Reset repository and upload final project (part 3)

.gitattributes

@@ -62,3 +62,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 .venv_haddock/bin/python3 filter=lfs diff=lfs merge=lfs -text
 .venv_haddock/bin/python3.12 filter=lfs diff=lfs merge=lfs -text
 .venv_haddock/lib/python3.12/site-packages/Bio/Align/_pairwisealigner.cpython-312-darwin.so filter=lfs diff=lfs merge=lfs -text
+.venv_haddock/lib/python3.12/site-packages/Bio/Cluster/_cluster.cpython-312-darwin.so filter=lfs diff=lfs merge=lfs -text

.venv_haddock/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data/PAM30

@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 30 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -5.06, Entropy = 2.57 bits
+#
+# Lowest score = -17, Highest score = 13
+#
+    A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V   B   Z   X   *
+A   6  -7  -4  -3  -6  -4  -2  -2  -7  -5  -6  -7  -5  -8  -2   0  -1 -13  -8  -2  -3  -3  -3 -17
+R  -7   8  -6 -10  -8  -2  -9  -9  -2  -5  -8   0  -4  -9  -4  -3  -6  -2 -10  -8  -7  -4  -6 -17
+N  -4  -6   8   2 -11  -3  -2  -3   0  -5  -7  -1  -9  -9  -6   0  -2  -8  -4  -8   6  -3  -3 -17
+D  -3 -10   2   8 -14  -2   2  -3  -4  -7 -12  -4 -11 -15  -8  -4  -5 -15 -11  -8   6   1  -5 -17
+C  -6  -8 -11 -14  10 -14 -14  -9  -7  -6 -15 -14 -13 -13  -8  -3  -8 -15  -4  -6 -12 -14  -9 -17
+Q  -4  -2  -3  -2 -14   8   1  -7   1  -8  -5  -3  -4 -13  -3  -5  -5 -13 -12  -7  -3   6  -5 -17
+E  -2  -9  -2   2 -14   1   8  -4  -5  -5  -9  -4  -7 -14  -5  -4  -6 -17  -8  -6   1   6  -5 -17
+G  -2  -9  -3  -3  -9  -7  -4   6  -9 -11 -10  -7  -8  -9  -6  -2  -6 -15 -14  -5  -3  -5  -5 -17
+H  -7  -2   0  -4  -7   1  -5  -9   9  -9  -6  -6 -10  -6  -4  -6  -7  -7  -3  -6  -1  -1  -5 -17
+I  -5  -5  -5  -7  -6  -8  -5 -11  -9   8  -1  -6  -1  -2  -8  -7  -2 -14  -6   2  -6  -6  -5 -17
+L  -6  -8  -7 -12 -15  -5  -9 -10  -6  -1   7  -8   1  -3  -7  -8  -7  -6  -7  -2  -9  -7  -6 -17
+K  -7   0  -1  -4 -14  -3  -4  -7  -6  -6  -8   7  -2 -14  -6  -4  -3 -12  -9  -9  -2  -4  -5 -17
+M  -5  -4  -9 -11 -13  -4  -7  -8 -10  -1   1  -2  11  -4  -8  -5  -4 -13 -11  -1 -10  -5  -5 -17
+F  -8  -9  -9 -15 -13 -13 -14  -9  -6  -2  -3 -14  -4   9 -10  -6  -9  -4   2  -8 -10 -13  -8 -17
+P  -2  -4  -6  -8  -8  -3  -5  -6  -4  -8  -7  -6  -8 -10   8  -2  -4 -14 -13  -6  -7  -4  -5 -17
+S   0  -3   0  -4  -3  -5  -4  -2  -6  -7  -8  -4  -5  -6  -2   6   0  -5  -7  -6  -1  -5  -3 -17
+T  -1  -6  -2  -5  -8  -5  -6  -6  -7  -2  -7  -3  -4  -9  -4   0   7 -13  -6  -3  -3  -6  -4 -17
+W -13  -2  -8 -15 -15 -13 -17 -15  -7 -14  -6 -12 -13  -4 -14  -5 -13  13  -5 -15 -10 -14 -11 -17
+Y  -8 -10  -4 -11  -4 -12  -8 -14  -3  -6  -7  -9 -11   2 -13  -7  -6  -5  10  -7  -6  -9  -7 -17
+V  -2  -8  -8  -8  -6  -7  -6  -5  -6   2  -2  -9  -1  -8  -6  -6  -3 -15  -7   7  -8  -6  -5 -17
+B  -3  -7   6   6 -12  -3   1  -3  -1  -6  -9  -2 -10 -10  -7  -1  -3 -10  -6  -8   6   0  -5 -17
+Z  -3  -4  -3   1 -14   6   6  -5  -1  -6  -7  -4  -5 -13  -4  -5  -6 -14  -9  -6   0   6  -5 -17
+X  -3  -6  -3  -5  -9  -5  -5  -5  -5  -5  -6  -5  -5  -8  -5  -3  -4 -11  -7  -5  -5  -5  -5 -17
+* -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17   1

.venv_haddock/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data/PAM70

@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 70 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -2.77, Entropy = 1.60 bits
+#
+# Lowest score = -11, Highest score = 13
+#
+    A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V   B   Z   X   *
+A   5  -4  -2  -1  -4  -2  -1   0  -4  -2  -4  -4  -3  -6   0   1   1  -9  -5  -1  -1  -1  -2 -11
+R  -4   8  -3  -6  -5   0  -5  -6   0  -3  -6   2  -2  -7  -2  -1  -4   0  -7  -5  -4  -2  -3 -11
+N  -2  -3   6   3  -7  -1   0  -1   1  -3  -5   0  -5  -6  -3   1   0  -6  -3  -5   5  -1  -2 -11
+D  -1  -6   3   6  -9   0   3  -1  -1  -5  -8  -2  -7 -10  -4  -1  -2 -10  -7  -5   5   2  -3 -11
+C  -4  -5  -7  -9   9  -9  -9  -6  -5  -4 -10  -9  -9  -8  -5  -1  -5 -11  -2  -4  -8  -9  -6 -11
+Q  -2   0  -1   0  -9   7   2  -4   2  -5  -3  -1  -2  -9  -1  -3  -3  -8  -8  -4  -1   5  -2 -11
+E  -1  -5   0   3  -9   2   6  -2  -2  -4  -6  -2  -4  -9  -3  -2  -3 -11  -6  -4   2   5  -3 -11
+G   0  -6  -1  -1  -6  -4  -2   6  -6  -6  -7  -5  -6  -7  -3   0  -3 -10  -9  -3  -1  -3  -3 -11
+H  -4   0   1  -1  -5   2  -2  -6   8  -6  -4  -3  -6  -4  -2  -3  -4  -5  -1  -4   0   1  -3 -11
+I  -2  -3  -3  -5  -4  -5  -4  -6  -6   7   1  -4   1   0  -5  -4  -1  -9  -4   3  -4  -4  -3 -11
+L  -4  -6  -5  -8 -10  -3  -6  -7  -4   1   6  -5   2  -1  -5  -6  -4  -4  -4   0  -6  -4  -4 -11
+K  -4   2   0  -2  -9  -1  -2  -5  -3  -4  -5   6   0  -9  -4  -2  -1  -7  -7  -6  -1  -2  -3 -11
+M  -3  -2  -5  -7  -9  -2  -4  -6  -6   1   2   0  10  -2  -5  -3  -2  -8  -7   0  -6  -3  -3 -11
+F  -6  -7  -6 -10  -8  -9  -9  -7  -4   0  -1  -9  -2   8  -7  -4  -6  -2   4  -5  -7  -9  -5 -11
+P   0  -2  -3  -4  -5  -1  -3  -3  -2  -5  -5  -4  -5  -7   7   0  -2  -9  -9  -3  -4  -2  -3 -11
+S   1  -1   1  -1  -1  -3  -2   0  -3  -4  -6  -2  -3  -4   0   5   2  -3  -5  -3   0  -2  -1 -11
+T   1  -4   0  -2  -5  -3  -3  -3  -4  -1  -4  -1  -2  -6  -2   2   6  -8  -4  -1  -1  -3  -2 -11
+W  -9   0  -6 -10 -11  -8 -11 -10  -5  -9  -4  -7  -8  -2  -9  -3  -8  13  -3 -10  -7 -10  -7 -11
+Y  -5  -7  -3  -7  -2  -8  -6  -9  -1  -4  -4  -7  -7   4  -9  -5  -4  -3   9  -5  -4  -7  -5 -11
+V  -1  -5  -5  -5  -4  -4  -4  -3  -4   3   0  -6   0  -5  -3  -3  -1 -10  -5   6  -5  -4  -2 -11
+B  -1  -4   5   5  -8  -1   2  -1   0  -4  -6  -1  -6  -7  -4   0  -1  -7  -4  -5   5   1  -2 -11
+Z  -1  -2  -1   2  -9   5   5  -3   1  -4  -4  -2  -3  -9  -2  -2  -3 -10  -7  -4   1   5  -3 -11
+X  -2  -3  -2  -3  -6  -2  -3  -3  -3  -3  -4  -3  -3  -5  -3  -1  -2  -7  -5  -2  -2  -3  -3 -11
+* -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11   1

.venv_haddock/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data/RAO

@@ -0,0 +1,27 @@
+#  J.K. Mohana Rao:
+#  "New scoring matrix for amino acid residue exchanges based on residue
+#  characteristic physical parameters."
+#  International Journal of Peptide and Protein Research: 29(2): 276-281 (1987).
+#  Figure 1, lower triangle.
+#  PMID 3570667
+   A  C  D  E  F  G  H  I  K  L  M  N  P  Q  R  S  T  V  W  Y
+A 16 11  9 10 10  8 11  9 10 11 11  9  6 11  8 10 10  9 11  9 
+C 11 16  8  9 10  8 10  8  9 11 10  9  7 10  8 10 10  8 11 10 
+D  9  8 16 11  4  9  9  3 11  6  5 11  8 11 10 10  9  3  6  7 
+E 10  9 11 16  6  6 11  4 11  7  8 10  5 11  9  9  8  4  7  6 
+F 10 10  4  6 16  7  9 12  6 11 10  6  4  7  5  8 10 11 11 10 
+G  8  8  9  6  7 16  7  6  7  6  4 10 11  8  7 11 10  6  8 10 
+H 11 10  9 11  9  7 16  8 11 10 10 10  5 11 10 10 10  9 10  9 
+I  9  8  3  4 12  6  8 16  4 10  9  5  3  6  4  8 10 12 11 10 
+K 10  9 11 11  6  7 11  4 16  7  8 11  6 12 11 10  9  5  7  7 
+L 11 11  6  7 11  6 10 10  7 16 11  7  4  9  6  8  9 10 11  9 
+M 11 10  5  8 10  4 10  9  8 11 16  6  2  9  6  7  8  9 10  8 
+N  9  9 11 10  6 10 10  5 11  7  6 16  9 11 10 11 10  5  8  8 
+P  6  7  8  5  4 11  5  3  6  4  2  9 16  7  6 10  8  3  6  8 
+Q 11 10 11 11  7  8 11  6 12  9  9 11  7 16 10 10 10  6  9  8 
+R  8  8 10  9  5  7 10  4 11  6  6 10  6 10 16  9  9  5  7  7 
+S 10 10 10  9  8 11 10  8 10  8  7 11 10 10  9 16 11  8 10 11 
+T 10 10  9  8 10 10 10 10  9  9  8 10  8 10  9 11 16 10 11 11 
+V  9  8  3  4 11  6  9 12  5 10  9  5  3  6  5  8 10 16 11 10 
+W 11 11  6  7 11  8 10 11  7 11 10  8  6  9  7 10 11 11 16 11 
+Y  9 10  7  6 10 10  9 10  7  9  8  8  8  8  7 11 11 10 11 16 

.venv_haddock/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data/RISLER

@@ -0,0 +1,27 @@
+#  J.L. Risler, M.O. Delorme, H. Delacroix, A. Henaut:
+#  "Amino acid substitutions in structurally related proteins. A pattern
+#  recognition approach. Determination of a new and efficient scoring matrix."
+#  Journal of Molecular Biology 204(4): 1019-1029 (1988).
+#  Figure 5.
+#  PMID 3221397
+     A    C    D    E    F    G    H    I    K    L    M    N    P    Q    R    S    T    V    W    Y
+A  2.2 -1.5  0.2  1.7  0.6  0.6 -0.6  1.7  1.4  1.3  1.0  1.3 -0.2  1.8  1.5  2.0  1.9  2.0 -0.9  0.2 
+C -1.5  2.2 -1.7 -1.5 -1.6 -1.7 -1.8 -1.6 -1.6 -1.5 -1.6 -1.6 -1.8 -1.4 -1.5 -1.3 -1.4 -1.4 -1.8 -1.1 
+D  0.2 -1.7  2.2  1.0 -0.3 -0.4 -1.3  0.0  0.1 -0.2 -0.5  0.8 -1.2  0.6 -0.1  0.7  0.0  0.0 -1.4 -0.4 
+E  1.7 -1.5  1.0  2.2  0.6  0.3 -0.6  1.5  1.4  0.9  0.6  1.4 -0.1  2.1  1.9  1.8  1.6  1.6 -1.0  0.2 
+F  0.6 -1.6 -0.3  0.6  2.2 -0.4 -1.1  1.0  0.1  1.0 -0.2  0.4 -1.1  0.7  0.4  0.5  0.3  0.8 -0.9  2.0 
+G  0.6 -1.7 -0.4  0.3 -0.4  2.2 -1.2  0.0 -0.1 -0.2 -0.4  0.2 -1.2  0.2  0.1  0.7  0.2  0.1 -1.3 -0.2 
+H -0.6 -1.8 -1.3 -0.6 -1.1 -1.2  2.2 -0.8 -1.0 -0.9 -1.2 -0.3 -1.6 -0.5 -0.4 -0.4 -0.9 -0.7 -1.7 -0.8 
+I  1.7 -1.6  0.0  1.5  1.0  0.0 -0.8  2.2  1.0  2.1  0.9  0.9 -0.6  1.4  1.4  1.6  1.6  2.2 -0.7  0.4 
+K  1.4 -1.6  0.1  1.4  0.1 -0.1 -1.0  1.0  2.2  0.7  0.4  1.0 -0.7  1.7  2.1  1.4  1.2  1.2 -1.1  0.5 
+L  1.3 -1.5 -0.2  0.9  1.0 -0.2 -0.9  2.1  0.7  2.2  1.8  0.8 -0.8  1.1  1.2  1.3  1.2  2.0 -0.8  0.5 
+M  1.0 -1.6 -0.5  0.6 -0.2 -0.4 -1.2  0.9  0.4  1.8  2.2  0.0 -1.2  1.2  1.1  0.6  0.8  0.8 -1.3 -0.2 
+N  1.3 -1.6  0.8  1.4  0.4  0.2 -0.3  0.9  1.0  0.8  0.0  2.2 -1.0  1.6  1.2  1.9  1.1  1.1 -1.1 -0.1 
+P -0.2 -1.8 -1.2 -0.1 -1.1 -1.2 -1.6 -0.6 -0.7 -0.8 -1.2 -1.0  2.2 -0.6 -0.3 -0.3 -0.5 -0.6 -1.6 -1.2 
+Q  1.8 -1.4  0.6  2.1  0.7  0.2 -0.5  1.4  1.7  1.1  1.2  1.6 -0.6  2.2  2.0  1.8  1.7  1.5 -1.0  0.5 
+R  1.5 -1.5 -0.1  1.9  0.4  0.1 -0.4  1.4  2.1  1.2  1.1  1.2 -0.3  2.0  2.2  2.0  1.9  1.5 -0.8  0.8 
+S  2.0 -1.3  0.7  1.8  0.5  0.7 -0.4  1.6  1.4  1.3  0.6  1.9 -0.3  1.8  2.0  2.2  2.1  1.8 -0.8  0.4 
+T  1.9 -1.4  0.0  1.6  0.3  0.2 -0.9  1.6  1.2  1.2  0.8  1.1 -0.5  1.7  1.9  2.1  2.2  1.6 -1.0  0.3 
+V  2.0 -1.4  0.0  1.6  0.8  0.1 -0.7  2.2  1.2  2.0  0.8  1.1 -0.6  1.5  1.5  1.8  1.6  2.2 -0.7  0.3 
+W -0.9 -1.8 -1.4 -1.0 -0.9 -1.3 -1.7 -0.7 -1.1 -0.8 -1.3 -1.1 -1.6 -1.0 -0.8 -0.8 -1.0 -0.7  2.2 -0.6 
+Y  0.2 -1.1 -0.4  0.2  2.0 -0.2 -0.8  0.4  0.5  0.5 -0.2 -0.1 -1.2  0.5  0.8  0.4  0.3  0.3 -0.6  2.2 

.venv_haddock/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data/SCHNEIDER

@@ -0,0 +1,70 @@
+# Adrian Schneider, Gina M. Cannarozzi, and Gaston H. Gonnet:
+# "Empirical codon substitution matrix."
+# BMC Bioinformatics 6:134 (2005).
+# Additional File 3.
+# PMID 15927081
+      AAA   AAC   AAG   AAT   ACA   ACC   ACG   ACT   AGA   AGC   AGG   AGT   ATA   ATC   ATG   ATT   CAA   CAC   CAG   CAT   CCA   CCC   CCG   CCT   CGA   CGC   CGG   CGT   CTA   CTC   CTG   CTT   GAA   GAC   GAG   GAT   GCA   GCC   GCG   GCT   GGA   GGC   GGG   GGT   GTA   GTC   GTG   GTT   TAA   TAC   TAG   TAT   TCA   TCC   TCG   TCT   TGA   TGC   TGG   TGT   TTA   TTC   TTG   TTT
+AAA  11.6  -2.7   9.7  -1.7  -2.7  -6.4  -3.9  -5.6   5.1  -5.0   3.6  -4.2  -6.3 -13.0  -7.1 -11.5   0.4  -6.0  -1.9  -5.3  -8.5 -11.2  -8.9 -10.8   2.1   0.0   1.4   0.2 -10.2 -13.5 -13.0 -12.5  -2.6  -8.5  -5.0  -8.1  -6.3  -9.9  -7.5  -9.0  -7.1 -10.2  -8.2  -9.2  -8.2 -12.5 -11.1 -11.4 -50.0 -14.8 -50.0 -13.8  -7.3 -10.1  -8.4  -9.1 -50.0 -13.0 -13.5 -12.4 -10.7 -18.1 -11.8 -17.2 
+AAC  -2.7  13.0  -3.3  10.9  -3.5  -0.4  -3.3  -1.8  -5.4   4.6  -5.5   3.0 -10.2  -7.9  -9.9  -9.6  -5.0   0.5  -5.5  -1.0 -10.3  -8.1  -9.4  -9.6  -8.1  -5.0  -7.3  -6.3 -13.4 -11.3 -14.4 -12.9  -6.3   0.8  -6.4  -1.1  -7.4  -5.0  -6.2  -6.5  -5.6  -1.6  -4.7  -3.0 -10.8  -8.7 -11.9 -10.0 -50.0  -6.2 -50.0  -7.5  -6.3  -4.3  -6.2  -5.4 -50.0  -7.0 -16.3  -8.2 -13.2 -12.3 -13.1 -13.3 
+AAG   9.7  -3.3  11.6  -2.8  -4.5  -6.7  -3.1  -6.9   3.3  -5.5   4.8  -5.1  -8.9 -13.2  -5.7 -12.6  -1.5  -6.1  -0.6  -6.1 -10.0 -11.8  -8.6 -11.9   1.2   0.5   2.2   0.1 -11.8 -14.0 -11.9 -13.4  -4.9  -9.1  -3.4  -8.9  -8.0 -10.0  -7.2 -10.0  -9.1 -10.2  -7.1  -9.9 -10.1 -13.0 -10.6 -12.7 -50.0 -14.9 -50.0 -14.4  -8.9 -10.8  -8.9 -10.4 -50.0 -13.1 -11.8 -13.0 -12.4 -19.4 -11.5 -17.8 
+AAT  -1.7  10.9  -2.8  12.9  -2.7  -2.2  -2.8   0.2  -4.8   2.9  -5.2   5.2  -9.1  -9.5  -9.0  -7.0  -4.0  -1.0  -5.0   1.0  -9.0  -8.8  -8.9  -7.7  -7.0  -6.8  -7.1  -4.3 -12.4 -12.9 -13.9 -10.0  -4.9  -0.7  -5.6   1.4  -6.0  -6.5  -6.2  -4.8  -5.1  -3.2  -5.0  -1.2  -9.8  -9.9 -11.3  -8.2 -50.0  -7.6 -50.0  -5.1  -5.5  -5.8  -5.9  -4.2 -50.0  -8.3 -15.5  -5.9 -11.6 -14.2 -12.0 -11.6 
+ACA  -2.7  -3.5  -4.5  -2.7  11.7   9.0  10.6   9.6  -3.2  -0.7  -5.1  -0.4   0.7  -4.6  -0.4  -3.6  -4.8  -8.9  -6.5  -7.8  -1.4  -4.1  -2.9  -3.3  -8.0  -9.1  -8.0  -8.2  -6.0  -9.3  -7.7  -8.5  -6.4 -10.1  -7.5  -8.6   2.8  -0.7   0.9   0.1  -5.9  -7.3  -6.5  -6.5  -0.4  -3.9  -2.6  -3.1 -50.0 -14.6 -50.0 -12.6   2.9   0.1   1.8   1.0 -50.0  -9.2 -13.6  -7.7  -4.8 -12.2  -6.2 -11.0 
+ACC  -6.4  -0.4  -6.7  -2.2   9.0  12.3   9.8   9.6  -7.1   2.4  -7.2   0.3  -2.9  -1.2  -3.0  -3.3  -7.6  -6.7  -8.1  -7.9  -4.9  -1.9  -4.5  -3.8  -9.5  -7.8  -9.3  -8.9  -9.4  -7.1  -9.0  -9.0  -9.4  -7.5  -9.3  -9.2  -0.7   2.6   0.2  -0.1  -8.0  -4.6  -7.7  -6.1  -3.6  -1.0  -4.1  -3.1 -50.0 -11.6 -50.0 -11.6   0.2   2.3   0.4   0.5 -50.0  -6.5 -15.3  -7.8  -8.4  -9.5  -8.3 -11.1 
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+ACT  -5.6  -1.8  -6.9   0.2   9.6   9.6   9.8  11.6  -6.6   0.9  -7.2   2.5  -2.3  -3.4  -2.3  -0.6  -6.5  -8.2  -8.0  -6.3  -3.7  -3.5  -3.9  -1.6  -9.9  -8.9  -9.6  -7.0  -8.6  -8.9  -8.8  -6.8  -8.6  -8.2  -8.8  -6.8   0.3   0.1   0.2   2.4  -7.4  -6.2  -6.9  -4.4  -2.9  -2.9  -3.5  -0.9 -50.0 -12.2 -50.0 -10.1   1.2   0.6   1.2   2.4 -50.0  -7.6 -16.1  -5.8  -7.2 -10.8  -7.4  -9.0 
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+AGT  -4.2   3.0  -5.1   5.2  -0.4   0.3  -0.2   2.5  -1.9  11.0  -2.1  13.2  -7.6  -8.5  -8.0  -5.3  -5.6  -4.5  -6.8  -2.4  -7.8  -7.9  -7.9  -6.2  -5.7  -5.1  -5.4  -2.1 -12.4 -12.3 -13.1 -10.1  -6.6  -4.4  -6.9  -2.6  -3.6  -3.8  -3.7  -2.0  -1.4   0.8  -0.9   3.0  -8.2  -8.1  -9.2  -5.8 -50.0 -10.1 -50.0  -7.4  -1.7  -2.0  -1.5  -0.5 -50.0  -2.1 -12.6  -0.4 -11.6 -13.9 -11.4 -11.1 
+ATA  -6.3 -10.2  -8.9  -9.1   0.7  -2.9  -1.7  -2.3  -5.7  -8.4  -7.7  -7.6  13.2   9.6   3.5   9.7  -8.7 -12.4 -10.7 -10.7  -7.8 -10.2  -8.8  -9.6  -9.5 -11.9 -10.9 -10.5   2.3  -0.4  -0.2  -0.3  -9.7 -15.5 -11.4 -13.7  -3.0  -6.4  -4.1  -5.4  -9.6 -11.9 -10.5 -11.8   6.2   3.3   3.7   3.6 -50.0 -13.6 -50.0 -11.9  -5.6  -8.8  -7.2  -8.9 -50.0 -12.4 -14.1 -11.6   2.8  -6.4   0.5  -5.2 
+ATC -13.0  -7.9 -13.2  -9.5  -4.6  -1.2  -4.1  -3.4 -12.5  -6.3 -12.5  -8.5   9.6  12.7   0.2  10.5 -12.4 -11.6 -13.2 -12.0 -12.4 -10.1 -11.6 -12.0 -15.1 -13.1 -14.3 -13.4  -1.4   1.4  -1.6  -0.5 -14.9 -14.3 -15.2 -16.8  -7.7  -4.7  -6.3  -6.6 -14.6 -10.8 -12.8 -13.0   2.3   6.0   2.5   3.6 -50.0 -11.2 -50.0 -11.9 -10.5  -9.2 -10.5 -10.5 -50.0 -10.3 -16.2 -11.3  -1.7  -3.7  -2.5  -5.4 
+ATG  -7.1  -9.9  -5.7  -9.0  -0.4  -3.0   0.9  -2.3  -7.2  -8.3  -5.3  -8.0   3.5   0.2  14.3   1.0  -7.3 -11.2  -6.9  -9.7  -8.5 -10.2  -7.7  -9.8 -10.0 -10.4  -8.4 -10.2   1.0  -0.6   1.7  -0.5 -11.1 -14.8  -9.7 -14.5  -3.7  -5.8  -3.1  -5.6 -10.4 -11.5  -8.2 -11.1   0.6  -1.6   1.6  -1.1 -50.0 -12.4 -50.0 -11.5  -5.5  -8.0  -4.9  -7.2 -50.0 -12.4 -10.3 -11.6   0.7  -6.8   2.4  -6.0 
+ATT -11.5  -9.6 -12.6  -7.0  -3.6  -3.3  -3.5  -0.6 -11.6  -7.7 -11.9  -5.3   9.7  10.5   1.0  12.6 -12.0 -12.2 -12.5  -9.7 -11.1 -11.2 -11.9  -9.4 -12.9 -14.3 -14.0 -11.9  -1.0  -0.4  -1.6   1.2 -13.9 -15.4 -13.7 -12.6  -6.2  -6.7  -6.3  -4.4 -13.0 -12.2 -13.0 -10.4   2.9   3.8   2.5   5.8 -50.0 -12.5 -50.0 -10.2  -9.6  -9.7  -9.6  -8.3 -50.0 -11.6 -15.4  -9.4  -1.1  -5.4  -1.6  -3.3 
+CAA   0.4  -5.0  -1.5  -4.0  -4.8  -7.6  -5.9  -6.5  -0.7  -6.1  -2.2  -5.6  -8.7 -12.4  -7.3 -12.0  12.8   2.3  10.2   3.0   0.0  -3.4  -0.7  -3.2   2.5  -0.8   0.9   0.2  -3.0  -7.2  -5.7  -6.1  -0.2  -6.6  -1.8  -6.0  -5.3  -8.2  -5.7  -7.6  -6.7  -9.6  -7.5  -9.3  -7.1 -10.5  -9.6  -9.4 -50.0  -8.1 -50.0  -7.2  -4.3  -6.8  -5.7  -6.3 -50.0  -9.5  -9.6  -8.9  -6.2 -12.8  -6.8 -11.8 
+CAC  -6.0   0.5  -6.1  -1.0  -8.9  -6.7  -8.9  -8.2  -4.8  -2.9  -4.4  -4.5 -12.4 -11.6 -11.2 -12.2   2.3  14.6   1.9  12.9  -5.5  -2.6  -4.1  -4.7  -1.2   3.0  -1.1   1.6  -8.0  -4.7  -8.7  -6.0  -8.2  -4.7  -7.8  -6.7 -10.0  -8.3  -8.9  -9.9 -10.8  -7.1 -10.0  -9.2 -11.6 -10.1 -12.3 -11.9 -50.0   2.2 -50.0   0.9  -7.9  -5.9  -7.4  -6.9 -50.0  -4.6 -11.6  -5.6  -9.7  -5.9  -9.9  -7.3 
+CAG  -1.9  -5.5  -0.6  -5.0  -6.5  -8.1  -5.6  -8.0  -3.1  -6.5  -1.9  -6.8 -10.7 -13.2  -6.9 -12.5  10.2   1.9  11.9   2.1  -2.3  -4.1  -0.5  -4.6  -0.1  -0.9   2.4  -0.8  -5.1  -6.9  -4.8  -6.7  -2.3  -7.1  -0.8  -7.2  -7.2  -8.0  -5.6  -8.5  -9.4  -9.7  -7.2  -9.8  -9.2 -11.1  -9.5 -10.7 -50.0  -8.7 -50.0  -8.6  -6.1  -7.5  -5.5  -7.7 -50.0 -10.4  -7.7 -10.0  -7.3 -13.6  -6.4 -13.3 
+CAT  -5.3  -1.0  -6.1   1.0  -7.8  -7.9  -8.5  -6.3  -4.3  -4.2  -4.8  -2.4 -10.7 -12.0  -9.7  -9.7   3.0  12.9   2.1  14.7  -4.9  -3.8  -4.0  -2.4  -1.0   0.8  -1.3   3.4  -7.6  -5.7  -8.1  -3.5  -6.8  -5.8  -7.2  -4.2  -8.9 -10.2  -8.4  -8.2  -9.9  -8.4  -9.7  -6.4 -11.1 -11.1 -11.8 -10.0 -50.0   0.4 -50.0   2.6  -7.2  -7.0  -7.4  -5.1 -50.0  -5.7  -9.8  -3.2  -8.4  -7.4  -8.9  -5.9 
+CCA  -8.5 -10.3 -10.0  -9.0  -1.4  -4.9  -3.9  -3.7 -10.0  -8.5 -10.2  -7.8  -7.8 -12.4  -8.5 -11.1   0.0  -5.5  -2.3  -4.9  12.6  10.0  11.1  10.5  -6.0  -8.3  -6.9  -7.5  -2.2  -7.4  -5.3  -5.9  -8.9 -12.5  -9.4 -11.6  -0.7  -3.9  -2.3  -3.0  -9.1  -9.8  -9.2  -9.5  -5.6  -9.0  -8.0  -8.5 -50.0 -15.3 -50.0 -14.1   2.3  -1.4   0.3  -0.5 -50.0 -13.6 -14.3 -11.5  -5.3 -13.7  -6.1 -12.7 
+CCC -11.2  -8.1 -11.8  -8.8  -4.1  -1.9  -3.9  -3.5 -11.6  -5.9 -11.5  -7.9 -10.2 -10.1 -10.2 -11.2  -3.4  -2.6  -4.1  -3.8  10.0  13.1  10.7  10.6  -8.1  -5.2  -8.0  -6.7  -6.1  -3.7  -7.5  -5.6 -11.1 -10.3 -10.6 -11.9  -3.2  -1.0  -2.2  -2.8 -10.5  -8.1  -9.4  -9.5  -8.3  -6.9  -9.4  -8.8 -50.0 -11.3 -50.0 -12.8  -0.6   2.2  -0.3   0.1 -50.0 -10.1 -17.5 -11.1  -8.6  -9.9  -8.6 -11.9 
+CCG  -8.9  -9.4  -8.6  -8.9  -2.9  -4.5  -2.2  -3.9  -8.8  -7.5  -8.1  -7.9  -8.8 -11.6  -7.7 -11.9  -0.7  -4.1  -0.5  -4.0  11.1  10.7  13.2  10.4  -5.7  -5.8  -3.5  -6.1  -3.6  -6.5  -3.3  -5.5  -9.4 -11.0  -8.7 -11.2  -1.8  -2.7   0.7  -3.0  -9.1  -8.2  -7.3  -9.4  -7.2  -8.2  -7.2  -8.2 -50.0 -13.2 -50.0 -13.3   0.5  -0.9   1.8  -0.6 -50.0 -11.4 -11.1 -10.5  -6.1 -12.9  -5.0 -11.9 
+CCT -10.8  -9.6 -11.9  -7.7  -3.3  -3.8  -4.5  -1.6 -11.7  -7.7 -12.0  -6.2  -9.6 -12.0  -9.8  -9.4  -3.2  -4.7  -4.6  -2.4  10.5  10.6  10.4  12.6  -8.2  -7.9  -9.0  -4.7  -6.1  -6.0  -7.5  -2.9 -10.9 -12.2 -11.2 -10.9  -2.4  -2.9  -2.7  -0.9 -10.4  -9.7 -10.2  -8.0  -8.4  -9.1  -9.3  -6.5 -50.0 -13.3 -50.0 -11.0  -0.0  -0.4  -0.4   2.3 -50.0 -10.9 -17.2  -8.3  -8.3 -12.7  -7.8  -9.3 
+CGA   2.1  -8.1   1.2  -7.0  -8.0  -9.5  -7.3  -9.9  10.5  -5.5   9.3  -5.7  -9.5 -15.1 -10.0 -12.9   2.5  -1.2  -0.1  -1.0  -6.0  -8.1  -5.7  -8.2  13.8  11.3  11.8  12.1  -6.0  -9.1  -9.0  -9.5  -8.9 -13.4 -10.0 -13.1  -9.9 -11.7  -9.8 -12.8  -5.9  -9.4  -6.5  -8.1 -10.7 -14.0 -13.3 -13.9 -50.0 -11.9 -50.0  -9.7  -8.9 -10.8  -9.0 -11.1 -50.0  -6.5  -5.3  -6.3 -10.5 -16.2 -10.4 -15.2 
+CGC   0.0  -5.0   0.5  -6.8  -9.1  -7.8  -7.5  -8.9   7.7  -2.4   8.2  -5.1 -11.9 -13.1 -10.4 -14.3  -0.8   3.0  -0.9   0.8  -8.3  -5.2  -5.8  -7.9  11.3  15.0  11.2  12.8  -9.7  -5.3  -9.2  -7.8 -11.7 -10.6 -10.1 -12.2 -11.7  -8.8  -8.9 -11.8  -9.3  -5.0  -8.0  -8.2 -13.6 -11.4 -12.8 -13.0 -50.0  -7.2 -50.0  -8.4 -11.0  -7.7  -8.7 -10.2 -50.0  -1.5  -7.1  -4.9 -11.2 -11.6 -11.6 -15.0 
+CGG   1.4  -7.3   2.2  -7.1  -8.0  -9.3  -6.4  -9.6   9.1  -5.5  10.0  -5.4 -10.9 -14.3  -8.4 -14.0   0.9  -1.1   2.4  -1.3  -6.9  -8.0  -3.5  -9.0  11.8  11.2  13.4  11.4  -7.3  -8.8  -6.5  -8.5 -10.0 -12.5  -7.8 -12.5  -9.6 -11.0  -7.1 -10.7  -7.9  -8.0  -4.3  -9.4 -11.4 -12.3 -10.9 -12.9 -50.0 -11.8 -50.0 -11.2  -9.4  -9.8  -7.3 -10.5 -50.0  -6.2  -2.2  -6.7  -9.8 -15.2  -8.5 -14.9 
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+GTC -12.5  -8.7 -13.0  -9.9  -3.9  -1.0  -3.4  -2.9 -12.5  -6.3 -11.6  -8.1   3.3   6.0  -1.6   3.8 -10.5 -10.1 -11.1 -11.1  -9.0  -6.9  -8.2  -9.1 -14.0 -11.4 -12.3 -12.1  -3.1   0.2  -3.2  -2.2 -10.4  -9.1 -10.4 -11.5  -2.1   1.2  -1.1  -1.4  -9.4  -5.6  -8.1  -8.0   8.6  12.4   8.6   9.5 -50.0 -10.4 -50.0 -11.6  -7.2  -5.7  -7.5  -7.4 -50.0  -8.6 -15.7  -9.7  -3.0  -3.7  -3.2  -5.9 
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+TCA  -7.3  -6.3  -8.9  -5.5   2.9   0.2   1.5   1.2  -8.5  -2.3 -10.0  -1.7  -5.6 -10.5  -5.5  -9.6  -4.3  -7.9  -6.1  -7.2   2.3  -0.6   0.5  -0.0  -8.9 -11.0  -9.4  -9.3  -4.6  -9.4  -7.3  -8.1  -7.8  -9.8  -8.9  -9.2   2.8   0.1   1.2   0.8  -5.9  -6.8  -5.9  -6.3  -4.1  -7.2  -6.1  -6.2 -50.0  -9.9 -50.0  -8.6  12.5   9.4  11.0   9.8 -50.0  -4.8  -8.7  -3.5  -0.0  -8.6  -2.1  -7.0 
+TCC -10.1  -4.3 -10.8  -5.8   0.1   2.3   0.7   0.6 -10.4  -0.2 -10.8  -2.0  -8.8  -9.2  -8.0  -9.7  -6.8  -5.9  -7.5  -7.0  -1.4   2.2  -0.9  -0.4 -10.8  -7.7  -9.8  -8.8  -8.9  -7.3  -9.6  -9.1 -10.5  -8.3 -10.2 -10.0  -0.0   2.5   0.7   0.5  -7.5  -5.1  -7.1  -6.7  -7.4  -5.7  -8.1  -7.0 -50.0  -5.8 -50.0  -7.0   9.4  12.7  10.1  10.0 -50.0  -1.5 -11.3  -3.3  -5.4  -4.2  -5.6  -6.8 
+TCG  -8.4  -6.2  -8.9  -5.9   1.8   0.4   2.7   1.2  -9.1  -1.2  -8.8  -1.5  -7.2 -10.5  -4.9  -9.6  -5.7  -7.4  -5.5  -7.4   0.3  -0.3   1.8  -0.4  -9.0  -8.7  -7.3  -8.9  -5.9  -9.4  -6.4  -8.7  -8.7  -9.1  -8.5  -9.4   1.4   0.7   3.5   0.7  -6.6  -5.3  -4.7  -5.8  -5.7  -7.5  -5.5  -7.1 -50.0  -8.9 -50.0  -8.4  11.0  10.1  13.2  10.2 -50.0  -4.2  -6.1  -3.6  -3.5  -8.4  -1.2  -6.8 
+TCT  -9.1  -5.4 -10.4  -4.2   1.0   0.5   0.6   2.4  -9.6  -1.5 -10.5  -0.5  -8.9 -10.5  -7.2  -8.3  -6.3  -6.9  -7.7  -5.1  -0.5   0.1  -0.6   2.3 -11.1 -10.2 -10.5  -7.0  -8.3  -9.4  -9.4  -6.6  -9.6  -9.7 -10.0  -7.9   0.7   0.6   0.8   2.3  -7.1  -6.5  -7.2  -5.0  -6.5  -7.4  -7.5  -5.4 -50.0  -7.6 -50.0  -4.8   9.8  10.0  10.2  12.1 -50.0  -3.1 -11.4  -0.7  -4.6  -6.6  -4.9  -3.9 
+TGA -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0  29.2 -50.0  28.5 -50.0 -50.0 -50.0 -50.0 -50.0  33.3 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 -50.0 
+TGC -13.0  -7.0 -13.1  -8.3  -9.2  -6.5  -8.9  -7.6  -9.8  -0.7  -9.2  -2.1 -12.4 -10.3 -12.4 -11.6  -9.5  -4.6 -10.4  -5.7 -13.6 -10.1 -11.4 -10.9  -6.5  -1.5  -6.2  -3.6 -12.8  -8.0 -12.3  -9.7 -16.5 -12.7 -15.6 -14.3  -8.7  -6.0  -7.1  -7.5  -9.5  -4.1  -8.4  -6.1 -11.0  -8.6 -11.3  -9.3 -50.0  -1.5 -50.0  -3.0  -4.8  -1.5  -4.2  -3.1 -50.0  16.4  -5.1  14.2 -10.1  -4.3 -10.0  -5.4 
+TGG -13.5 -16.3 -11.8 -15.5 -13.6 -15.3 -12.1 -16.1  -7.7 -13.3  -4.2 -12.6 -14.1 -16.2 -10.3 -15.4  -9.6 -11.6  -7.7  -9.8 -14.3 -17.5 -11.1 -17.2  -5.3  -7.1  -2.2  -7.1  -9.6 -11.9  -8.7 -11.4 -17.1 -20.6 -15.3 -19.9 -14.1 -14.8 -12.4 -16.5 -11.7 -12.8  -6.4 -13.4 -14.3 -15.7 -12.7 -14.0 -50.0  -7.8 -50.0  -7.1  -8.7 -11.3  -6.1 -11.4 -50.0  -5.1  18.6  -4.8  -8.6  -8.1  -4.5  -7.3 
+TGT -12.4  -8.2 -13.0  -5.9  -7.7  -7.8  -7.4  -5.8  -8.8  -2.0  -9.3  -0.4 -11.6 -11.3 -11.6  -9.4  -8.9  -5.6 -10.0  -3.2 -11.5 -11.1 -10.5  -8.3  -6.3  -4.9  -6.7  -1.2 -10.6  -9.7 -11.3  -8.0 -14.8 -13.1 -15.5 -11.4  -7.5  -7.5  -7.1  -5.9  -8.4  -5.8  -8.1  -3.6  -9.9  -9.7 -10.1  -8.2 -50.0  -3.0 -50.0  -0.1  -3.5  -3.3  -3.6  -0.7 -50.0  14.2  -4.8  16.4  -8.9  -5.8  -8.9  -3.4 
+TTA -10.7 -13.2 -12.4 -11.6  -4.8  -8.4  -6.1  -7.2 -10.3 -11.8 -11.0 -11.6   2.8  -1.7   0.7  -1.1  -6.2  -9.7  -7.3  -8.4  -5.3  -8.6  -6.1  -8.3 -10.5 -11.2  -9.8 -10.2   9.5   6.5   7.6   6.8 -12.1 -16.0 -13.0 -16.2  -5.2  -8.6  -7.1  -7.8 -12.5 -14.4 -12.1 -13.0   1.4  -3.0  -1.6  -2.4 -50.0  -8.1 -50.0  -7.3  -0.0  -5.4  -3.5  -4.6 -50.0 -10.1  -8.6  -8.9  13.2  -0.9   9.7  -0.3 
+TTC -18.1 -12.3 -19.4 -14.2 -12.2  -9.5 -11.5 -10.8 -17.9 -11.9 -18.2 -13.9  -6.4  -3.7  -6.8  -5.4 -12.8  -5.9 -13.6  -7.4 -13.7  -9.9 -12.9 -12.7 -16.2 -11.6 -15.2 -12.7  -3.2   0.5  -3.3  -1.8 -18.9 -16.6 -18.8 -19.2 -12.5  -9.4 -10.6 -11.1 -17.3 -14.1 -16.2 -16.0  -7.9  -3.7  -7.8  -6.3 -50.0   3.6 -50.0   2.3  -8.6  -4.2  -8.4  -6.6 -50.0  -4.3  -8.1  -5.8  -0.9  14.2  -1.8  11.6 
+TTG -11.8 -13.1 -11.5 -12.0  -6.2  -8.3  -5.4  -7.4 -11.8 -12.3 -11.1 -11.4   0.5  -2.5   2.4  -1.6  -6.8  -9.9  -6.4  -8.9  -6.1  -8.6  -5.0  -7.8 -10.4 -11.6  -8.5  -9.9   8.2   6.4   8.7   6.9 -12.4 -17.0 -12.6 -15.8  -6.5  -8.5  -5.0  -7.8 -13.2 -13.6 -10.3 -13.7  -0.7  -3.2  -0.3  -2.4 -50.0  -9.4 -50.0  -8.7  -2.1  -5.6  -1.2  -4.9 -50.0 -10.0  -4.5  -8.9   9.7  -1.8  11.3  -0.9 
+TTT -17.2 -13.3 -17.8 -11.6 -11.0 -11.1 -10.4  -9.0 -16.0 -12.7 -16.1 -11.1  -5.2  -5.4  -6.0  -3.3 -11.8  -7.3 -13.3  -5.9 -12.7 -11.9 -11.9  -9.3 -15.2 -15.0 -14.9 -11.0  -2.8  -1.8  -2.9   0.4 -17.4 -18.4 -18.3 -15.9 -10.7 -11.2 -10.6  -9.0 -15.4 -14.8 -15.8 -13.3  -6.8  -5.9  -7.2  -3.9 -50.0   2.0 -50.0   3.9  -7.0  -6.8  -6.8  -3.9 -50.0  -5.4  -7.3  -3.4  -0.3  11.6  -0.9  14.1 

.venv_haddock/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data/STR

@@ -0,0 +1,26 @@
+#  Steven Henikoff and Jorja G. Henikoff:
+#  "Performance evaluation of amino acid substitution matrices."
+#  Proteins: Structure, Function, and Genetics: 17(1): 49-61 (1993).
+#  Figure 1, lower triangle.
+#  PMID 8234244
+   A  C  D  E  F  G  H  I  K  L  M  N  P  Q  R  S  T  V  W  Y
+A  4 -2 -1  0 -3  0 -2 -2 -1 -2  0 -1 -1  0 -1  0 -1  0 -3 -3 
+C -2 11 -7 -3 -2 -6 -6 -4 -4 -6 -5 -6 -8 -3 -2 -4 -5 -4 -6 -6 
+D -1 -7  6  2 -5 -1  0 -3 -1 -6 -4  2 -1  0 -2  0 -1 -4 -6 -3 
+E  0 -3  2  5 -4 -2 -2 -3  1 -4 -2  0 -1  2  0 -1  0 -2 -6 -2 
+F -3 -2 -5 -4  7 -6 -2  1 -3  2  0 -3 -5 -4 -4 -3 -3 -1  2  3 
+G  0 -6 -1 -2 -6  5 -3 -5 -3 -5 -4 -1 -2 -2 -2 -1 -3 -4 -4 -3 
+H -2 -6  0 -2 -2 -3  8 -5  0 -3 -2  2 -3  0  0 -2 -2 -2 -3  0 
+I -2 -4 -3 -3  1 -5 -5  6 -3  2  1 -3 -4 -5 -3 -3 -2  2 -2 -1 
+K -1 -4 -1  1 -3 -3  0 -3  5 -2 -1  0 -1  1  2 -1  0 -3 -3 -2 
+L -2 -6 -6 -4  2 -5 -3  2 -2  5  3 -3 -3 -3 -3 -4 -3  1 -1 -2 
+M  0 -5 -4 -2  0 -4 -2  1 -1  3  8 -2 -6  1 -4 -4 -2  0 -2 -1 
+N -1 -6  2  0 -3 -1  2 -3  0 -3 -2  5 -2  0 -1  0  0 -4 -5 -1 
+P -1 -8 -1 -1 -5 -2 -3 -4 -1 -3 -6 -2  7 -2 -2 -1 -1 -4 -4 -6 
+Q  0 -3  0  2 -4 -2  0 -5  1 -3  1  0 -2  6  1 -1  0 -2 -5 -3 
+R -1 -2 -2  0 -4 -2  0 -3  2 -3 -4 -1 -2  1  7  0 -1 -3 -2 -1 
+S  0 -4  0 -1 -3 -1 -2 -3 -1 -4 -4  0 -1 -1  0  4  1 -3 -5 -2 
+T -1 -5 -1  0 -3 -3 -2 -2  0 -3 -2  0 -1  0 -1  1  5 -1 -5 -2 
+V  0 -4 -4 -2 -1 -4 -2  2 -3  1  0 -4 -4 -2 -3 -3 -1  5 -4 -1 
+W -3 -6 -6 -6  2 -4 -3 -2 -3 -1 -2 -5 -4 -5 -2 -5 -5 -4 10  2 
+Y -3 -6 -3 -2  3 -3  0 -1 -2 -2 -1 -1 -6 -3 -1 -2 -2 -1  2  7 

.venv_haddock/lib/python3.12/site-packages/Bio/Align/substitution_matrices/data/TRANS

@@ -0,0 +1,12 @@
+#  David Wheeler,
+#  Department of Cell Biology, Baylor College of Medicine, Houston, Texas:
+#  "Weight matrices for sequence similarity scoring."
+#  Version 2.0, May 1996.
+#  David Wheeler defined the Transition/Transversion Matrix as a penalty
+#  matrix; the matrix below is a similarity matrix where
+#  similarity = 5 - penalty.
+   A  T  C  G
+A  5  0  0  4
+T  0  5  4  0
+C  0  4  5  0
+G  4  0  0  5

.venv_haddock/lib/python3.12/site-packages/Bio/Align/tabular.py

@@ -0,0 +1,408 @@
+# Copyright 2021 by Michiel de Hoon.  All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+"""Bio.Align support for tabular output from BLAST or FASTA.
+
+This module contains a parser for tabular output from BLAST run with the
+'-outfmt 7' argument, as well as tabular output from William Pearson's
+FASTA alignment tools using the '-m 8CB' or '-m 8CC' arguments.
+"""
+
+import enum
+import re
+
+import numpy as np
+
+from Bio.Align import Alignment
+from Bio.Align import interfaces
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+
+
+class State(enum.Enum):
+    """Enumerate alignment states needed when parsing a BTOP string."""
+
+    MATCH = enum.auto()
+    QUERY_GAP = enum.auto()
+    TARGET_GAP = enum.auto()
+    NONE = enum.auto()
+
+
+class AlignmentIterator(interfaces.AlignmentIterator):
+    """Alignment iterator for tabular output from BLAST or FASTA.
+
+    For reading (pairwise) alignments from tabular output generated by BLAST
+    run with the '-outfmt 7' argument, as well as tabular output generated by
+    William Pearson's FASTA alignment programs with the '-m 8CB' or '-m 8CC'
+    output formats.
+    """
+
+    fmt = "Tabular"
+
+    def _read_header(self, stream):
+        line = stream.readline()
+        if not line:
+            raise ValueError("Empty file.")
+        if not line.startswith("# "):
+            raise ValueError("Missing header.")
+        line = line.rstrip()
+        self._parse_header(stream, line)
+
+    def _parse_header(self, stream, line):
+        metadata = {}
+        blast_programs = (
+            "BLASTN",
+            "BLASTP",
+            "BLASTX",
+            "TBLASTN",
+            "TBLASTX",
+            "DELTABLAST",
+            "PSIBLAST",
+            "RPSBLAST",
+            "RPSTBLASTN",
+        )
+        try:
+            program, version = line[2:].split(None, 1)
+            if program not in blast_programs:
+                raise ValueError("Not a BLAST program")
+        except ValueError:
+            # FASTA
+            metadata["Command line"] = line[2:]
+            line = stream.readline()
+            assert line.startswith("# ")
+            metadata["Program"], metadata["Version"] = line[2:].rstrip().split(None, 1)
+            self._final_prefix = "# FASTA processed "
+        else:
+            # BLAST
+            metadata["Program"], metadata["Version"] = program, version
+            self._final_prefix = "# BLAST processed "
+        for line in stream:
+            line = line.strip()
+            assert line.startswith("# ")
+            try:
+                prefix, value = line[2:].split(": ")
+            except ValueError:
+                suffix = " hits found"
+                assert line.endswith(suffix)
+                hits = int(line[2 : -len(suffix)])
+                break
+            if prefix == "Query":
+                if metadata["Program"] == "FASTA":
+                    query_line, query_size = value.rsplit(" - ", 1)
+                    query_size, unit = query_size.split()
+                    self._query_size = int(query_size)
+                    assert unit in ("nt", "aa")
+                else:
+                    query_line = value
+                    self._query_size = None
+                try:
+                    self._query_id, self._query_description = query_line.split(None, 1)
+                except ValueError:
+                    self._query_id = query_line.strip()
+                    self._query_description = None
+            elif prefix == "Database":
+                metadata["Database"] = value
+            elif prefix == "Fields":
+                self._fields = value.split(", ")
+            elif prefix == "RID":
+                metadata["RID"] = value
+        self.metadata = metadata
+
+    def _read_next_alignment(self, stream):
+        for line in stream:
+            line = line.rstrip()
+            if line.startswith("# "):
+                if line.startswith(self._final_prefix) and line.endswith(" queries"):
+                    del self._fields
+                    del self._query_id
+                    del self._query_description
+                    del self._query_size
+                    del self._final_prefix
+                    return
+                self._parse_header(stream, line)
+            else:
+                break
+        alignment_length = None
+        identical = None
+        btop = None
+        cigar = None
+        score = None
+        query_id = None
+        target_id = None
+        query_start = None
+        query_end = None
+        target_start = None
+        target_end = None
+        query_sequence = None
+        target_sequence = None
+        target_length = None
+        coordinates = None
+        query_size = self._query_size
+        columns = line.split("\t")
+        assert len(columns) == len(self._fields)
+        annotations = {}
+        query_annotations = {}
+        target_annotations = {}
+        for column, field in zip(columns, self._fields):
+            if field == "query id":
+                query_id = column
+                if self._query_id is not None:
+                    assert query_id == self._query_id
+            elif field == "subject id":
+                target_id = column
+            elif field == "% identity":
+                annotations[field] = float(column)
+            elif field == "alignment length":
+                alignment_length = int(column)
+            elif field == "mismatches":
+                annotations[field] = int(column)
+            elif field == "gap opens":
+                annotations[field] = int(column)
+            elif field == "q. start":
+                query_start = int(column)
+            elif field == "q. end":
+                query_end = int(column)
+            elif field == "s. start":
+                target_start = int(column)
+            elif field == "s. end":
+                target_end = int(column)
+            elif field == "evalue":
+                annotations["evalue"] = float(column)
+            elif field == "bit score":
+                annotations["bit score"] = float(column)
+            elif field == "BTOP":
+                coordinates = self.parse_btop(column)
+            elif field == "aln_code":
+                coordinates = self.parse_cigar(column)
+            elif field == "query gi":
+                query_annotations["gi"] = column
+            elif field == "query acc.":
+                query_annotations["acc."] = column
+            elif field == "query acc.ver":
+                query_annotations["acc.ver"] = column
+                if query_id is None:
+                    query_id = column
+            elif field == "query length":
+                if query_size is None:
+                    query_size = int(column)
+                else:
+                    assert query_size == int(column)
+            elif field == "subject ids":
+                target_annotations["ids"] = column
+            elif field == "subject gi":
+                target_annotations["gi"] = column
+            elif field == "subject gis":
+                target_annotations["gis"] = column
+            elif field == "subject acc.":
+                target_annotations["acc."] = column
+            elif field == "subject accs.":
+                target_annotations["accs."] = column
+            elif field == "subject tax ids":
+                target_annotations["tax ids"] = column
+            elif field == "subject sci names":
+                target_annotations["sci names"] = column
+            elif field == "subject com names":
+                target_annotations["com names"] = column
+            elif field == "subject blast names":
+                target_annotations["blast names"] = column
+            elif field == "subject super kingdoms":
+                target_annotations["super kingdoms"] = column
+            elif field == "subject title":
+                target_annotations["title"] = column
+            elif field == "subject titles":
+                target_annotations["titles"] = column
+            elif field == "subject strand":
+                target_annotations["strand"] = column
+            elif field == "% subject coverage":
+                target_annotations["% coverage"] = float(column)
+            elif field == "subject acc.ver":
+                target_annotations["acc.ver"] = column
+                if target_id is None:
+                    target_id = column
+            elif field == "subject length":
+                target_length = int(column)
+            elif field == "query seq":
+                query_sequence = column
+            elif field == "subject seq":
+                target_sequence = column
+            elif field == "score":
+                score = int(column)
+            elif field == "identical":
+                identical = int(column)
+                annotations[field] = identical
+            elif field == "positives":
+                annotations[field] = int(column)
+            elif field == "gaps":
+                annotations[field] = int(column)
+            elif field == "% positives":
+                annotations[field] = float(column)
+            elif field == "% hsp coverage":
+                annotations[field] = float(column)
+            elif field == "query/sbjct frames":
+                annotations[field] = column
+            elif field == "query frame":
+                query_annotations["frame"] = column
+            elif field == "sbjct frame":
+                target_annotations["frame"] = column
+            else:
+                raise ValueError("Unexpected field '%s'" % field)
+        program = self.metadata["Program"]
+        if coordinates is None:
+            if alignment_length is not None:
+                annotations["alignment length"] = alignment_length
+                # otherwise, get it from alignment.shape
+        if query_start is not None and query_end is not None:
+            if query_start < query_end:
+                query_start -= 1
+            else:
+                query_end -= 1
+        if target_start is not None and target_end is not None:
+            if target_start < target_end:
+                target_start -= 1
+            else:
+                target_end -= 1
+        if coordinates is None or program in ("BLASTX", "TBLASTX"):
+            if query_start is not None:
+                query_annotations["start"] = query_start
+            if query_end is not None:
+                query_annotations["end"] = query_end
+        elif coordinates is not None:
+            if query_start < query_end:
+                coordinates[1, :] += query_start
+            else:
+                # mapped to reverse strand
+                coordinates[1, :] = query_start - coordinates[1, :]
+        if coordinates is None or program in ("TBLASTN", "TBLASTX"):
+            if target_start is not None:
+                target_annotations["start"] = target_start
+            if target_end is not None:
+                target_annotations["end"] = target_end
+        elif coordinates is not None:
+            coordinates[0, :] += target_start
+        if query_sequence is None:
+            if query_size is None:
+                query_seq = None
+            else:
+                query_seq = Seq(None, length=query_size)
+        else:
+            query_sequence = query_sequence.replace("-", "")
+            if program == "TBLASTN":
+                assert len(query_sequence) == query_end - query_start
+                query_seq = Seq({query_start: query_sequence}, length=query_size)
+            elif program == "TBLASTX":
+                query_annotations["start"] = query_start
+                query_annotations["end"] = query_end
+                query_seq = Seq(query_sequence)
+            else:
+                raise Exception("Unknown program %s" % program)
+        query = SeqRecord(query_seq, id=query_id)
+        if self._query_description is not None:
+            query.description = self._query_description
+        if query_annotations:
+            query.annotations = query_annotations
+        if self.metadata["Program"] in ("TBLASTN", "TBLASTX"):
+            target_annotations["length"] = target_length
+            if target_sequence is None:
+                target_seq = None
+            else:
+                target_sequence = target_sequence.replace("-", "")
+                target_seq = Seq(target_sequence)
+        else:
+            if target_sequence is None:
+                if target_end is None:
+                    target_seq = None
+                else:
+                    target_seq = Seq(None, length=target_end)
+            else:
+                target_sequence = target_sequence.replace("-", "")
+                if target_start is not None and target_end is not None:
+                    assert len(target_sequence) == target_end - target_start
+                    target_seq = Seq({target_start: target_sequence}, length=target_end)
+        target = SeqRecord(target_seq, id=target_id)
+        if target_annotations:
+            target.annotations = target_annotations
+        records = [target, query]
+        alignment = Alignment(records, coordinates)
+        alignment.annotations = annotations
+        if score is not None:
+            alignment.score = score
+        return alignment
+
+    def parse_btop(self, btop):
+        """Parse a BTOP string and return alignment coordinates.
+
+        A BTOP (Blast trace-back operations) string is used by BLAST to
+        describe a sequence alignment.
+        """
+        target_coordinates = []
+        query_coordinates = []
+        target_coordinates.append(0)
+        query_coordinates.append(0)
+        state = State.NONE
+        tokens = re.findall("([A-Z-*]{2}|\\d+)", btop)
+        # each token is now
+        # - an integer
+        # - a pair of characters, which may include dashes
+        for token in tokens:
+            if token.startswith("-"):
+                if state != State.QUERY_GAP:
+                    target_coordinates.append(target_coordinates[-1])
+                    query_coordinates.append(query_coordinates[-1])
+                    state = State.QUERY_GAP
+                target_coordinates[-1] += 1
+            elif token.endswith("-"):
+                if state != State.TARGET_GAP:
+                    target_coordinates.append(target_coordinates[-1])
+                    query_coordinates.append(query_coordinates[-1])
+                    state = State.TARGET_GAP
+                query_coordinates[-1] += 1
+            else:
+                try:
+                    length = int(token)
+                except ValueError:
+                    # pair of mismatched letters
+                    length = 1
+                if state == State.MATCH:
+                    target_coordinates[-1] += length
+                    query_coordinates[-1] += length
+                else:
+                    target_coordinates.append(target_coordinates[-1] + length)
+                    query_coordinates.append(query_coordinates[-1] + length)
+                    state = State.MATCH
+        coordinates = np.array([target_coordinates, query_coordinates], np.intp)
+        return coordinates
+
+    def parse_cigar(self, cigar):
+        """Parse a CIGAR string and return alignment coordinates.
+
+        A CIGAR string, as defined by the SAM Sequence Alignment/Map format,
+        describes a sequence alignment as a series of lengths and operation
+        (alignment/insertion/deletion) codes.
+        """
+        target_coordinates = []
+        query_coordinates = []
+        target_coordinate = 0
+        query_coordinate = 0
+        target_coordinates.append(target_coordinate)
+        query_coordinates.append(query_coordinate)
+        state = State.NONE
+        tokens = re.findall("(M|D|I|\\d+)", cigar)
+        # each token is now
+        # - the length of the operation
+        # - the operation
+        for length, operation in zip(tokens[::2], tokens[1::2]):
+            length = int(length)
+            if operation == "M":
+                target_coordinate += length
+                query_coordinate += length
+            elif operation == "I":
+                target_coordinate += length
+            elif operation == "D":
+                query_coordinate += length
+            target_coordinates.append(target_coordinate)
+            query_coordinates.append(query_coordinate)
+        coordinates = np.array([target_coordinates, query_coordinates], np.intp)
+        return coordinates

.venv_haddock/lib/python3.12/site-packages/Bio/AlignIO/ClustalIO.py

@@ -0,0 +1,313 @@
+# Copyright 2006-2016 by Peter Cock.  All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+"""Bio.AlignIO support for "clustal" output from CLUSTAL W and other tools.
+
+You are expected to use this module via the Bio.AlignIO functions (or the
+Bio.SeqIO functions if you want to work directly with the gapped sequences).
+"""
+
+from Bio.Align import MultipleSeqAlignment
+from Bio.AlignIO.Interfaces import AlignmentIterator
+from Bio.AlignIO.Interfaces import SequentialAlignmentWriter
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+
+
+class ClustalWriter(SequentialAlignmentWriter):
+    """Clustalw alignment writer."""
+
+    def write_alignment(self, alignment):
+        """Use this to write (another) single alignment to an open file."""
+        if len(alignment) == 0:
+            raise ValueError("Must have at least one sequence")
+        if alignment.get_alignment_length() == 0:
+            # This doubles as a check for an alignment object
+            raise ValueError("Non-empty sequences are required")
+
+        # Old versions of the parser in Bio.Clustalw used a ._version property
+        try:
+            version = str(alignment._version)
+        except AttributeError:
+            version = ""
+        if not version:
+            version = "1.81"
+        if version.startswith("2."):
+            # e.g. 2.0.x
+            output = f"CLUSTAL {version} multiple sequence alignment\n\n\n"
+        else:
+            # e.g. 1.81 or 1.83
+            output = f"CLUSTAL X ({version}) multiple sequence alignment\n\n\n"
+
+        cur_char = 0
+        max_length = len(alignment[0])
+
+        if max_length <= 0:
+            raise ValueError("Non-empty sequences are required")
+
+        if "clustal_consensus" in alignment.column_annotations:
+            star_info = alignment.column_annotations["clustal_consensus"]
+        else:
+            try:
+                # This was originally stored by Bio.Clustalw as ._star_info
+                star_info = alignment._star_info
+            except AttributeError:
+                star_info = None
+
+        # keep displaying sequences until we reach the end
+        while cur_char != max_length:
+            # calculate the number of sequences to show, which will
+            # be less if we are at the end of the sequence
+            if (cur_char + 50) > max_length:
+                show_num = max_length - cur_char
+            else:
+                show_num = 50
+
+            # go through all of the records and print out the sequences
+            # when we output, we do a nice 80 column output, although this
+            # may result in truncation of the ids.
+            for record in alignment:
+                # Make sure we don't get any spaces in the record
+                # identifier when output in the file by replacing
+                # them with underscores:
+                line = record.id[0:30].replace(" ", "_").ljust(36)
+                line += str(record.seq[cur_char : (cur_char + show_num)])
+                output += line + "\n"
+
+            # now we need to print out the star info, if we've got it
+            if star_info:
+                output += (
+                    (" " * 36) + star_info[cur_char : (cur_char + show_num)] + "\n"
+                )
+
+            output += "\n"
+            cur_char += show_num
+
+        # Want a trailing blank new line in case the output is concatenated
+        self.handle.write(output + "\n")
+
+
+class ClustalIterator(AlignmentIterator):
+    """Clustalw alignment iterator."""
+
+    _header = None  # for caching lines between __next__ calls
+
+    def __next__(self):
+        """Parse the next alignment from the handle."""
+        handle = self.handle
+
+        if self._header is None:
+            line = handle.readline()
+        else:
+            # Header we saved from when we were parsing
+            # the previous alignment.
+            line = self._header
+            self._header = None
+
+        if not line:
+            raise StopIteration
+
+        # Whitelisted headers we know about
+        known_headers = [
+            "CLUSTAL",
+            "PROBCONS",
+            "MUSCLE",
+            "MSAPROBS",
+            "Kalign",
+            "Biopython",
+        ]
+        if line.strip().split()[0] not in known_headers:
+            raise ValueError(
+                "%s is not a known CLUSTAL header: %s"
+                % (line.strip().split()[0], ", ".join(known_headers))
+            )
+
+        # find the clustal version in the header line
+        version = None
+        for word in line.split():
+            if word[0] == "(" and word[-1] == ")":
+                word = word[1:-1]
+            if word[0] in "0123456789":
+                version = word
+                break
+
+        # There should be two blank lines after the header line
+        line = handle.readline()
+        while line.strip() == "":
+            line = handle.readline()
+
+        # If the alignment contains entries with the same sequence
+        # identifier (not a good idea - but seems possible), then this
+        # dictionary based parser will merge their sequences.  Fix this?
+        ids = []
+        seqs = []
+        consensus = ""
+        seq_cols = None  # Used to extract the consensus
+
+        # Use the first block to get the sequence identifiers
+        while True:
+            if line[0] != " " and line.strip() != "":
+                # Sequences identifier...
+                fields = line.rstrip().split()
+
+                # We expect there to be two fields, there can be an optional
+                # "sequence number" field containing the letter count.
+                if len(fields) < 2 or len(fields) > 3:
+                    raise ValueError(f"Could not parse line:\n{line}")
+
+                ids.append(fields[0])
+                seqs.append(fields[1])
+
+                # Record the sequence position to get the consensus
+                if seq_cols is None:
+                    start = len(fields[0]) + line[len(fields[0]) :].find(fields[1])
+                    end = start + len(fields[1])
+                    seq_cols = slice(start, end)
+                    del start, end
+                assert fields[1] == line[seq_cols]
+
+                if len(fields) == 3:
+                    # This MAY be an old style file with a letter count...
+                    try:
+                        letters = int(fields[2])
+                    except ValueError:
+                        raise ValueError(
+                            f"Could not parse line, bad sequence number:\n{line}"
+                        ) from None
+                    if len(fields[1].replace("-", "")) != letters:
+                        raise ValueError(
+                            f"Could not parse line, invalid sequence number:\n{line}"
+                        )
+            elif line[0] == " ":
+                # Sequence consensus line...
+                assert len(ids) == len(seqs)
+                assert len(ids) > 0
+                assert seq_cols is not None
+                consensus = line[seq_cols]
+                assert not line[: seq_cols.start].strip()
+                assert not line[seq_cols.stop :].strip()
+                # Check for blank line (or end of file)
+                line = handle.readline()
+                assert line.strip() == ""
+                break
+            else:
+                # No consensus
+                break
+            line = handle.readline()
+            if not line:
+                break  # end of file
+
+        assert line.strip() == ""
+        assert seq_cols is not None
+
+        # Confirm all same length
+        for s in seqs:
+            assert len(s) == len(seqs[0])
+        if consensus:
+            assert len(consensus) == len(seqs[0])
+
+        # Loop over any remaining blocks...
+        done = False
+        while not done:
+            # There should be a blank line between each block.
+            # Also want to ignore any consensus line from the
+            # previous block.
+            while (not line) or line.strip() == "":
+                line = handle.readline()
+                if not line:
+                    break  # end of file
+            if not line:
+                break  # end of file
+
+            if line.split(None, 1)[0] in known_headers:
+                # Found concatenated alignment.
+                self._header = line
+                break
+
+            for i in range(len(ids)):
+                if line[0] == " ":
+                    raise ValueError(f"Unexpected line:\n{line!r}")
+                fields = line.rstrip().split()
+
+                # We expect there to be two fields, there can be an optional
+                # "sequence number" field containing the letter count.
+                if len(fields) < 2 or len(fields) > 3:
+                    raise ValueError(f"Could not parse line:\n{line!r}")
+
+                if fields[0] != ids[i]:
+                    raise ValueError(
+                        "Identifiers out of order? Got '%s' but expected '%s'"
+                        % (fields[0], ids[i])
+                    )
+
+                if fields[1] != line[seq_cols]:
+                    start = len(fields[0]) + line[len(fields[0]) :].find(fields[1])
+                    if start != seq_cols.start:
+                        raise ValueError("Old location %s -> %i:XX" % (seq_cols, start))
+                    end = start + len(fields[1])
+                    seq_cols = slice(start, end)
+                    del start, end
+
+                # Append the sequence
+                seqs[i] += fields[1]
+                assert len(seqs[i]) == len(seqs[0])
+
+                if len(fields) == 3:
+                    # This MAY be an old style file with a letter count...
+                    try:
+                        letters = int(fields[2])
+                    except ValueError:
+                        raise ValueError(
+                            f"Could not parse line, bad sequence number:\n{line}"
+                        ) from None
+                    if len(seqs[i].replace("-", "")) != letters:
+                        raise ValueError(
+                            f"Could not parse line, invalid sequence number:\n{line}"
+                        )
+
+                # Read in the next line
+                line = handle.readline()
+            # There should now be a consensus line
+            if consensus:
+                assert line[0] == " "
+                assert seq_cols is not None
+                consensus += line[seq_cols]
+                assert len(consensus) == len(seqs[0])
+                assert not line[: seq_cols.start].strip()
+                assert not line[seq_cols.stop :].strip()
+                # Read in the next line
+                line = handle.readline()
+
+        assert len(ids) == len(seqs)
+        if len(seqs) == 0 or len(seqs[0]) == 0:
+            raise StopIteration
+
+        if (
+            self.records_per_alignment is not None
+            and self.records_per_alignment != len(ids)
+        ):
+            raise ValueError(
+                "Found %i records in this alignment, told to expect %i"
+                % (len(ids), self.records_per_alignment)
+            )
+
+        records = (SeqRecord(Seq(s), id=i, description=i) for (i, s) in zip(ids, seqs))
+        alignment = MultipleSeqAlignment(records)
+        # TODO - Handle alignment annotation better, for now
+        # mimic the old parser in Bio.Clustalw
+        if version:
+            alignment._version = version
+        if consensus:
+            alignment_length = len(seqs[0])
+            if len(consensus) != alignment_length:
+                raise ValueError(
+                    "Alignment length is %i, consensus length is %i, '%s'"
+                    % (alignment_length, len(consensus), consensus)
+                )
+            alignment.column_annotations["clustal_consensus"] = consensus
+            # For backward compatibility prior to .column_annotations:
+            alignment._star_info = consensus
+        return alignment

.venv_haddock/lib/python3.12/site-packages/Bio/AlignIO/EmbossIO.py

@@ -0,0 +1,220 @@
+# Copyright 2008-2016 by Peter Cock.  All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+"""Bio.AlignIO support for "emboss" alignment output from EMBOSS tools.
+
+You are expected to use this module via the Bio.AlignIO functions (or the
+Bio.SeqIO functions if you want to work directly with the gapped sequences).
+
+This module contains a parser for the EMBOSS pairs/simple file format, for
+example from the alignret, water and needle tools.
+"""
+
+from Bio.Align import MultipleSeqAlignment
+from Bio.AlignIO.Interfaces import AlignmentIterator
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+
+
+class EmbossIterator(AlignmentIterator):
+    """Emboss alignment iterator.
+
+    For reading the (pairwise) alignments from EMBOSS tools in what they
+    call the "pairs" and "simple" formats.
+    """
+
+    _header = None  # for caching lines between __next__ calls
+
+    def __next__(self):
+        """Parse the next alignment from the handle."""
+        handle = self.handle
+
+        if self._header is None:
+            line = handle.readline()
+        else:
+            # Header we saved from when we were parsing
+            # the previous alignment.
+            line = self._header
+            self._header = None
+
+        if not line:
+            raise StopIteration
+
+        while line.rstrip() != "#=======================================":
+            line = handle.readline()
+            if not line:
+                raise StopIteration
+
+        length_of_seqs = None
+        number_of_seqs = None
+        ids = []
+        header_dict = {}
+
+        while line[0] == "#":
+            # Read in the rest of this alignment header,
+            # try and discover the number of records expected
+            # and their length
+            parts = line[1:].split(":", 1)
+            key = parts[0].lower().strip()
+            if key == "aligned_sequences":
+                number_of_seqs = int(parts[1].strip())
+                assert len(ids) == 0
+                # Should now expect the record identifiers...
+                for i in range(number_of_seqs):
+                    line = handle.readline()
+                    parts = line[1:].strip().split(":", 1)
+                    assert i + 1 == int(parts[0].strip())
+                    ids.append(parts[1].strip())
+                assert len(ids) == number_of_seqs
+            if key == "length":
+                length_of_seqs = int(parts[1].strip())
+
+            # Parse the rest of the header
+            if key == "identity":
+                header_dict["identity"] = int(parts[1].strip().split("/")[0])
+            if key == "similarity":
+                header_dict["similarity"] = int(parts[1].strip().split("/")[0])
+            if key == "gaps":
+                header_dict["gaps"] = int(parts[1].strip().split("/")[0])
+            if key == "score":
+                header_dict["score"] = float(parts[1].strip())
+
+            # And read in another line...
+            line = handle.readline()
+
+        if number_of_seqs is None:
+            raise ValueError("Number of sequences missing!")
+        if length_of_seqs is None:
+            raise ValueError("Length of sequences missing!")
+
+        if (
+            self.records_per_alignment is not None
+            and self.records_per_alignment != number_of_seqs
+        ):
+            raise ValueError(
+                "Found %i records in this alignment, told to expect %i"
+                % (number_of_seqs, self.records_per_alignment)
+            )
+
+        seqs = [""] * len(ids)
+        seq_starts = []
+        index = 0
+
+        # Parse the seqs
+        while line:
+            if len(line) > 21:
+                id_start = line[:21].strip().split(None, 1)
+                seq_end = line[21:].strip().split(None, 1)
+                if len(id_start) == 2 and len(seq_end) == 2:
+                    # identifier, seq start position, seq, seq end position
+                    # (an aligned seq is broken up into multiple lines)
+                    id, start = id_start
+                    seq, end = seq_end
+                    if start >= end:
+                        # Special case, either a single letter is present,
+                        # or no letters at all.
+                        if seq.replace("-", "") == "":
+                            start = int(start)
+                            end = int(end)
+                        else:
+                            start = int(start) - 1
+                            end = int(end)
+                    else:
+                        assert seq.replace("-", "") != "", repr(line)
+                        start = int(start) - 1  # python counting
+                        end = int(end)
+
+                    if index < 0 or index >= number_of_seqs:
+                        raise ValueError(
+                            "Expected index %i in range [0,%i)"
+                            % (index, number_of_seqs)
+                        )
+                    # The identifier is truncated...
+                    assert id == ids[index] or id == ids[index][: len(id)]
+
+                    if len(seq_starts) == index:
+                        # Record the start
+                        seq_starts.append(start)
+
+                    # Check the start...
+                    if start >= end:
+                        assert seq.replace("-", "") == "", line
+                    elif start - seq_starts[index] != len(seqs[index].replace("-", "")):
+                        raise ValueError(
+                            "Found %i chars so far for sequence %i (%s, %r), line says start %i:\n%s"
+                            % (
+                                len(seqs[index].replace("-", "")),
+                                index,
+                                id,
+                                seqs[index],
+                                start,
+                                line,
+                            )
+                        )
+                    seqs[index] += seq
+
+                    # Check the end ...
+                    if end != seq_starts[index] + len(seqs[index].replace("-", "")):
+                        raise ValueError(
+                            "Found %i chars so far for sequence %i (%s, %r, start=%i), file says end %i:\n%s"
+                            % (
+                                len(seqs[index].replace("-", "")),
+                                index,
+                                id,
+                                seqs[index],
+                                seq_starts[index],
+                                end,
+                                line,
+                            )
+                        )
+
+                    index += 1
+                    if index >= number_of_seqs:
+                        index = 0
+                else:
+                    # just a start value, this is just alignment annotation (?)
+                    # print("Skipping: " + line.rstrip())
+                    pass
+            elif line.strip() == "":
+                # Just a spacer?
+                pass
+            else:
+                raise ValueError(f"Unrecognised EMBOSS pairwise line: {line!r}\n")
+
+            line = handle.readline()
+            if (
+                line.rstrip() == "#---------------------------------------"
+                or line.rstrip() == "#======================================="
+            ):
+                # End of alignment
+                self._header = line
+                break
+
+        assert index == 0
+
+        if (
+            self.records_per_alignment is not None
+            and self.records_per_alignment != len(ids)
+        ):
+            raise ValueError(
+                "Found %i records in this alignment, told to expect %i"
+                % (len(ids), self.records_per_alignment)
+            )
+
+        records = []
+        for id, seq in zip(ids, seqs):
+            if len(seq) != length_of_seqs:
+                # EMBOSS 2.9.0 is known to use spaces instead of minus signs
+                # for leading gaps, and thus fails to parse.  This old version
+                # is still used as of Dec 2008 behind the EBI SOAP webservice:
+                # http://www.ebi.ac.uk/Tools/webservices/wsdl/WSEmboss.wsdl
+                raise ValueError(
+                    "Error parsing alignment - sequences of "
+                    "different length? You could be using an "
+                    "old version of EMBOSS."
+                )
+            records.append(SeqRecord(Seq(seq), id=id, description=id))
+        return MultipleSeqAlignment(records, annotations=header_dict)

.venv_haddock/lib/python3.12/site-packages/Bio/AlignIO/FastaIO.py

@@ -0,0 +1,346 @@
+# Copyright 2008-2016 by Peter Cock.  All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+"""Bio.AlignIO support for "fasta-m10" output from Bill Pearson's FASTA tools.
+
+You are expected to use this module via the Bio.AlignIO functions (or the
+Bio.SeqIO functions if you want to work directly with the gapped sequences).
+
+This module contains a parser for the pairwise alignments produced by Bill
+Pearson's FASTA tools, for use from the Bio.AlignIO interface where it is
+referred to as the "fasta-m10" file format (as we only support the machine
+readable output format selected with the -m 10 command line option).
+
+This module does NOT cover the generic "fasta" file format originally
+developed as an input format to the FASTA tools.  The Bio.AlignIO and
+Bio.SeqIO both use the Bio.SeqIO.FastaIO module to deal with these files,
+which can also be used to store a multiple sequence alignments.
+"""
+
+from Bio.Align import MultipleSeqAlignment
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+
+
+def _extract_alignment_region(alignment_seq_with_flanking, annotation):
+    """Extract alignment region (PRIVATE).
+
+    Helper function for the main parsing code.
+
+    To get the actual pairwise alignment sequences, we must first
+    translate the un-gapped sequence based coordinates into positions
+    in the gapped sequence (which may have a flanking region shown
+    using leading - characters).  To date, I have never seen any
+    trailing flanking region shown in the m10 file, but the
+    following code should also cope with that.
+
+    Note that this code seems to work fine even when the "sq_offset"
+    entries are present as a result of using the -X command line option.
+    """
+    align_stripped = alignment_seq_with_flanking.strip("-")
+    display_start = int(annotation["al_display_start"])
+    if int(annotation["al_start"]) <= int(annotation["al_stop"]):
+        start = int(annotation["al_start"]) - display_start
+        end = int(annotation["al_stop"]) - display_start + 1
+    else:
+        # FASTA has flipped this sequence...
+        start = display_start - int(annotation["al_start"])
+        end = display_start - int(annotation["al_stop"]) + 1
+
+    end += align_stripped.count("-")
+    if start < 0 or start >= end or end > len(align_stripped):
+        raise ValueError(
+            "Problem with sequence start/stop,\n%s[%i:%i]\n%s"
+            % (alignment_seq_with_flanking, start, end, annotation)
+        )
+    return align_stripped[start:end]
+
+
+def FastaM10Iterator(handle, seq_count=None):
+    """Alignment iterator for the FASTA tool's pairwise alignment output.
+
+    This is for reading the pairwise alignments output by Bill Pearson's
+    FASTA program when called with the -m 10 command line option for machine
+    readable output.  For more details about the FASTA tools, see the website
+    http://fasta.bioch.virginia.edu/ and the paper:
+
+         W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448
+
+    This class is intended to be used via the Bio.AlignIO.parse() function
+    by specifying the format as "fasta-m10" as shown in the following code::
+
+        from Bio import AlignIO
+        handle = ...
+        for a in AlignIO.parse(handle, "fasta-m10"):
+            assert len(a) == 2, "Should be pairwise!"
+            print("Alignment length %i" % a.get_alignment_length())
+            for record in a:
+                print("%s %s %s" % (record.seq, record.name, record.id))
+
+    Note that this is not a full blown parser for all the information
+    in the FASTA output - for example, most of the header and all of the
+    footer is ignored.  Also, the alignments are not batched according to
+    the input queries.
+
+    Also note that there can be up to about 30 letters of flanking region
+    included in the raw FASTA output as contextual information.  This is NOT
+    part of the alignment itself, and is not included in the resulting
+    MultipleSeqAlignment objects returned.
+    """
+    state_PREAMBLE = -1
+    state_NONE = 0
+    state_QUERY_HEADER = 1
+    state_ALIGN_HEADER = 2
+    state_ALIGN_QUERY = 3
+    state_ALIGN_MATCH = 4
+    state_ALIGN_CONS = 5
+
+    def build_hsp():
+        if not query_tags and not match_tags:
+            raise ValueError(f"No data for query {query_id!r}, match {match_id!r}")
+        assert query_tags, query_tags
+        assert match_tags, match_tags
+        evalue = align_tags.get("fa_expect")
+        tool = global_tags.get("tool", "").upper()
+
+        q = _extract_alignment_region(query_seq, query_tags)
+        if tool in ["TFASTX"] and len(match_seq) == len(q):
+            m = match_seq
+            # Quick hack until I can work out how -, * and / characters
+            # and the apparent mix of aa and bp coordinates works.
+        else:
+            m = _extract_alignment_region(match_seq, match_tags)
+        if len(q) != len(m):
+            raise ValueError(
+                f"""\
+Darn... amino acids vs nucleotide coordinates?
+tool: {tool}
+query_seq: {query_seq}
+query_tags: {query_tags}
+{q} length: {len(q)}
+match_seq: {match_seq}
+match_tags: {match_tags}
+{m} length: {len(m)}
+handle.name: {handle.name}
+"""
+            )
+
+        annotations = {}
+        records = []
+
+        # Want to record both the query header tags, and the alignment tags.
+        annotations.update(header_tags)
+        annotations.update(align_tags)
+
+        # Query
+        # =====
+        record = SeqRecord(
+            Seq(q),
+            id=query_id,
+            name="query",
+            description=query_descr,
+            annotations={"original_length": int(query_tags["sq_len"])},
+        )
+        # TODO - handle start/end coordinates properly. Short term hack for now:
+        record._al_start = int(query_tags["al_start"])
+        record._al_stop = int(query_tags["al_stop"])
+
+        # TODO - Can FASTA output RNA?
+        if "sq_type" in query_tags:
+            if query_tags["sq_type"] == "D":
+                record.annotations["molecule_type"] = "DNA"
+            elif query_tags["sq_type"] == "p":
+                record.annotations["molecule_type"] = "protein"
+
+        records.append(record)
+
+        # Match
+        # =====
+        record = SeqRecord(
+            Seq(m),
+            id=match_id,
+            name="match",
+            description=match_descr,
+            annotations={"original_length": int(match_tags["sq_len"])},
+        )
+        # TODO - handle start/end coordinates properly. Short term hack for now:
+        record._al_start = int(match_tags["al_start"])
+        record._al_stop = int(match_tags["al_stop"])
+
+        if "sq_type" in match_tags:
+            if match_tags["sq_type"] == "D":
+                record.annotations["molecule_type"] = "DNA"
+            elif match_tags["sq_type"] == "p":
+                record.annotations["molecule_type"] = "protein"
+
+        records.append(record)
+
+        return MultipleSeqAlignment(records, annotations=annotations)
+
+    state = state_PREAMBLE
+    query_id = None
+    match_id = None
+    query_descr = ""
+    match_descr = ""
+    global_tags = {}
+    header_tags = {}
+    align_tags = {}
+    query_tags = {}
+    match_tags = {}
+    query_seq = ""
+    match_seq = ""
+    cons_seq = ""
+    for line in handle:
+        if ">>>" in line and not line.startswith(">>>"):
+            if query_id and match_id:
+                # This happens on old FASTA output which lacked an end of
+                # query >>><<< marker line.
+                yield build_hsp()
+            state = state_NONE
+            query_descr = line[line.find(">>>") + 3 :].strip()
+            query_id = query_descr.split(None, 1)[0]
+            match_id = None
+            header_tags = {}
+            align_tags = {}
+            query_tags = {}
+            match_tags = {}
+            query_seq = ""
+            match_seq = ""
+            cons_seq = ""
+        elif line.startswith("!! No "):
+            # e.g.
+            # !! No library sequences with E() < 0.5
+            # or on more recent versions,
+            # No sequences with E() < 0.05
+            assert state == state_NONE
+            assert not header_tags
+            assert not align_tags
+            assert not match_tags
+            assert not query_tags
+            assert match_id is None
+            assert not query_seq
+            assert not match_seq
+            assert not cons_seq
+            query_id = None
+        elif line.strip() in [">>><<<", ">>>///"]:
+            # End of query, possible end of all queries
+            if query_id and match_id:
+                yield build_hsp()
+            state = state_NONE
+            query_id = None
+            match_id = None
+            header_tags = {}
+            align_tags = {}
+            query_tags = {}
+            match_tags = {}
+            query_seq = ""
+            match_seq = ""
+            cons_seq = ""
+        elif line.startswith(">>>"):
+            # Should be start of a match!
+            assert query_id is not None
+            assert line[3:].split(", ", 1)[0] == query_id, line
+            assert match_id is None
+            assert not header_tags
+            assert not align_tags
+            assert not query_tags
+            assert not match_tags
+            assert not match_seq
+            assert not query_seq
+            assert not cons_seq
+            state = state_QUERY_HEADER
+        elif line.startswith(">>"):
+            # Should now be at start of a match alignment!
+            if query_id and match_id:
+                yield build_hsp()
+            align_tags = {}
+            query_tags = {}
+            match_tags = {}
+            query_seq = ""
+            match_seq = ""
+            cons_seq = ""
+            match_descr = line[2:].strip()
+            match_id = match_descr.split(None, 1)[0]
+            state = state_ALIGN_HEADER
+        elif line.startswith(">--"):
+            # End of one HSP
+            assert query_id and match_id, line
+            yield build_hsp()
+            # Clean up read for next HSP
+            # but reuse header_tags
+            align_tags = {}
+            query_tags = {}
+            match_tags = {}
+            query_seq = ""
+            match_seq = ""
+            cons_seq = ""
+            state = state_ALIGN_HEADER
+        elif line.startswith(">"):
+            if state == state_ALIGN_HEADER:
+                # Should be start of query alignment seq...
+                assert query_id is not None, line
+                assert match_id is not None, line
+                assert query_id.startswith(line[1:].split(None, 1)[0]), line
+                state = state_ALIGN_QUERY
+            elif state == state_ALIGN_QUERY:
+                # Should be start of match alignment seq
+                assert query_id is not None, line
+                assert match_id is not None, line
+                assert match_id.startswith(line[1:].split(None, 1)[0]), line
+                state = state_ALIGN_MATCH
+            elif state == state_NONE:
+                # Can get > as the last line of a histogram
+                pass
+            else:
+                raise RuntimeError("state %i got %r" % (state, line))
+        elif line.startswith("; al_cons"):
+            assert state == state_ALIGN_MATCH, line
+            state = state_ALIGN_CONS
+            # Next line(s) should be consensus seq...
+        elif line.startswith("; "):
+            if ": " in line:
+                key, value = (s.strip() for s in line[2:].split(": ", 1))
+            else:
+                import warnings
+
+                from Bio import BiopythonParserWarning
+
+                # Seen in lalign36, specifically version 36.3.4 Apr, 2011
+                # Fixed in version 36.3.5b Oct, 2011(preload8)
+                warnings.warn(
+                    f"Missing colon in line: {line!r}", BiopythonParserWarning
+                )
+                try:
+                    key, value = (s.strip() for s in line[2:].split(" ", 1))
+                except ValueError:
+                    raise ValueError(f"Bad line: {line!r}") from None
+            if state == state_QUERY_HEADER:
+                header_tags[key] = value
+            elif state == state_ALIGN_HEADER:
+                align_tags[key] = value
+            elif state == state_ALIGN_QUERY:
+                query_tags[key] = value
+            elif state == state_ALIGN_MATCH:
+                match_tags[key] = value
+            else:
+                raise RuntimeError(f"Unexpected state {state!r}, {line!r}")
+        elif state == state_ALIGN_QUERY:
+            query_seq += line.strip()
+        elif state == state_ALIGN_MATCH:
+            match_seq += line.strip()
+        elif state == state_ALIGN_CONS:
+            cons_seq += line.strip("\n")
+        elif state == state_PREAMBLE:
+            if line.startswith("#"):
+                global_tags["command"] = line[1:].strip()
+            elif line.startswith(" version "):
+                global_tags["version"] = line[9:].strip()
+            elif " compares a " in line:
+                global_tags["tool"] = line[: line.find(" compares a ")].strip()
+            elif " searches a " in line:
+                global_tags["tool"] = line[: line.find(" searches a ")].strip()
+        else:
+            pass

.venv_haddock/lib/python3.12/site-packages/Bio/AlignIO/Interfaces.py

@@ -0,0 +1,158 @@
+# Copyright 2008-2018 by Peter Cock.  All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+"""AlignIO support module (not for general use).
+
+Unless you are writing a new parser or writer for Bio.AlignIO, you should not
+use this module.  It provides base classes to try and simplify things.
+"""
+
+
+class AlignmentIterator:
+    """Base class for building MultipleSeqAlignment iterators.
+
+    You should write a next() method to return Alignment
+    objects.  You may wish to redefine the __init__
+    method as well.
+    """
+
+    def __init__(self, handle, seq_count=None):
+        """Create an AlignmentIterator object.
+
+        Arguments:
+         - handle   - input file
+         - count    - optional, expected number of records per alignment
+           Recommend for fasta file format.
+
+        Note when subclassing:
+         - there should be a single non-optional argument, the handle,
+           and optional count IN THAT ORDER.
+         - you can add additional optional arguments.
+
+        """
+        self.handle = handle
+        self.records_per_alignment = seq_count
+        #####################################################
+        # You may want to subclass this, for example        #
+        # to read through the file to find the first record,#
+        # or if additional arguments are required.          #
+        #####################################################
+
+    def __next__(self):
+        """Return the next alignment in the file.
+
+        This method should be replaced by any derived class to do something
+        useful.
+        """
+        raise NotImplementedError("This object should be subclassed")
+        #####################################################
+        # You SHOULD subclass this, to split the file up    #
+        # into your individual alignments and convert these #
+        # into MultipleSeqAlignment objects.                #
+        #####################################################
+
+    def __iter__(self):
+        """Iterate over the entries as MultipleSeqAlignment objects.
+
+        Example usage for (concatenated) PHYLIP files::
+
+            with open("many.phy","r") as myFile:
+                for alignment in PhylipIterator(myFile):
+                    print("New alignment:")
+                    for record in alignment:
+                        print(record.id)
+                        print(record.seq)
+
+        """
+        return iter(self.__next__, None)
+
+
+class AlignmentWriter:
+    """Base class for building MultipleSeqAlignment writers.
+
+    You should write a write_alignment() method.
+    You may wish to redefine the __init__ method as well.
+    """
+
+    def __init__(self, handle):
+        """Initialize the class."""
+        self.handle = handle
+
+    def write_file(self, alignments):
+        """Use this to write an entire file containing the given alignments.
+
+        Arguments:
+         - alignments - A list or iterator returning MultipleSeqAlignment objects
+
+        In general, this method can only be called once per file.
+
+        This method should be replaced by any derived class to do something
+        useful.  It should return the number of alignments..
+        """
+        raise NotImplementedError("This object should be subclassed")
+        #####################################################
+        # You SHOULD subclass this, to write the alignment  #
+        # objects to the file handle                        #
+        #####################################################
+
+    def clean(self, text):
+        """Use this to avoid getting newlines in the output."""
+        return text.replace("\n", " ").replace("\r", " ")
+
+
+class SequentialAlignmentWriter(AlignmentWriter):
+    """Base class for building MultipleSeqAlignment writers.
+
+    This assumes each alignment can be simply appended to the file.
+    You should write a write_alignment() method.
+    You may wish to redefine the __init__ method as well.
+    """
+
+    def __init__(self, handle):
+        """Initialize the class."""
+        self.handle = handle
+
+    def write_file(self, alignments):
+        """Use this to write an entire file containing the given alignments.
+
+        Arguments:
+         - alignments - A list or iterator returning MultipleSeqAlignment objects
+
+        In general, this method can only be called once per file.
+        """
+        self.write_header()
+        count = 0
+        for alignment in alignments:
+            self.write_alignment(alignment)
+            count += 1
+        self.write_footer()
+        return count
+
+    def write_header(self):
+        """Use this to write any header.
+
+        This method should be replaced by any derived class to do something
+        useful.
+        """
+
+    def write_footer(self):
+        """Use this to write any footer.
+
+        This method should be replaced by any derived class to do something
+        useful.
+        """
+
+    def write_alignment(self, alignment):
+        """Use this to write a single alignment.
+
+        This method should be replaced by any derived class to do something
+        useful.
+        """
+        raise NotImplementedError("This object should be subclassed")
+        #####################################################
+        # You SHOULD subclass this, to write the alignment  #
+        # objects to the file handle                        #
+        #####################################################

.venv_haddock/lib/python3.12/site-packages/Bio/AlignIO/MafIO.py

@@ -0,0 +1,869 @@
+# Copyright 2011, 2012 by Andrew Sczesnak.  All rights reserved.
+# Revisions Copyright 2011, 2017 by Peter Cock.  All rights reserved.
+# Revisions Copyright 2014, 2015 by Adam Novak.  All rights reserved.
+# Revisions Copyright 2015, 2017 by Blaise Li.  All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+"""Bio.AlignIO support for the "maf" multiple alignment format.
+
+The Multiple Alignment Format, described by UCSC, stores a series of
+multiple alignments in a single file. It is suitable for whole-genome
+to whole-genome alignments, metadata such as source chromosome, start
+position, size, and strand can be stored.
+
+See http://genome.ucsc.edu/FAQ/FAQformat.html#format5
+
+You are expected to use this module via the Bio.AlignIO functions(or the
+Bio.SeqIO functions if you want to work directly with the gapped sequences).
+
+Coordinates in the MAF format are defined in terms of zero-based start
+positions (like Python) and aligning region sizes.
+
+A minimal aligned region of length one and starting at first position in the
+source sequence would have ``start == 0`` and ``size == 1``.
+
+As we can see on this example, ``start + size`` will give one more than the
+zero-based end position. We can therefore manipulate ``start`` and
+``start + size`` as python list slice boundaries.
+
+For an inclusive end coordinate, we need to use ``end = start + size - 1``.
+A 1-column wide alignment would have ``start == end``.
+"""
+
+import os
+from itertools import islice
+
+try:
+    from sqlite3 import dbapi2
+except ImportError:
+    dbapi2 = None  # type: ignore
+
+from Bio.Align import MultipleSeqAlignment
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+
+from .Interfaces import SequentialAlignmentWriter
+
+MAFINDEX_VERSION = 2
+
+
+class MafWriter(SequentialAlignmentWriter):
+    """Accepts a MultipleSeqAlignment object, writes a MAF file."""
+
+    def write_header(self):
+        """Write the MAF header."""
+        self.handle.write("##maf version=1 scoring=none\n")
+        self.handle.write("# generated by Biopython\n\n")
+
+    def _write_record(self, record):
+        """Write a single SeqRecord object to an 's' line in a MAF block (PRIVATE)."""
+        # convert biopython-style 1/-1 strand to MAF-style +/- strand
+        if record.annotations.get("strand") == 1:
+            strand = "+"
+        elif record.annotations.get("strand") == -1:
+            strand = "-"
+        else:
+            # TODO: issue warning?
+            strand = "+"
+
+        fields = [
+            "s",
+            # In the MAF file format, spaces are not allowed in the id
+            "%-40s" % record.id.replace(" ", "_"),
+            "%15s" % record.annotations.get("start", 0),
+            "%5s"
+            % record.annotations.get("size", len(str(record.seq).replace("-", ""))),
+            strand,
+            "%15s" % record.annotations.get("srcSize", 0),
+            str(record.seq),
+        ]
+        self.handle.write(f"{' '.join(fields)}\n")
+
+    def write_alignment(self, alignment):
+        """Write a complete alignment to a MAF block.
+
+        Writes every SeqRecord in a MultipleSeqAlignment object to its own
+        MAF block (beginning with an 'a' line, containing 's' lines).
+        """
+        if not isinstance(alignment, MultipleSeqAlignment):
+            raise TypeError("Expected an alignment object")
+
+        if len({len(x) for x in alignment}) > 1:
+            raise ValueError("Sequences must all be the same length")
+
+        # We allow multiple sequences with the same IDs; for example, there may
+        # be a MAF aligning the + and - strands of the same sequence together.
+
+        # for now, use ._annotations private property, but restrict keys to those
+        # specifically supported by the MAF format, according to spec
+        try:
+            anno = " ".join(
+                [
+                    f"{x}={y}"
+                    for x, y in alignment._annotations.items()
+                    if x in ("score", "pass")
+                ]
+            )
+        except AttributeError:
+            anno = "score=0.00"
+
+        self.handle.write(f"a {anno}\n")
+
+        recs_out = 0
+
+        for record in alignment:
+            self._write_record(record)
+
+            recs_out += 1
+
+        self.handle.write("\n")
+
+        return recs_out
+
+
+# Invalid function name according to pylint, but kept for compatibility
+# with Bio* conventions.
+def MafIterator(handle, seq_count=None):
+    """Iterate over a MAF file handle as MultipleSeqAlignment objects.
+
+    Iterates over lines in a MAF file-like object (handle), yielding
+    MultipleSeqAlignment objects. SeqRecord IDs generally correspond to
+    species names.
+    """
+    in_a_bundle = False
+
+    annotations = []
+    records = []
+
+    while True:
+        # allows parsing of the last bundle without duplicating code
+        line = handle.readline()
+
+        try:
+            # Will be in binary mode if called via the indexing code
+            # (which needs the raw offsets for cross platform indexing)
+            line = line.decode("ASCII")
+        except AttributeError:
+            pass
+
+        if in_a_bundle:
+            if line.startswith("s"):
+                # add a SeqRecord to the bundle
+                line_split = line.strip().split()
+
+                if len(line_split) != 7:
+                    raise ValueError(
+                        "Error parsing alignment - 's' line must have 7 fields"
+                    )
+
+                # convert MAF-style +/- strand to biopython-type 1/-1
+                if line_split[4] == "+":
+                    strand = 1
+                elif line_split[4] == "-":
+                    strand = -1
+                else:
+                    # TODO: issue warning, set to 0?
+                    strand = 1
+
+                # s (literal), src (ID), start, size, strand, srcSize, text (sequence)
+                anno = {
+                    "start": int(line_split[2]),
+                    "size": int(line_split[3]),
+                    "strand": strand,
+                    "srcSize": int(line_split[5]),
+                }
+
+                sequence = line_split[6]
+
+                # interpret a dot/period to mean the same as the first sequence
+                if "." in sequence:
+                    if not records:
+                        raise ValueError(
+                            "Found dot/period in first sequence of alignment"
+                        )
+
+                    ref = records[0].seq
+                    new = []
+
+                    for letter, ref_letter in zip(sequence, ref):
+                        new.append(ref_letter if letter == "." else letter)
+
+                    sequence = "".join(new)
+
+                records.append(
+                    SeqRecord(
+                        Seq(sequence),
+                        id=line_split[1],
+                        name=line_split[1],
+                        description="",
+                        annotations=anno,
+                    )
+                )
+            elif line.startswith("i"):
+                # TODO: information about what is in the aligned species DNA before
+                # and after the immediately preceding "s" line
+                pass
+            elif line.startswith("e"):
+                # TODO: information about the size of the gap between the alignments
+                # that span the current block
+                pass
+            elif line.startswith("q"):
+                # TODO: quality of each aligned base for the species.
+                # Need to find documentation on this, looks like ASCII 0-9 or gap?
+                # Can then store in each SeqRecord's .letter_annotations dictionary,
+                # perhaps as the raw string or turned into integers / None for gap?
+                pass
+            elif line.startswith("#"):
+                # ignore comments
+                # (not sure whether comments
+                # are in the maf specification, though)
+                pass
+            elif not line.strip():
+                # end a bundle of records
+                if seq_count is not None:
+                    assert len(records) == seq_count
+
+                alignment = MultipleSeqAlignment(records)
+                # TODO - Introduce an annotated alignment class?
+                # See also Bio/AlignIO/FastaIO.py for same requirement.
+                # For now, store the annotation a new private property:
+                alignment._annotations = annotations
+
+                yield alignment
+
+                in_a_bundle = False
+
+                annotations = []
+                records = []
+            else:
+                raise ValueError(f"Error parsing alignment - unexpected line:\n{line}")
+        elif line.startswith("a"):
+            # start a bundle of records
+            in_a_bundle = True
+            annot_strings = line.strip().split()[1:]
+            if len(annot_strings) != line.count("="):
+                raise ValueError("Error parsing alignment - invalid key in 'a' line")
+            annotations = dict(a_string.split("=") for a_string in annot_strings)
+        elif line.startswith("#"):
+            # ignore comments
+            pass
+        elif not line:
+            break
+
+
+class MafIndex:
+    """Index for a MAF file.
+
+    The index is a sqlite3 database that is built upon creation of the object
+    if necessary, and queried when methods *search* or *get_spliced* are
+    used.
+    """
+
+    def __init__(self, sqlite_file, maf_file, target_seqname):
+        """Indexes or loads the index of a MAF file."""
+        if dbapi2 is None:
+            # Python was compiled without sqlite3 support
+            from Bio import MissingPythonDependencyError
+
+            raise MissingPythonDependencyError(
+                "Python was compiled without the sqlite3 module"
+            )
+
+        self._target_seqname = target_seqname
+        # example: Tests/MAF/ucsc_mm9_chr10.mafindex
+        self._index_filename = sqlite_file
+        # example: /home/bli/src/biopython/Tests/MAF
+        self._relative_path = os.path.abspath(os.path.dirname(sqlite_file))
+        # example: Tests/MAF/ucsc_mm9_chr10.maf
+        self._maf_file = maf_file
+
+        # Opening in bytes mode as want real offsets, not where
+        # Python attempts to hide cross-platform newline differences etc
+        self._maf_fp = open(self._maf_file, "rb")
+
+        # if sqlite_file exists, use the existing db, otherwise index the file
+        if os.path.isfile(sqlite_file):
+            self._con = dbapi2.connect(sqlite_file)
+            try:
+                self._record_count = self.__check_existing_db()
+            except ValueError as err:
+                self._maf_fp.close()
+                self._con.close()
+                raise err from None
+        else:
+            self._con = dbapi2.connect(sqlite_file)
+            try:
+                self._record_count = self.__make_new_index()
+            except ValueError as err:
+                self._maf_fp.close()
+                self._con.close()
+                raise err from None
+
+        # lastly, setup a MafIterator pointing at the open maf_file
+        self._mafiter = MafIterator(self._maf_fp)
+
+    def close(self):
+        """Close the file handle being used to read the data.
+
+        Once called, further use of the index won't work. The sole
+        purpose of this method is to allow explicit handle closure
+        - for example if you wish to delete the file, on Windows
+        you must first close all open handles to that file.
+        """
+        self._con.close()
+        self._record_count = 0
+
+    def __check_existing_db(self):
+        """Perform basic sanity checks upon loading an existing index (PRIVATE)."""
+        try:
+            idx_version = int(
+                self._con.execute(
+                    "SELECT value FROM meta_data WHERE key = 'version'"
+                ).fetchone()[0]
+            )
+            if idx_version != MAFINDEX_VERSION:
+                msg = "\n".join(
+                    [
+                        "Index version (%s) incompatible with this version "
+                        "of MafIndex" % idx_version,
+                        "You might erase the existing index %s "
+                        "for it to be rebuilt." % self._index_filename,
+                    ]
+                )
+                raise ValueError(msg)
+
+            filename = self._con.execute(
+                "SELECT value FROM meta_data WHERE key = 'filename'"
+            ).fetchone()[0]
+            # Compute absolute path of the original maf file
+            if os.path.isabs(filename):
+                # It was already stored as absolute
+                tmp_mafpath = filename
+            else:
+                # It should otherwise have been stored as relative to the index
+                # Would be stored with Unix / path separator, so convert
+                # it to the local OS path separator here:
+                tmp_mafpath = os.path.join(
+                    self._relative_path, filename.replace("/", os.path.sep)
+                )
+            if tmp_mafpath != os.path.abspath(self._maf_file):
+                # Original and given absolute paths differ.
+                raise ValueError(
+                    f"Index uses a different file ({filename} != {self._maf_file})"
+                )
+
+            db_target = self._con.execute(
+                "SELECT value FROM meta_data WHERE key = 'target_seqname'"
+            ).fetchone()[0]
+            if db_target != self._target_seqname:
+                raise ValueError(
+                    "Provided database indexed for %s, expected %s"
+                    % (db_target, self._target_seqname)
+                )
+
+            record_count = int(
+                self._con.execute(
+                    "SELECT value FROM meta_data WHERE key = 'record_count'"
+                ).fetchone()[0]
+            )
+            if record_count == -1:
+                raise ValueError("Unfinished/partial database provided")
+
+            records_found = int(
+                self._con.execute("SELECT COUNT(*) FROM offset_data").fetchone()[0]
+            )
+            if records_found != record_count:
+                raise ValueError(
+                    "Expected %s records, found %s.  Corrupt index?"
+                    % (record_count, records_found)
+                )
+
+            return records_found
+
+        except (dbapi2.OperationalError, dbapi2.DatabaseError) as err:
+            raise ValueError(f"Problem with SQLite database: {err}") from None
+
+    def __make_new_index(self):
+        """Read MAF file and generate SQLite index (PRIVATE)."""
+        # make the tables
+        self._con.execute("CREATE TABLE meta_data (key TEXT, value TEXT);")
+        self._con.execute(
+            "INSERT INTO meta_data (key, value) VALUES (?, ?);",
+            ("version", MAFINDEX_VERSION),
+        )
+        self._con.execute(
+            "INSERT INTO meta_data (key, value) VALUES ('record_count', -1);"
+        )
+        self._con.execute(
+            "INSERT INTO meta_data (key, value) VALUES (?, ?);",
+            ("target_seqname", self._target_seqname),
+        )
+        # Determine whether to store maf file as relative to the index or absolute
+        # See https://github.com/biopython/biopython/pull/381
+        if not os.path.isabs(self._maf_file) and not os.path.isabs(
+            self._index_filename
+        ):
+            # Since the user gave both maf file and index as relative paths,
+            # we will store the maf file relative to the index.
+            # Note for cross platform use (e.g. shared drive over SAMBA),
+            # convert any Windows slash into Unix style for rel paths.
+            # example: ucsc_mm9_chr10.maf
+            mafpath = os.path.relpath(self._maf_file, self._relative_path).replace(
+                os.path.sep, "/"
+            )
+        elif (
+            os.path.dirname(os.path.abspath(self._maf_file)) + os.path.sep
+        ).startswith(self._relative_path + os.path.sep):
+            # Since maf file is in same directory or sub directory,
+            # might as well make this into a relative path:
+            mafpath = os.path.relpath(self._maf_file, self._relative_path).replace(
+                os.path.sep, "/"
+            )
+        else:
+            # Default to storing as an absolute path
+            # example: /home/bli/src/biopython/Tests/MAF/ucsc_mm9_chr10.maf
+            mafpath = os.path.abspath(self._maf_file)
+        self._con.execute(
+            "INSERT INTO meta_data (key, value) VALUES (?, ?);",
+            ("filename", mafpath),
+        )
+        self._con.execute(
+            "CREATE TABLE offset_data (bin INTEGER, start INTEGER, end INTEGER, offset INTEGER);"
+        )
+
+        insert_count = 0
+
+        # iterate over the entire file and insert in batches
+        mafindex_func = self.__maf_indexer()
+
+        while True:
+            batch = list(islice(mafindex_func, 100))
+            if not batch:
+                break
+
+            # batch is made from self.__maf_indexer(),
+            # which yields zero-based "inclusive" start and end coordinates
+            self._con.executemany(
+                "INSERT INTO offset_data (bin, start, end, offset) VALUES (?,?,?,?);",
+                batch,
+            )
+            self._con.commit()
+            insert_count += len(batch)
+
+        # then make indexes on the relevant fields
+        self._con.execute("CREATE INDEX IF NOT EXISTS bin_index ON offset_data(bin);")
+        self._con.execute(
+            "CREATE INDEX IF NOT EXISTS start_index ON offset_data(start);"
+        )
+        self._con.execute("CREATE INDEX IF NOT EXISTS end_index ON offset_data(end);")
+
+        self._con.execute(
+            f"UPDATE meta_data SET value = '{insert_count}' WHERE key = 'record_count'"
+        )
+
+        self._con.commit()
+
+        return insert_count
+
+    def __maf_indexer(self):
+        """Return index information for each bundle (PRIVATE).
+
+        Yields index information for each bundle in the form of
+        (bin, start, end, offset) tuples where start and end are
+        0-based inclusive coordinates.
+        """
+        line = self._maf_fp.readline()
+
+        while line:
+            if line.startswith(b"a"):
+                # note the offset
+                offset = self._maf_fp.tell() - len(line)
+
+                # search the following lines for a match to target_seqname
+                while True:
+                    line = self._maf_fp.readline()
+
+                    if not line.strip() or line.startswith(b"a"):
+                        # Empty line or new alignment record
+                        raise ValueError(
+                            "Target for indexing (%s) not found in this bundle"
+                            % (self._target_seqname,)
+                        )
+                    elif line.startswith(b"s"):
+                        # s (literal), src (ID), start, size, strand, srcSize, text (sequence)
+                        line_split = line.decode("ASCII").strip().split()
+
+                        if line_split[1] == self._target_seqname:
+                            start = int(line_split[2])
+                            size = int(line_split[3])
+                            if size != len(line_split[6].replace("-", "")):
+                                raise ValueError(
+                                    "Invalid length for target coordinates "
+                                    "(expected %s, found %s)"
+                                    % (size, len(line_split[6].replace("-", "")))
+                                )
+
+                            # "inclusive" end position is start + length - 1
+                            end = start + size - 1
+
+                            # _ucscbin takes end-exclusive coordinates
+                            yield (self._ucscbin(start, end + 1), start, end, offset)
+
+                            break
+
+            line = self._maf_fp.readline()
+
+    # TODO: check coordinate correctness for the two bin-related static methods
+    @staticmethod
+    def _region2bin(start, end):
+        """Find bins that a region may belong to (PRIVATE).
+
+        Converts a region to a list of bins that it may belong to, including largest
+        and smallest bins.
+        """
+        bins = [0, 1]
+
+        bins.extend(range(1 + (start >> 26), 2 + ((end - 1) >> 26)))
+        bins.extend(range(9 + (start >> 23), 10 + ((end - 1) >> 23)))
+        bins.extend(range(73 + (start >> 20), 74 + ((end - 1) >> 20)))
+        bins.extend(range(585 + (start >> 17), 586 + ((end - 1) >> 17)))
+
+        return set(bins)
+
+    @staticmethod
+    def _ucscbin(start, end):
+        """Return the smallest bin a given region will fit into (PRIVATE).
+
+        Adapted from http://genomewiki.ucsc.edu/index.php/Bin_indexing_system
+        """
+        bin_offsets = [512 + 64 + 8 + 1, 64 + 8 + 1, 8 + 1, 1, 0]
+
+        _bin_first_shift = 17
+        _bin_next_shift = 3
+
+        start_bin = start
+        end_bin = end - 1
+
+        start_bin >>= _bin_first_shift
+        end_bin >>= _bin_first_shift
+
+        for bin_offset in bin_offsets:
+            if start_bin == end_bin:
+                return bin_offset + start_bin
+            start_bin >>= _bin_next_shift
+            end_bin >>= _bin_next_shift
+
+        return 0
+
+    def _get_record(self, offset):
+        """Retrieve a single MAF record located at the offset provided (PRIVATE)."""
+        self._maf_fp.seek(offset)
+        return next(self._mafiter)
+
+    def search(self, starts, ends):
+        """Search index database for MAF records overlapping ranges provided.
+
+        Returns *MultipleSeqAlignment* results in order by start, then end, then
+        internal offset field.
+
+        *starts* should be a list of 0-based start coordinates of segments in the reference.
+        *ends* should be the list of the corresponding segment ends
+        (in the half-open UCSC convention:
+        http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/).
+        """
+        # verify the provided exon coordinates
+        if len(starts) != len(ends):
+            raise ValueError("Every position in starts must have a match in ends")
+
+        # Could it be safer to sort the (exonstart, exonend) pairs?
+        for exonstart, exonend in zip(starts, ends):
+            exonlen = exonend - exonstart
+            if exonlen < 1:
+                raise ValueError(
+                    "Exon coordinates (%d, %d) invalid: exon length (%d) < 1"
+                    % (exonstart, exonend, exonlen)
+                )
+        con = self._con
+
+        # Keep track of what blocks have already been yielded
+        # in order to avoid duplicating them
+        # (see https://github.com/biopython/biopython/issues/1083)
+        yielded_rec_coords = set()
+        # search for every exon
+        for exonstart, exonend in zip(starts, ends):
+            try:
+                possible_bins = ", ".join(
+                    map(str, self._region2bin(exonstart, exonend))
+                )
+            except TypeError:
+                raise TypeError(
+                    "Exon coordinates must be integers "
+                    "(start=%d, end=%d)" % (exonstart, exonend)
+                ) from None
+
+            # https://www.sqlite.org/lang_expr.html
+            # -----
+            # The BETWEEN operator
+            #
+            # The BETWEEN operator is logically equivalent to a pair of
+            # comparisons. "x BETWEEN y AND z" is equivalent to "x>=y AND x<=z"
+            # except that with BETWEEN, the x expression is only evaluated
+            # once. The precedence of the BETWEEN operator is the same as the
+            # precedence as operators == and != and LIKE and groups left to
+            # right.
+            # -----
+
+            # We are testing overlap between the query segment and records in
+            # the index, using non-strict coordinates comparisons.
+            # The query segment end must be passed as end-inclusive
+            # The index should also have been build with end-inclusive
+            # end coordinates.
+            # See https://github.com/biopython/biopython/pull/1086#issuecomment-285069073
+
+            result = con.execute(
+                "SELECT DISTINCT start, end, offset FROM offset_data "
+                "WHERE bin IN (%s) "
+                "AND (end BETWEEN %s AND %s OR %s BETWEEN start AND end) "
+                "ORDER BY start, end, offset ASC;"
+                % (possible_bins, exonstart, exonend - 1, exonend - 1)
+            )
+
+            rows = result.fetchall()
+
+            # rows come from the sqlite index,
+            # which should have been written using __make_new_index,
+            # so rec_start and rec_end should be zero-based "inclusive" coordinates
+            for rec_start, rec_end, offset in rows:
+                # Avoid yielding multiple time the same block
+                if (rec_start, rec_end) in yielded_rec_coords:
+                    continue
+                else:
+                    yielded_rec_coords.add((rec_start, rec_end))
+                # Iterate through hits, fetching alignments from the MAF file
+                # and checking to be sure we've retrieved the expected record.
+
+                fetched = self._get_record(int(offset))
+
+                for record in fetched:
+                    if record.id == self._target_seqname:
+                        # start and size come from the maf lines
+                        start = record.annotations["start"]
+                        # "inclusive" end is start + length - 1
+                        end = start + record.annotations["size"] - 1
+
+                        if not (start == rec_start and end == rec_end):
+                            raise ValueError(
+                                "Expected %s-%s @ offset %s, found %s-%s"
+                                % (rec_start, rec_end, offset, start, end)
+                            )
+
+                yield fetched
+
+    def get_spliced(self, starts, ends, strand=1):
+        """Return a multiple alignment of the exact sequence range provided.
+
+        Accepts two lists of start and end positions on target_seqname, representing
+        exons to be spliced in silico.  Returns a *MultipleSeqAlignment* of the
+        desired sequences spliced together.
+
+        *starts* should be a list of 0-based start coordinates of segments in the reference.
+        *ends* should be the list of the corresponding segment ends
+        (in the half-open UCSC convention:
+        http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/).
+
+        To ask for the alignment portion corresponding to the first 100
+        nucleotides of the reference sequence, you would use
+        ``search([0], [100])``
+        """
+        # validate strand
+        if strand not in (1, -1):
+            raise ValueError(f"Strand must be 1 or -1, got {strand}")
+
+        # pull all alignments that span the desired intervals
+        fetched = list(self.search(starts, ends))
+
+        # keep track of the expected letter count
+        # (sum of lengths of [start, end) segments,
+        # where [start, end) half-open)
+        expected_letters = sum(end - start for start, end in zip(starts, ends))
+
+        # if there's no alignment, return filler for the assembly of the length given
+        if len(fetched) == 0:
+            return MultipleSeqAlignment(
+                [SeqRecord(Seq("N" * expected_letters), id=self._target_seqname)]
+            )
+
+        # find the union of all IDs in these alignments
+        all_seqnames = {sequence.id for multiseq in fetched for sequence in multiseq}
+
+        # split every record by base position
+        # key: sequence name
+        # value: dictionary
+        #        key: position in the reference sequence
+        #        value: letter(s) (including letters
+        #               aligned to the "-" preceding the letter
+        #               at the position in the reference, if any)
+        split_by_position = {seq_name: {} for seq_name in all_seqnames}
+
+        # keep track of what the total number of (unspliced) letters should be
+        total_rec_length = 0
+
+        # track first strand encountered on the target seqname
+        ref_first_strand = None
+
+        for multiseq in fetched:
+            # find the target_seqname in this MultipleSeqAlignment and use it to
+            # set the parameters for the rest of this iteration
+            for seqrec in multiseq:
+                if seqrec.id == self._target_seqname:
+                    try:
+                        if ref_first_strand is None:
+                            ref_first_strand = seqrec.annotations["strand"]
+
+                            if ref_first_strand not in (1, -1):
+                                raise ValueError("Strand must be 1 or -1")
+                        elif ref_first_strand != seqrec.annotations["strand"]:
+                            raise ValueError(
+                                "Encountered strand='%s' on target seqname, "
+                                "expected '%s'"
+                                % (seqrec.annotations["strand"], ref_first_strand)
+                            )
+                    except KeyError:
+                        raise ValueError(
+                            "No strand information for target seqname (%s)"
+                            % self._target_seqname
+                        ) from None
+                    # length including gaps (i.e. alignment length)
+                    rec_length = len(seqrec)
+                    rec_start = seqrec.annotations["start"]
+                    ungapped_length = seqrec.annotations["size"]
+                    # inclusive end in zero-based coordinates of the reference
+                    rec_end = rec_start + ungapped_length - 1
+                    # This is length in terms of actual letters in the reference
+                    total_rec_length += ungapped_length
+
+                    # blank out these positions for every seqname
+                    for seqrec in multiseq:
+                        for pos in range(rec_start, rec_end + 1):
+                            split_by_position[seqrec.id][pos] = ""
+
+                    break
+            # http://psung.blogspot.fr/2007/12/for-else-in-python.html
+            # https://docs.python.org/2/tutorial/controlflow.html#break-and-continue-statements-and-else-clauses-on-loops
+            else:
+                raise ValueError(
+                    f"Did not find {self._target_seqname} in alignment bundle"
+                )
+
+            # the true, chromosome/contig/etc position in the target seqname
+            real_pos = rec_start
+
+            # loop over the alignment to fill split_by_position
+            for gapped_pos in range(rec_length):
+                for seqrec in multiseq:
+                    # keep track of this position's value for the target seqname
+                    if seqrec.id == self._target_seqname:
+                        track_val = seqrec.seq[gapped_pos]
+
+                    # Here, a real_pos that corresponds to just after a series of "-"
+                    # in the reference will "accumulate" the letters found in other sequences
+                    # in front of the "-"s
+                    split_by_position[seqrec.id][real_pos] += seqrec.seq[gapped_pos]
+
+                # increment the real_pos counter only when non-gaps are found in
+                # the target_seqname, and we haven't reached the end of the record
+                if track_val != "-" and real_pos < rec_end:
+                    real_pos += 1
+
+        # make sure the number of bp entries equals the sum of the record lengths
+        if len(split_by_position[self._target_seqname]) != total_rec_length:
+            raise ValueError(
+                "Target seqname (%s) has %s records, expected %s"
+                % (
+                    self._target_seqname,
+                    len(split_by_position[self._target_seqname]),
+                    total_rec_length,
+                )
+            )
+
+        # translates a position in the target_seqname sequence to its gapped length
+        realpos_to_len = {
+            pos: len(gapped_fragment)
+            for pos, gapped_fragment in split_by_position[self._target_seqname].items()
+            if len(gapped_fragment) > 1
+        }
+
+        # splice together the exons
+        subseq = {}
+
+        for seqid in all_seqnames:
+            seq_split = split_by_position[seqid]
+            seq_splice = []
+
+            filler_char = "N" if seqid == self._target_seqname else "-"
+
+            # iterate from start to end, taking bases from split_by_position when
+            # they exist, using N or - for gaps when there is no alignment.
+            append = seq_splice.append
+
+            for exonstart, exonend in zip(starts, ends):
+                # exonend is exclusive
+                for real_pos in range(exonstart, exonend):
+                    # if this seqname has this position, add it
+                    if real_pos in seq_split:
+                        append(seq_split[real_pos])
+                    # if not, but it's in the target_seqname, add length-matched filler
+                    elif real_pos in realpos_to_len:
+                        append(filler_char * realpos_to_len[real_pos])
+                    # it's not in either, so add a single filler character
+                    else:
+                        append(filler_char)
+
+            subseq[seqid] = "".join(seq_splice)
+
+        # make sure we're returning the right number of letters
+        if len(subseq[self._target_seqname].replace("-", "")) != expected_letters:
+            raise ValueError(
+                "Returning %s letters for target seqname (%s), expected %s"
+                % (
+                    len(subseq[self._target_seqname].replace("-", "")),
+                    self._target_seqname,
+                    expected_letters,
+                )
+            )
+
+        # check to make sure all sequences are the same length as the target seqname
+        ref_subseq_len = len(subseq[self._target_seqname])
+
+        for seqid, seq in subseq.items():
+            if len(seq) != ref_subseq_len:
+                raise ValueError(
+                    "Returning length %s for %s, expected %s"
+                    % (len(seq), seqid, ref_subseq_len)
+                )
+
+        # finally, build a MultipleSeqAlignment object for our final sequences
+        result_multiseq = []
+
+        for seqid, seq in subseq.items():
+            seq = Seq(seq)
+
+            seq = seq if strand == ref_first_strand else seq.reverse_complement()
+
+            result_multiseq.append(SeqRecord(seq, id=seqid, name=seqid, description=""))
+
+        return MultipleSeqAlignment(result_multiseq)
+
+    def __repr__(self):
+        """Return a string representation of the index."""
+        return "MafIO.MafIndex(%r, target_seqname=%r)" % (
+            self._maf_fp.name,
+            self._target_seqname,
+        )
+
+    def __len__(self):
+        """Return the number of records in the index."""
+        return self._record_count

.venv_haddock/lib/python3.12/site-packages/Bio/AlignIO/MauveIO.py

@@ -0,0 +1,343 @@
+# Copyright 2015-2015 by Eric Rasche.  All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+"""Bio.AlignIO support for "xmfa" output from Mauve/ProgressiveMauve.
+
+You are expected to use this module via the Bio.AlignIO functions (or the
+Bio.SeqIO functions if you want to work directly with the gapped sequences).
+
+For example, consider a progressiveMauve alignment file containing the following::
+
+    #FormatVersion Mauve1
+    #Sequence1File	a.fa
+    #Sequence1Entry	1
+    #Sequence1Format	FastA
+    #Sequence2File	b.fa
+    #Sequence2Entry	2
+    #Sequence2Format	FastA
+    #Sequence3File	c.fa
+    #Sequence3Entry	3
+    #Sequence3Format	FastA
+    #BackboneFile	three.xmfa.bbcols
+    > 1:0-0 + a.fa
+    --------------------------------------------------------------------------------
+    --------------------------------------------------------------------------------
+    --------------------------------------------------------------------------------
+    > 2:5417-5968 + b.fa
+    TTTAAACATCCCTCGGCCCGTCGCCCTTTTATAATAGCAGTACGTGAGAGGAGCGCCCTAAGCTTTGGGAAATTCAAGC-
+    --------------------------------------------------------------------------------
+    CTGGAACGTACTTGCTGGTTTCGCTACTATTTCAAACAAGTTAGAGGCCGTTACCTCGGGCGAACGTATAAACCATTCTG
+    > 3:9476-10076 - c.fa
+    TTTAAACACCTTTTTGGATG--GCCCAGTTCGTTCAGTTGTG-GGGAGGAGATCGCCCCAAACGTATGGTGAGTCGGGCG
+    TTTCCTATAGCTATAGGACCAATCCACTTACCATACGCCCGGCGTCGCCCAGTCCGGTTCGGTACCCTCCATGACCCACG
+    ---------------------------------------------------------AAATGAGGGCCCAGGGTATGCTT
+    =
+    > 2:5969-6015 + b.fa
+    -----------------------
+    GGGCGAACGTATAAACCATTCTG
+    > 3:9429-9476 - c.fa
+    TTCGGTACCCTCCATGACCCACG
+    AAATGAGGGCCCAGGGTATGCTT
+
+This is a multiple sequence alignment with multiple aligned sections, so you
+would probably load this using the Bio.AlignIO.parse() function:
+
+    >>> from Bio import AlignIO
+    >>> align = AlignIO.parse("Mauve/simple_short.xmfa", "mauve")
+    >>> alignments = list(align)
+    >>> for aln in alignments:
+    ...     print(aln)
+    ...
+    Alignment with 3 rows and 240 columns
+    --------------------------------------------...--- a.fa
+    TTTAAACATCCCTCGGCCCGTCGCCCTTTTATAATAGCAGTACG...CTG b.fa/5416-5968
+    TTTAAACACCTTTTTGGATG--GCCCAGTTCGTTCAGTTGTG-G...CTT c.fa/9475-10076
+    Alignment with 2 rows and 46 columns
+    -----------------------GGGCGAACGTATAAACCATTCTG b.fa/5968-6015
+    TTCGGTACCCTCCATGACCCACGAAATGAGGGCCCAGGGTATGCTT c.fa/9428-9476
+
+Additional information is extracted from the XMFA file and available through
+the annotation attribute of each record::
+
+    >>> for record in alignments[0]:
+    ...     print(record.id, len(record))
+    ...     print("  start: %d, end: %d, strand: %d" %(
+    ...         record.annotations['start'], record.annotations['end'],
+    ...         record.annotations['strand']))
+    ...
+    a.fa 240
+      start: 0, end: 0, strand: 1
+    b.fa/5416-5968 240
+      start: 5416, end: 5968, strand: 1
+    c.fa/9475-10076 240
+      start: 9475, end: 10076, strand: -1
+
+"""
+
+import re
+
+from Bio.Align import MultipleSeqAlignment
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+
+from .Interfaces import AlignmentIterator
+from .Interfaces import SequentialAlignmentWriter
+
+XMFA_HEADER_REGEX = re.compile(
+    r"> (?P<id>\d+):(?P<start>\d+)-(?P<end>\d+) (?P<strand>[+-]) (?P<name>.*)"
+)
+XMFA_HEADER_REGEX_BIOPYTHON = re.compile(
+    r"> (?P<id>\d+):(?P<start>\d+)-(?P<end>\d+) (?P<strand>[+-]) (?P<name>[^#]*) # (?P<realname>.*)"
+)
+ID_LINE_FMT = "> {seq_name}:{start}-{end} {strand} {filename} # {ugly_hack}"
+
+
+def _identifier_split(identifier):
+    """Return (name, start, end) string tuple from an identifier (PRIVATE)."""
+    id, loc, strand = identifier.split(":")
+    start, end = map(int, loc.split("-"))
+    start -= 1
+    return id, start, end, strand
+
+
+class MauveWriter(SequentialAlignmentWriter):
+    """Mauve/XMFA alignment writer."""
+
+    def __init__(self, *args, **kwargs):
+        """Initialize the class."""
+        super().__init__(*args, **kwargs)
+        self._wrote_header = False
+        self._wrote_first = False
+
+    def write_alignment(self, alignment):
+        """Use this to write (another) single alignment to an open file.
+
+        Note that sequences and their annotation are recorded
+        together (rather than having a block of annotation followed
+        by a block of aligned sequences).
+        """
+        count = len(alignment)
+
+        self._length_of_sequences = alignment.get_alignment_length()
+
+        # NOTE - For now, the alignment object does not hold any per column
+        # or per alignment annotation - only per sequence.
+
+        if count == 0:
+            raise ValueError("Must have at least one sequence")
+        if self._length_of_sequences == 0:
+            raise ValueError("Non-empty sequences are required")
+
+        if not self._wrote_header:
+            self._wrote_header = True
+            self.handle.write("#FormatVersion Mauve1\n")
+            # There are some more headers, but we ignore those for now.
+            # Sequence1File	unknown.fa
+            # Sequence1Entry	1
+            # Sequence1Format	FastA
+            for i in range(1, count + 1):
+                self.handle.write(f"#Sequence{i}Entry\t{i}\n")
+
+        for idx, record in enumerate(alignment):
+            self._write_record(record, record_idx=idx)
+        self.handle.write("=\n")
+
+    def _write_record(self, record, record_idx=0):
+        """Write a single SeqRecord to the file (PRIVATE)."""
+        if self._length_of_sequences != len(record.seq):
+            raise ValueError("Sequences must all be the same length")
+
+        seq_name = record.name
+        try:
+            seq_name = str(int(record.name))
+        except ValueError:
+            seq_name = str(record_idx + 1)
+
+        # We remove the "/{start}-{end}" before writing, as it cannot be part
+        # of the produced XMFA file.
+        if "start" in record.annotations and "end" in record.annotations:
+            suffix0 = f"/{record.annotations['start']}-{record.annotations['end']}"
+            suffix1 = f"/{record.annotations['start'] + 1}-{record.annotations['end']}"
+            if seq_name[-len(suffix0) :] == suffix0:
+                seq_name = seq_name[: -len(suffix0)]
+            if seq_name[-len(suffix1) :] == suffix1:
+                seq_name = seq_name[: -len(suffix1)]
+
+        if (
+            "start" in record.annotations
+            and "end" in record.annotations
+            and "strand" in record.annotations
+        ):
+            id_line = ID_LINE_FMT.format(
+                seq_name=seq_name,
+                start=record.annotations["start"] + 1,
+                end=record.annotations["end"],
+                strand=("+" if record.annotations["strand"] == 1 else "-"),
+                filename=record.name + ".fa",
+                ugly_hack=record.id,
+            )
+            lacking_annotations = False
+        else:
+            id_line = ID_LINE_FMT.format(
+                seq_name=seq_name,
+                start=0,
+                end=0,
+                strand="+",
+                filename=record.name + ".fa",
+                ugly_hack=record.id,
+            )
+            lacking_annotations = True
+
+        # If the sequence is an empty one, skip writing it out
+        if (":0-0 " in id_line or ":1-0 " in id_line) and not lacking_annotations:
+            # Except in the first LCB
+            if not self._wrote_first:
+                self._wrote_first = True
+                # The first LCB we write out is special, and must list ALL
+                # sequences, for the Mauve GUI
+                # http://darlinglab.org/mauve/user-guide/files.html#non-standard-xmfa-formatting-used-by-the-mauve-gui
+                id_line = ID_LINE_FMT.format(
+                    seq_name=seq_name,
+                    start=0,
+                    end=0,
+                    strand="+",
+                    filename=record.name + ".fa",
+                    ugly_hack=record.id,
+                )
+                id_line = id_line.replace("\n", " ").replace("\r", " ")
+                self.handle.write(id_line + "\n\n")
+            # Alignments lacking a start/stop/strand were generated by
+            # Biopython on load, and shouldn't exist according to XMFA
+        else:
+            # In other blocks, we only write sequences if they exist in a given
+            # alignment.
+            id_line = id_line.replace("\n", " ").replace("\r", " ")
+            self.handle.write(id_line + "\n")
+            for i in range(0, len(record.seq), 80):
+                self.handle.write(f"{record.seq[i : i + 80]}\n")
+
+
+class MauveIterator(AlignmentIterator):
+    """Mauve xmfa alignment iterator."""
+
+    _ids: list[str] = []  # for caching IDs between __next__ calls
+
+    def __next__(self):
+        """Parse the next alignment from the handle."""
+        handle = self.handle
+        line = handle.readline()
+
+        if not line:
+            raise StopIteration
+
+        # Strip out header comments
+        while line and line.strip().startswith("#"):
+            line = handle.readline()
+
+        seqs = {}
+        seq_regions = {}
+        passed_end_alignment = False
+
+        latest_id = None
+        while True:
+            if not line:
+                break  # end of file
+            line = line.strip()
+
+            if line.startswith("="):
+                # There may be more data, but we've reached the end of this
+                # alignment
+                break
+            elif line.startswith(">"):
+                m = XMFA_HEADER_REGEX_BIOPYTHON.match(line)
+                if not m:
+                    m = XMFA_HEADER_REGEX.match(line)
+                    if not m:
+                        raise ValueError("Malformed header line: %s", line)
+
+                parsed_id = m.group("id")
+                parsed_data = {}
+                for key in ("start", "end", "id", "strand", "name", "realname"):
+                    try:
+                        value = m.group(key)
+                        if key == "start":
+                            value = int(value)
+                            # Convert to zero based counting
+                            if value > 0:
+                                value -= 1
+
+                        if key == "end":
+                            value = int(value)
+                        parsed_data[key] = value
+                    except IndexError:
+                        # This will occur if we're asking for a group that
+                        # doesn't exist. It's fine.
+                        pass
+                seq_regions[parsed_id] = parsed_data
+
+                if parsed_id not in self._ids:
+                    self._ids.append(parsed_id)
+
+                seqs.setdefault(parsed_id, "")
+                latest_id = parsed_id
+            else:
+                assert not passed_end_alignment
+                if latest_id is None:
+                    raise ValueError("Saw sequence before definition line")
+                seqs[latest_id] += line
+            line = handle.readline()
+
+        assert len(seqs) <= len(self._ids)
+
+        self.ids = self._ids
+        self.sequences = seqs
+
+        if self._ids and seqs:
+            alignment_length = max(map(len, list(seqs.values())))
+            records = []
+            for id in self._ids:
+                if id not in seqs or len(seqs[id]) == 0 or len(seqs[id]) == 0:
+                    seq = "-" * alignment_length
+                else:
+                    seq = seqs[id]
+
+                if alignment_length != len(seq):
+                    raise ValueError(
+                        "Sequences have different lengths, or repeated identifier"
+                    )
+
+                # Sometimes we don't see a particular sequence in the
+                # alignment, so we skip that record since it isn't present in
+                # that LCB/alignment
+                if id not in seq_regions:
+                    continue
+
+                if seq_regions[id]["start"] != 0 or seq_regions[id]["end"] != 0:
+                    suffix = "/{start}-{end}".format(**seq_regions[id])
+                    if "realname" in seq_regions[id]:
+                        corrected_id = seq_regions[id]["realname"]
+                    else:
+                        corrected_id = seq_regions[id]["name"]
+                    if corrected_id.count(suffix) == 0:
+                        corrected_id += suffix
+                else:
+                    if "realname" in seq_regions[id]:
+                        corrected_id = seq_regions[id]["realname"]
+                    else:
+                        corrected_id = seq_regions[id]["name"]
+
+                record = SeqRecord(Seq(seq), id=corrected_id, name=id)
+
+                record.annotations["start"] = seq_regions[id]["start"]
+                record.annotations["end"] = seq_regions[id]["end"]
+                record.annotations["strand"] = (
+                    1 if seq_regions[id]["strand"] == "+" else -1
+                )
+
+                records.append(record)
+            return MultipleSeqAlignment(records)
+        else:
+            raise StopIteration

.venv_haddock/lib/python3.12/site-packages/Bio/AlignIO/MsfIO.py

@@ -0,0 +1,333 @@
+# Copyright 2019, National Marrow Donor Program (NMPD).  All rights reserved.
+# Written by Peter Cock, The James Hutton Institute, under contract to NMDP.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+"""Bio.AlignIO support for GCG MSF format.
+
+The file format was produced by the GCG PileUp and and LocalPileUp tools,
+and later tools such as T-COFFEE and MUSCLE support it as an optional
+output format.
+
+The original GCG tool would write gaps at ends of each sequence which could
+be missing data as tildes (``~``), whereas internal gaps were periods (``.``)
+instead. This parser replaces both with minus signs (``-``) for consistency
+with the rest of ``Bio.AlignIO``.
+
+You are expected to use this module via the Bio.AlignIO functions (or the
+Bio.SeqIO functions if you want to work directly with the gapped sequences).
+"""
+
+from Bio.Align import MultipleSeqAlignment
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+
+from .Interfaces import AlignmentIterator
+
+
+class MsfIterator(AlignmentIterator):
+    """GCG MSF alignment iterator."""
+
+    _header = None  # for caching lines between __next__ calls
+
+    def __next__(self):
+        """Parse the next alignment from the handle."""
+        handle = self.handle
+
+        if self._header is None:
+            line = handle.readline()
+        else:
+            # Header we saved from when we were parsing
+            # the previous alignment.
+            line = self._header
+            self._header = None
+
+        if not line:
+            raise StopIteration
+
+        # Whitelisted headers we know about.
+        known_headers = ["!!NA_MULTIPLE_ALIGNMENT", "!!AA_MULTIPLE_ALIGNMENT", "PileUp"]
+        # Examples in "Molecular Biology Software Training Manual GCG version 10"
+        # by BBSRC Bioscuences IT Services (BITS), Harpenden, UK, Copyright 1996-2001
+        # would often start as follows:
+        #
+        # !!AA_MUTIPLE_ALIGNMENT 1.0
+        # PileUp of: @/usr/users2/culhane/...
+        #
+        # etc with other seemingly free format text before getting to the
+        # MSF/Type/Check line and the following Name: lines block and // line.
+        #
+        # MUSCLE just has a line "PileUp", while other sources just use the line
+        # "!!AA_MULTIPLE_ALIGNMENT" (amino acid) or "!!NA_MULTIPLE_ALIGNMENT"
+        # (nucleotide).
+        if line.strip().split()[0] not in known_headers:
+            raise ValueError(
+                "%s is not a known GCG MSF header: %s"
+                % (line.strip().split()[0], ", ".join(known_headers))
+            )
+
+        while line and " MSF: " not in line:
+            line = handle.readline()
+
+        if not line:
+            raise ValueError("Reached end of file without MSF/Type/Check header line")
+
+        # Quoting from "Molecular Biology Software Training Manual GCG version 10"
+        # by BBSRC Bioscuences IT Services (BITS), Harpenden, UK. Copyright 1996-2001.
+        # Page 31:
+        #
+        # "Header information is before a .. (double dot) in a GCG format file.
+        #  The file will also have a checksum specific for that file."
+        #
+        # This was followed by a single non-aligned sequence, but this convention
+        # appears to also be used in the GCG MSF files. Quoting other examples in
+        # this reference, page 31:
+        #
+        # localpileup_17.msf  MSF: 195  Type: P  January 6, 2000 15:41  Check: 4365 ..
+        #
+        # Except from page 148:
+        #
+        # localpileup_106.msf  MSF: 457  Type: P  November 28, 2000 16:09  Check: 2396 ..
+        #
+        # Quoting output from MUSCLE v3.8, have two leading spaces and a zero checksum:
+        #
+        #   MSF: 689  Type: N  Check: 0000  ..
+        #
+        # By observation, the MSF value is the column count, type is N (nucleotide)
+        # or P (protein / amino acid).
+        #
+        # In a possible bug, EMBOSS v6.6.0.0 uses CompCheck: rather than Check: as shown,
+        #
+        # $ seqret -sequence Tests/Fasta/f002 -auto -stdout -osformat msf
+        # !!NA_MULTIPLE_ALIGNMENT 1.0
+        #
+        #   stdout MSF: 633 Type: N 01/08/19 CompCheck: 8543 ..
+        #
+        #   Name: G26680     Len: 633  Check: 4334 Weight: 1.00
+        #   Name: G26685     Len: 633  Check: 3818 Weight: 1.00
+        #   Name: G29385     Len: 633  Check:  391 Weight: 1.00
+        #
+        # //
+        #
+        parts = line.strip("\n").split()
+        offset = parts.index("MSF:")
+        if (
+            parts[offset + 2] != "Type:"
+            or parts[-3] not in ("Check:", "CompCheck:")
+            or parts[-1] != ".."
+        ):
+            raise ValueError(
+                "GCG MSF header line should be "
+                "'<optional text> MSF: <int> Type: <letter> <optional date> Check: <int> ..', "
+                " not: %r" % line
+            )
+        try:
+            aln_length = int(parts[offset + 1])
+        except ValueError:
+            aln_length = -1
+        if aln_length < 0:
+            raise ValueError(
+                "GCG MSF header line should have MDF: <int> for column count, not %r"
+                % parts[offset + 1]
+            )
+        seq_type = parts[offset + 3]
+        if seq_type not in ["P", "N"]:
+            raise ValueError(
+                "GCG MSF header line should have 'Type: P' (protein) "
+                "or 'Type: N' (nucleotide), not 'Type: %s'" % seq_type
+            )
+
+        # There should be a blank line after that header line, then the Name: lines
+        #
+        # In a possible bug, T-COFFEE v12.00 adds 'oo' after the names, as shown here,
+        #
+        # PileUp
+        #
+        #
+        #
+        #    MSF:  628  Type: P    Check:   147   ..
+        #
+        #  Name: AK1H_ECOLI/1-378 oo  Len:  628  Check:  3643  Weight:  1.000
+        #  Name: AKH_HAEIN/1-382 oo  Len:  628  Check:  6504  Weight:  1.000
+        #
+        # //
+        ids = []
+        lengths = []
+        checks = []
+        weights = []
+        line = handle.readline()
+        while line and line.strip() != "//":
+            line = handle.readline()
+            if line.strip().startswith("Name: "):
+                if " Len: " in line and " Check: " in line and " Weight: " in line:
+                    rest = line[line.index("Name: ") + 6 :].strip()
+                    name, rest = rest.split(" Len: ")
+                    length, rest = rest.split(" Check: ")
+                    check, weight = rest.split(" Weight: ")
+                    name = name.strip()
+                    if name.endswith(" oo"):
+                        # T-COFFEE oddity, ignore this
+                        name = name[:-3]
+                    if name in ids:
+                        raise ValueError(f"Duplicated ID of {name!r}")
+                    if " " in name:
+                        raise NotImplementedError(f"Space in ID {name!r}")
+                    ids.append(name)
+                    # Expect aln_length <= int(length.strip()), see below
+                    lengths.append(int(length.strip()))
+                    checks.append(int(check.strip()))
+                    weights.append(float(weight.strip()))
+                else:
+                    raise ValueError(f"Malformed GCG MSF name line: {line!r}")
+        if not line:
+            raise ValueError("End of file while looking for end of header // line.")
+
+        if aln_length != max(lengths):
+            # In broken examples from IMGTHLA was possible to continue
+            # https://github.com/ANHIG/IMGTHLA/issues/201
+            max_length = max(lengths)
+            max_count = sum(1 for _ in lengths if _ == max_length)
+            raise ValueError(
+                "GCG MSF header said alignment length %i, but %s of %i sequences said Len: %s"
+                % (aln_length, max_count, len(ids), max_length)
+            )
+
+        line = handle.readline()
+        if not line:
+            raise ValueError("End of file after // line, expected sequences.")
+        if line.strip():
+            raise ValueError("After // line, expected blank line before sequences.")
+
+        # Now load the sequences
+        seqs = [[] for _ in ids]  # list of empty lists
+        completed_length = 0
+        while completed_length < aln_length:
+            # Note might have a coordinate header line (seems to be optional)
+            for idx, name in enumerate(ids):
+                line = handle.readline()
+                if idx == 0 and not line.strip():
+                    # T-COFFEE uses two blank lines between blocks, rather than one
+                    while line and not line.strip():
+                        line = handle.readline()
+                if not line:
+                    raise ValueError("End of file where expecting sequence data.")
+                # print("Looking for seq for %s in line: %r" % (name, line))
+                words = line.strip().split()
+                # Should we use column numbers, rather than assuming no spaces in names?
+                if idx == 0 and words and words[0] != name:
+                    # print("Actually have a coord line")
+                    # Hopefully this is a coordinate header before the first seq
+                    try:
+                        i = int(words[0])
+                    except ValueError:
+                        i = -1
+                    if i != completed_length + 1:
+                        raise ValueError(
+                            "Expected GCG MSF coordinate line starting %i, got: %r"
+                            % (completed_length + 1, line)
+                        )
+                    if len(words) > 1:
+                        # Final block usually not full 50 chars, so expect start only.
+                        if len(words) != 2:
+                            i = -1
+                        else:
+                            try:
+                                i = int(words[1])
+                            except ValueError:
+                                i = -1
+                        if i != (
+                            completed_length + 50
+                            if completed_length + 50 < aln_length
+                            else aln_length
+                        ):
+                            raise ValueError(
+                                "Expected GCG MSF coordinate line %i to %i, got: %r"
+                                % (
+                                    completed_length + 1,
+                                    (
+                                        completed_length + 50
+                                        if completed_length + 50 < aln_length
+                                        else aln_length
+                                    ),
+                                    line,
+                                )
+                            )
+                    line = handle.readline()
+                    words = line.strip().split()
+                    # print("Still looking for seq for %s in line: %r" % (name, line))
+                # Dealt with any coordinate header line, should now be sequence
+                if not words:
+                    # Should be sequence here, but perhaps its a short one?
+                    if (
+                        lengths[idx] < aln_length
+                        and len("".join(seqs[idx])) == lengths[idx]
+                    ):
+                        # Is this actually allowed in the format? Personally I would
+                        # expect a line with name and a block of trailing ~ here.
+                        pass
+                    else:
+                        raise ValueError(f"Expected sequence for {name}, got: {line!r}")
+                elif words[0] == name:
+                    assert len(words) > 1, line
+                    # print(i, name, repr(words))
+                    seqs[idx].extend(words[1:])
+                else:
+                    raise ValueError(f"Expected sequence for {name!r}, got: {line!r}")
+            # TODO - check the sequence lengths thus far are consistent
+            # with blocks of 50?
+            completed_length += 50
+            line = handle.readline()
+            if line.strip():
+                raise ValueError(f"Expected blank line, got: {line!r}")
+
+        # Skip over any whitespace at the end...
+        while True:
+            line = handle.readline()
+            if not line:
+                # End of file, no more alignments
+                break
+            elif not line.strip():
+                # Blank line, ignore
+                pass
+            elif line.strip().split()[0] in known_headers:
+                # Looks like the start of another alignment:
+                self._header = line
+                break
+            else:
+                raise ValueError(f"Unexpected line after GCG MSF alignment: {line!r}")
+
+        # Combine list of strings into single string, remap gaps
+        seqs = ["".join(s).replace("~", "-").replace(".", "-") for s in seqs]
+
+        # Apply any trailing padding for short sequences
+        padded = False
+        for idx, (length, s) in enumerate(zip(lengths, seqs)):
+            if len(s) < aln_length and len(s) == length:
+                padded = True
+                seqs[idx] = s + "-" * (aln_length - len(s))
+        if padded:
+            import warnings
+
+            from Bio import BiopythonParserWarning
+
+            warnings.warn(
+                "One of more alignment sequences were truncated and have been gap padded",
+                BiopythonParserWarning,
+            )
+
+        records = (
+            SeqRecord(Seq(s), id=i, name=i, description=i, annotations={"weight": w})
+            for (i, s, w) in zip(ids, seqs, weights)
+        )
+
+        # This will check alignment lengths are self-consistent:
+        align = MultipleSeqAlignment(records)
+        # Check matches the header:
+        if align.get_alignment_length() != aln_length:
+            raise ValueError(
+                "GCG MSF headers said alignment length %i, but have %i"
+                % (aln_length, align.get_alignment_length())
+            )
+        return align

.venv_haddock/lib/python3.12/site-packages/Bio/AlignIO/NexusIO.py

@@ -0,0 +1,173 @@
+# Copyright 2008-2010, 2012-2014, 2016-2017 by Peter Cock.  All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+"""Bio.AlignIO support for the "nexus" file format.
+
+You are expected to use this module via the Bio.AlignIO functions (or the
+Bio.SeqIO functions if you want to work directly with the gapped sequences).
+
+See also the Bio.Nexus module (which this code calls internally),
+as this offers more than just accessing the alignment or its
+sequences as SeqRecord objects.
+"""
+
+from typing import IO
+from collections.abc import Iterator
+from typing import Optional
+
+from Bio.Align import MultipleSeqAlignment
+from Bio.AlignIO.Interfaces import AlignmentWriter
+from Bio.Nexus import Nexus
+from Bio.SeqRecord import SeqRecord
+
+# You can get a couple of example files here:
+# http://www.molecularevolution.org/resources/fileformats/
+
+
+# This is a generator function!
+def NexusIterator(
+    handle: IO[str], seq_count: int | None = None
+) -> Iterator[MultipleSeqAlignment]:
+    """Return SeqRecord objects from a Nexus file.
+
+    Thus uses the Bio.Nexus module to do the hard work.
+
+    You are expected to call this function via Bio.SeqIO or Bio.AlignIO
+    (and not use it directly).
+
+    NOTE - We only expect ONE alignment matrix per Nexus file,
+    meaning this iterator will only yield one MultipleSeqAlignment.
+    """
+    n = Nexus.Nexus(handle)
+    if not n.matrix:
+        # No alignment found
+        return
+
+    # Bio.Nexus deals with duplicated names by adding a '.copy' suffix.
+    # The original names and the modified names are kept in these two lists:
+    assert len(n.unaltered_taxlabels) == len(n.taxlabels)
+
+    if seq_count and seq_count != len(n.unaltered_taxlabels):
+        raise ValueError(
+            "Found %i sequences, but seq_count=%i"
+            % (len(n.unaltered_taxlabels), seq_count)
+        )
+
+    # TODO - Can we extract any annotation too?
+    annotations: SeqRecord._AnnotationsDict | None
+    if n.datatype in ("dna", "nucleotide"):
+        annotations = {"molecule_type": "DNA"}
+    elif n.datatype == "rna":
+        annotations = {"molecule_type": "RNA"}
+    elif n.datatype == "protein":
+        annotations = {"molecule_type": "protein"}
+    else:
+        annotations = None
+    records = (
+        SeqRecord(
+            n.matrix[new_name],
+            id=new_name,
+            name=old_name,
+            description="",
+            annotations=annotations,
+        )
+        for old_name, new_name in zip(n.unaltered_taxlabels, n.taxlabels)
+    )
+    # All done
+    yield MultipleSeqAlignment(records)
+
+
+class NexusWriter(AlignmentWriter):
+    """Nexus alignment writer.
+
+    Note that Nexus files are only expected to hold ONE alignment
+    matrix.
+
+    You are expected to call this class via the Bio.AlignIO.write() or
+    Bio.SeqIO.write() functions.
+    """
+
+    def write_file(self, alignments):
+        """Use this to write an entire file containing the given alignments.
+
+        Arguments:
+         - alignments - A list or iterator returning MultipleSeqAlignment objects.
+           This should hold ONE and only one alignment.
+
+        """
+        align_iter = iter(alignments)  # Could have been a list
+        try:
+            alignment = next(align_iter)
+        except StopIteration:
+            # Nothing to write!
+            return 0
+
+        # Check there is only one alignment...
+        try:
+            next(align_iter)
+            raise ValueError("We can only write one Alignment to a Nexus file.")
+        except StopIteration:
+            pass
+
+        # Good.  Actually write the single alignment,
+        self.write_alignment(alignment)
+        return 1  # we only support writing one alignment!
+
+    def write_alignment(self, alignment, interleave=None):
+        """Write an alignment to file.
+
+        Creates an empty Nexus object, adds the sequences
+        and then gets Nexus to prepare the output.
+        Default interleave behaviour: Interleave if columns > 1000
+        --> Override with interleave=[True/False]
+        """
+        if len(alignment) == 0:
+            raise ValueError("Must have at least one sequence")
+        columns = alignment.get_alignment_length()
+        if columns == 0:
+            raise ValueError("Non-empty sequences are required")
+        datatype = self._classify_mol_type_for_nexus(alignment)
+        minimal_record = (
+            "#NEXUS\nbegin data; dimensions ntax=0 nchar=0; format datatype=%s; end;"
+            % datatype
+        )
+        n = Nexus.Nexus(minimal_record)
+        for record in alignment:
+            # Sanity test sequences (should this be even stricter?)
+            if datatype == "dna" and "U" in record.seq:
+                raise ValueError(f"{record.id} contains U, but DNA alignment")
+            elif datatype == "rna" and "T" in record.seq:
+                raise ValueError(f"{record.id} contains T, but RNA alignment")
+            n.add_sequence(record.id, str(record.seq))
+
+        # Note: MrBayes may choke on large alignments if not interleaved
+        if interleave is None:
+            interleave = columns > 1000
+        n.write_nexus_data(self.handle, interleave=interleave)
+
+    def _classify_mol_type_for_nexus(self, alignment):
+        """Return 'protein', 'dna', or 'rna' based on records' molecule type (PRIVATE).
+
+        All the records must have a molecule_type annotation, and they must
+        agree.
+
+        Raises an exception if this is not possible.
+        """
+        values = {_.annotations.get("molecule_type", None) for _ in alignment}
+        if all(_ and "DNA" in _ for _ in values):
+            return "dna"  # could have been a mix of "DNA" and "gDNA"
+        elif all(_ and "RNA" in _ for _ in values):
+            return "rna"  # could have been a mix of "RNA" and "mRNA"
+        elif all(_ and "protein" in _ for _ in values):
+            return "protein"
+        else:
+            raise ValueError("Need the molecule type to be defined")
+
+
+if __name__ == "__main__":
+    from Bio._utils import run_doctest
+
+    run_doctest(verbose=0)

.venv_haddock/lib/python3.12/site-packages/Bio/AlignIO/PhylipIO.py

@@ -0,0 +1,454 @@
+# Copyright 2006-2016 by Peter Cock.  All rights reserved.
+# Revisions copyright 2011 Brandon Invergo. All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+"""AlignIO support for "phylip" format from Joe Felsenstein's PHYLIP tools.
+
+You are expected to use this module via the Bio.AlignIO functions (or the
+Bio.SeqIO functions if you want to work directly with the gapped sequences).
+
+Support for "relaxed phylip" format is also provided. Relaxed phylip differs
+from standard phylip format in the following ways:
+
+ - No whitespace is allowed in the sequence ID.
+ - No truncation is performed. Instead, sequence IDs are padded to the longest
+   ID length, rather than 10 characters. A space separates the sequence
+   identifier from the sequence.
+
+Relaxed phylip is supported by RAxML and PHYML.
+
+Note
+====
+
+In TREE_PUZZLE (Schmidt et al. 2003) and PHYML (Guindon and Gascuel 2003)
+a dot/period (".") in a sequence is interpreted as meaning the same
+character as in the first sequence.  The PHYLIP documentation from 3.3 to 3.69
+http://evolution.genetics.washington.edu/phylip/doc/sequence.html says:
+
+"a period was also previously allowed but it is no longer allowed,
+because it sometimes is used in different senses in other programs"
+
+Biopython 1.58 or later treats dots/periods in the sequence as invalid, both
+for reading and writing. Older versions did nothing special with a dot/period.
+"""
+
+import string
+
+from Bio.Align import MultipleSeqAlignment
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+
+from .Interfaces import AlignmentIterator
+from .Interfaces import SequentialAlignmentWriter
+
+_PHYLIP_ID_WIDTH = 10
+_NO_DOTS = "PHYLIP format no longer allows dots in sequence"
+
+
+class PhylipWriter(SequentialAlignmentWriter):
+    """Phylip alignment writer."""
+
+    def write_alignment(self, alignment, id_width=_PHYLIP_ID_WIDTH):
+        """Use this to write (another) single alignment to an open file.
+
+        This code will write interlaced alignments (when the sequences are
+        longer than 50 characters).
+
+        Note that record identifiers are strictly truncated to id_width,
+        defaulting to the value required to comply with the PHYLIP standard.
+
+        For more information on the file format, please see:
+        http://evolution.genetics.washington.edu/phylip/doc/sequence.html
+        http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles
+        """
+        handle = self.handle
+
+        if len(alignment) == 0:
+            raise ValueError("Must have at least one sequence")
+        length_of_seqs = alignment.get_alignment_length()
+        for record in alignment:
+            if length_of_seqs != len(record.seq):
+                raise ValueError("Sequences must all be the same length")
+        if length_of_seqs <= 0:
+            raise ValueError("Non-empty sequences are required")
+
+        # Check for repeated identifiers...
+        # Apply this test *after* cleaning the identifiers
+        names = []
+        seqs = []
+        for record in alignment:
+            """
+            Quoting the PHYLIP version 3.6 documentation:
+
+            The name should be ten characters in length, filled out to
+            the full ten characters by blanks if shorter. Any printable
+            ASCII/ISO character is allowed in the name, except for
+            parentheses ("(" and ")"), square brackets ("[" and "]"),
+            colon (":"), semicolon (";") and comma (","). If you forget
+            to extend the names to ten characters in length by blanks,
+            the program [i.e. PHYLIP] will get out of synchronization
+            with the contents of the data file, and an error message will
+            result.
+
+            Note that Tab characters count as only one character in the
+            species names. Their inclusion can cause trouble.
+            """
+            name = sanitize_name(record.id, id_width)
+            if name in names:
+                raise ValueError(
+                    "Repeated name %r (originally %r), possibly due to truncation"
+                    % (name, record.id)
+                )
+            names.append(name)
+            sequence = str(record.seq)
+            if "." in sequence:
+                # Do this check here (once per record, not once per block)
+                raise ValueError(_NO_DOTS)
+            seqs.append(sequence)
+
+        # From experimentation, the use of tabs is not understood by the
+        # EMBOSS suite.  The nature of the expected white space is not
+        # defined in the PHYLIP documentation, simply "These are in free
+        # format, separated by blanks".  We'll use spaces to keep EMBOSS
+        # happy.
+        handle.write(" %i %s\n" % (len(alignment), length_of_seqs))
+        block = 0
+        while True:
+            for name, sequence in zip(names, seqs):
+                if block == 0:
+                    # Write name (truncated/padded to id_width characters)
+                    # Now truncate and right pad to expected length.
+                    handle.write(name[:id_width].ljust(id_width))
+                else:
+                    # write indent
+                    handle.write(" " * id_width)
+                # Write five chunks of ten letters per line...
+                for chunk in range(5):
+                    i = block * 50 + chunk * 10
+                    seq_segment = sequence[i : i + 10]
+                    # TODO - Force any gaps to be '-' character?
+                    # TODO - How to cope with '?' or '.' in the sequence?
+                    handle.write(f" {seq_segment}")
+                    if i + 10 > length_of_seqs:
+                        break
+                handle.write("\n")
+            block += 1
+            if block * 50 >= length_of_seqs:
+                break
+            handle.write("\n")
+
+
+class PhylipIterator(AlignmentIterator):
+    """Reads a Phylip alignment file returning a MultipleSeqAlignment iterator.
+
+    Record identifiers are limited to at most 10 characters.
+
+    It only copes with interlaced phylip files!  Sequential files won't work
+    where the sequences are split over multiple lines.
+
+    For more information on the file format, please see:
+    http://evolution.genetics.washington.edu/phylip/doc/sequence.html
+    http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles
+    """
+
+    # Default truncation length
+    id_width = _PHYLIP_ID_WIDTH
+
+    _header = None  # for caching lines between __next__ calls
+
+    def _is_header(self, line):
+        line = line.strip()
+        parts = [x for x in line.split() if x]
+        if len(parts) != 2:
+            return False  # First line should have two integers
+        try:
+            number_of_seqs = int(parts[0])
+            length_of_seqs = int(parts[1])
+            return True
+        except ValueError:
+            return False  # First line should have two integers
+
+    def _split_id(self, line):
+        """Extract the sequence ID from a Phylip line (PRIVATE).
+
+        Returning a tuple containing: (sequence_id, sequence_residues)
+
+        The first 10 characters in the line are are the sequence id, the
+        remainder are sequence data.
+        """
+        seq_id = line[: self.id_width].strip()
+        seq = line[self.id_width :].strip().replace(" ", "")
+        return seq_id, seq
+
+    def __next__(self):
+        """Parse the next alignment from the handle."""
+        handle = self.handle
+
+        if self._header is None:
+            line = handle.readline()
+        else:
+            # Header we saved from when we were parsing
+            # the previous alignment.
+            line = self._header
+            self._header = None
+
+        if not line:
+            raise StopIteration
+        line = line.strip()
+        parts = [x for x in line.split() if x]
+        if len(parts) != 2:
+            raise ValueError("First line should have two integers")
+        try:
+            number_of_seqs = int(parts[0])
+            length_of_seqs = int(parts[1])
+        except ValueError:
+            raise ValueError("First line should have two integers") from None
+
+        assert self._is_header(line)
+
+        if (
+            self.records_per_alignment is not None
+            and self.records_per_alignment != number_of_seqs
+        ):
+            raise ValueError(
+                "Found %i records in this alignment, told to expect %i"
+                % (number_of_seqs, self.records_per_alignment)
+            )
+
+        ids = []
+        seqs = []
+
+        # By default, expects STRICT truncation / padding to 10 characters.
+        # Does not require any whitespace between name and seq.
+        for i in range(number_of_seqs):
+            line = handle.readline().rstrip()
+            sequence_id, s = self._split_id(line)
+            ids.append(sequence_id)
+            if "." in s:
+                raise ValueError(_NO_DOTS)
+            seqs.append([s])
+
+        # Look for further blocks
+        line = ""
+        while True:
+            # Skip any blank lines between blocks...
+            while "" == line.strip():
+                line = handle.readline()
+                if not line:
+                    break  # end of file
+            if not line:
+                break  # end of file
+
+            if self._is_header(line):
+                # Looks like the start of a concatenated alignment
+                self._header = line
+                break
+
+            # print("New block...")
+            for i in range(number_of_seqs):
+                s = line.strip().replace(" ", "")
+                if "." in s:
+                    raise ValueError(_NO_DOTS)
+                seqs[i].append(s)
+                line = handle.readline()
+                if (not line) and i + 1 < number_of_seqs:
+                    raise ValueError("End of file mid-block")
+            if not line:
+                break  # end of file
+
+        records = (
+            SeqRecord(Seq("".join(s)), id=i, name=i, description=i)
+            for (i, s) in zip(ids, seqs)
+        )
+        return MultipleSeqAlignment(records)
+
+
+# Relaxed Phylip
+class RelaxedPhylipWriter(PhylipWriter):
+    """Relaxed Phylip format writer."""
+
+    def write_alignment(self, alignment):
+        """Write a relaxed phylip alignment."""
+        # Check inputs
+        for name in (s.id.strip() for s in alignment):
+            if any(c in name for c in string.whitespace):
+                raise ValueError(f"Whitespace not allowed in identifier: {name}")
+
+        # Calculate a truncation length - maximum length of sequence ID plus a
+        # single character for padding
+        # If no sequences, set id_width to 1. super(...) call will raise a
+        # ValueError
+        if len(alignment) == 0:
+            id_width = 1
+        else:
+            id_width = max(len(s.id.strip()) for s in alignment) + 1
+        super().write_alignment(alignment, id_width)
+
+
+class RelaxedPhylipIterator(PhylipIterator):
+    """Relaxed Phylip format Iterator."""
+
+    def _split_id(self, line):
+        """Extract the sequence ID from a Phylip line (PRIVATE).
+
+        Returns a tuple containing: (sequence_id, sequence_residues)
+
+        For relaxed format split at the first whitespace character.
+        """
+        seq_id, sequence = line.split(None, 1)
+        sequence = sequence.strip().replace(" ", "")
+        return seq_id, sequence
+
+
+class SequentialPhylipWriter(SequentialAlignmentWriter):
+    """Sequential Phylip format Writer."""
+
+    def write_alignment(self, alignment, id_width=_PHYLIP_ID_WIDTH):
+        """Write a Phylip alignment to the handle."""
+        handle = self.handle
+
+        if len(alignment) == 0:
+            raise ValueError("Must have at least one sequence")
+        length_of_seqs = alignment.get_alignment_length()
+        for record in alignment:
+            if length_of_seqs != len(record.seq):
+                raise ValueError("Sequences must all be the same length")
+        if length_of_seqs <= 0:
+            raise ValueError("Non-empty sequences are required")
+
+        # Check for repeated identifiers...
+        # Apply this test *after* cleaning the identifiers
+        names = []
+        for record in alignment:
+            # Either remove the banned characters, or map them to something
+            # else like an underscore "_" or pipe "|" character...
+            name = sanitize_name(record.id, id_width)
+            if name in names:
+                raise ValueError(
+                    "Repeated name %r (originally %r), possibly due to truncation"
+                    % (name, record.id)
+                )
+            names.append(name)
+
+        # From experimentation, the use of tabs is not understood by the
+        # EMBOSS suite.  The nature of the expected white space is not
+        # defined in the PHYLIP documentation, simply "These are in free
+        # format, separated by blanks".  We'll use spaces to keep EMBOSS
+        # happy.
+        handle.write(" %i %s\n" % (len(alignment), length_of_seqs))
+        for name, record in zip(names, alignment):
+            sequence = str(record.seq)
+            if "." in sequence:
+                raise ValueError(_NO_DOTS)
+            handle.write(name[:id_width].ljust(id_width))
+            # Write the entire sequence to one line (see sequential format
+            # notes in the SequentialPhylipIterator docstring
+            handle.write(sequence)
+            handle.write("\n")
+
+
+class SequentialPhylipIterator(PhylipIterator):
+    """Sequential Phylip format Iterator.
+
+    The sequential format carries the same restrictions as the normal
+    interleaved one, with the difference being that the sequences are listed
+    sequentially, each sequence written in its entirety before the start of
+    the next. According to the PHYLIP documentation for input file
+    formatting, newlines and spaces may optionally be entered at any point
+    in the sequences.
+    """
+
+    _header = None  # for caching lines between __next__ calls
+
+    def __next__(self):
+        """Parse the next alignment from the handle."""
+        handle = self.handle
+
+        if self._header is None:
+            line = handle.readline()
+        else:
+            # Header we saved from when we were parsing
+            # the previous alignment.
+            line = self._header
+            self._header = None
+
+        if not line:
+            raise StopIteration
+        line = line.strip()
+        parts = [x for x in line.split() if x]
+        if len(parts) != 2:
+            raise ValueError("First line should have two integers")
+        try:
+            number_of_seqs = int(parts[0])
+            length_of_seqs = int(parts[1])
+        except ValueError:
+            raise ValueError("First line should have two integers") from None
+
+        assert self._is_header(line)
+
+        if (
+            self.records_per_alignment is not None
+            and self.records_per_alignment != number_of_seqs
+        ):
+            raise ValueError(
+                "Found %i records in this alignment, told to expect %i"
+                % (number_of_seqs, self.records_per_alignment)
+            )
+
+        ids = []
+        seqs = []
+
+        # By default, expects STRICT truncation / padding to 10 characters.
+        # Does not require any whitespace between name and seq.
+        for i in range(number_of_seqs):
+            line = handle.readline().rstrip()
+            sequence_id, s = self._split_id(line)
+            ids.append(sequence_id)
+            while len(s) < length_of_seqs:
+                # The sequence may be split into multiple lines
+                line = handle.readline().strip()
+                if not line:
+                    break
+                if line == "":
+                    continue
+                s = "".join([s, line.strip().replace(" ", "")])
+                if len(s) > length_of_seqs:
+                    raise ValueError(
+                        "Found a record of length %i, "
+                        "should be %i" % (len(s), length_of_seqs)
+                    )
+            if "." in s:
+                raise ValueError(_NO_DOTS)
+            seqs.append(s)
+        while True:
+            # Find other alignments in the file
+            line = handle.readline()
+            if not line:
+                break
+            if self._is_header(line):
+                self._header = line
+                break
+
+        records = (
+            SeqRecord(Seq(s), id=i, name=i, description=i) for (i, s) in zip(ids, seqs)
+        )
+        return MultipleSeqAlignment(records)
+
+
+def sanitize_name(name, width=None):
+    """Sanitise sequence identifier for output.
+
+    Removes the banned characters "[]()" and replaces the characters ":;"
+    with "|". The name is truncated to "width" characters if specified.
+    """
+    name = name.strip()
+    for char in "[](),":
+        name = name.replace(char, "")
+    for char in ":;":
+        name = name.replace(char, "|")
+    if width is not None:
+        name = name[:width]
+    return name

.venv_haddock/lib/python3.12/site-packages/Bio/AlignIO/StockholmIO.py

@@ -0,0 +1,620 @@
+# Copyright 2006-2016 by Peter Cock.  All rights reserved.
+# Revisions copyright 2015 by Ben Woodcroft.  All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+"""Bio.AlignIO support for "stockholm" format (used in the PFAM database).
+
+You are expected to use this module via the Bio.AlignIO functions (or the
+Bio.SeqIO functions if you want to work directly with the gapped sequences).
+
+For example, consider a Stockholm alignment file containing the following::
+
+    # STOCKHOLM 1.0
+    #=GC SS_cons       .................<<<<<<<<...<<<<<<<........>>>>>>>..
+    AP001509.1         UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-GAUGAGGGU
+    #=GR AP001509.1 SS -----------------<<<<<<<<---..<<-<<-------->>->>..--
+    AE007476.1         AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-CACGA-CGU
+    #=GR AE007476.1 SS -----------------<<<<<<<<-----<<.<<-------->>.>>----
+
+    #=GC SS_cons       ......<<<<<<<.......>>>>>>>..>>>>>>>>...............
+    AP001509.1         CUCUAC-AGGUA-CCGUAAA-UACCUAGCUACGAAAAGAAUGCAGUUAAUGU
+    #=GR AP001509.1 SS -------<<<<<--------->>>>>--->>>>>>>>---------------
+    AE007476.1         UUCUACAAGGUG-CCGG-AA-CACCUAACAAUAAGUAAGUCAGCAGUGAGAU
+    #=GR AE007476.1 SS ------.<<<<<--------->>>>>.-->>>>>>>>---------------
+    //
+
+This is a single multiple sequence alignment, so you would probably load this
+using the Bio.AlignIO.read() function:
+
+    >>> from Bio import AlignIO
+    >>> align = AlignIO.read("Stockholm/simple.sth", "stockholm")
+    >>> print(align)
+    Alignment with 2 rows and 104 columns
+    UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-G...UGU AP001509.1
+    AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-C...GAU AE007476.1
+    >>> for record in align:
+    ...     print("%s %i" % (record.id, len(record)))
+    AP001509.1 104
+    AE007476.1 104
+
+In addition to the sequences themselves, this example alignment also includes
+some GR lines for the secondary structure of the sequences.  These are
+strings, with one character for each letter in the associated sequence:
+
+    >>> for record in align:
+    ...     print(record.id)
+    ...     print(record.seq)
+    ...     print(record.letter_annotations['secondary_structure'])
+    AP001509.1
+    UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-GAUGAGGGUCUCUAC-AGGUA-CCGUAAA-UACCUAGCUACGAAAAGAAUGCAGUUAAUGU
+    -----------------<<<<<<<<---..<<-<<-------->>->>..---------<<<<<--------->>>>>--->>>>>>>>---------------
+    AE007476.1
+    AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-CACGA-CGUUUCUACAAGGUG-CCGG-AA-CACCUAACAAUAAGUAAGUCAGCAGUGAGAU
+    -----------------<<<<<<<<-----<<.<<-------->>.>>----------.<<<<<--------->>>>>.-->>>>>>>>---------------
+
+Any general annotation for each row is recorded in the SeqRecord's annotations
+dictionary.  Any per-column annotation for the entire alignment in in the
+alignment's column annotations dictionary, such as the secondary structure
+consensus in this example:
+
+    >>> sorted(align.column_annotations.keys())
+    ['secondary_structure']
+    >>> align.column_annotations["secondary_structure"]
+    '.................<<<<<<<<...<<<<<<<........>>>>>>>........<<<<<<<.......>>>>>>>..>>>>>>>>...............'
+
+You can output this alignment in many different file formats
+using Bio.AlignIO.write(), or the MultipleSeqAlignment object's format method:
+
+    >>> print(format(align, "fasta"))
+    >AP001509.1
+    UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-GAUGAGGGUCUCUAC-A
+    GGUA-CCGUAAA-UACCUAGCUACGAAAAGAAUGCAGUUAAUGU
+    >AE007476.1
+    AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-CACGA-CGUUUCUACAA
+    GGUG-CCGG-AA-CACCUAACAAUAAGUAAGUCAGCAGUGAGAU
+    <BLANKLINE>
+
+Most output formats won't be able to hold the annotation possible in a
+Stockholm file:
+
+    >>> print(format(align, "stockholm"))
+    # STOCKHOLM 1.0
+    #=GF SQ 2
+    AP001509.1 UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-GAUGAGGGUCUCUAC-AGGUA-CCGUAAA-UACCUAGCUACGAAAAGAAUGCAGUUAAUGU
+    #=GS AP001509.1 AC AP001509.1
+    #=GS AP001509.1 DE AP001509.1
+    #=GR AP001509.1 SS -----------------<<<<<<<<---..<<-<<-------->>->>..---------<<<<<--------->>>>>--->>>>>>>>---------------
+    AE007476.1 AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-CACGA-CGUUUCUACAAGGUG-CCGG-AA-CACCUAACAAUAAGUAAGUCAGCAGUGAGAU
+    #=GS AE007476.1 AC AE007476.1
+    #=GS AE007476.1 DE AE007476.1
+    #=GR AE007476.1 SS -----------------<<<<<<<<-----<<.<<-------->>.>>----------.<<<<<--------->>>>>.-->>>>>>>>---------------
+    #=GC SS_cons .................<<<<<<<<...<<<<<<<........>>>>>>>........<<<<<<<.......>>>>>>>..>>>>>>>>...............
+    //
+    <BLANKLINE>
+
+Note that when writing Stockholm files, AlignIO does not break long sequences
+up and interleave them (as in the input file shown above).  The standard
+allows this simpler layout, and it is more likely to be understood by other
+tools.
+
+Finally, as an aside, it can sometimes be useful to use Bio.SeqIO.parse() to
+iterate over the alignment rows as SeqRecord objects - rather than working
+with Alignnment objects.
+
+    >>> from Bio import SeqIO
+    >>> for record in SeqIO.parse("Stockholm/simple.sth", "stockholm"):
+    ...     print(record.id)
+    ...     print(record.seq)
+    ...     print(record.letter_annotations['secondary_structure'])
+    AP001509.1
+    UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-GAUGAGGGUCUCUAC-AGGUA-CCGUAAA-UACCUAGCUACGAAAAGAAUGCAGUUAAUGU
+    -----------------<<<<<<<<---..<<-<<-------->>->>..---------<<<<<--------->>>>>--->>>>>>>>---------------
+    AE007476.1
+    AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-CACGA-CGUUUCUACAAGGUG-CCGG-AA-CACCUAACAAUAAGUAAGUCAGCAGUGAGAU
+    -----------------<<<<<<<<-----<<.<<-------->>.>>----------.<<<<<--------->>>>>.-->>>>>>>>---------------
+
+Remember that if you slice a SeqRecord, the per-letter-annotations like the
+secondary structure string here, are also sliced:
+
+    >>> sub_record = record[10:20]
+    >>> print(sub_record.seq)
+    AUCGUUUUAC
+    >>> print(sub_record.letter_annotations['secondary_structure'])
+    -------<<<
+
+Likewise with the alignment object, as long as you are not dropping any rows,
+slicing specific columns of an alignment will slice any per-column-annotations:
+
+    >>> align.column_annotations["secondary_structure"]
+    '.................<<<<<<<<...<<<<<<<........>>>>>>>........<<<<<<<.......>>>>>>>..>>>>>>>>...............'
+    >>> part_align = align[:,10:20]
+    >>> part_align.column_annotations["secondary_structure"]
+    '.......<<<'
+
+You can also see this in the Stockholm output of this partial-alignment:
+
+    >>> print(format(part_align, "stockholm"))
+    # STOCKHOLM 1.0
+    #=GF SQ 2
+    AP001509.1 UCAACACUCU
+    #=GS AP001509.1 AC AP001509.1
+    #=GS AP001509.1 DE AP001509.1
+    #=GR AP001509.1 SS -------<<<
+    AE007476.1 AUCGUUUUAC
+    #=GS AE007476.1 AC AE007476.1
+    #=GS AE007476.1 DE AE007476.1
+    #=GR AE007476.1 SS -------<<<
+    #=GC SS_cons .......<<<
+    //
+    <BLANKLINE>
+
+"""
+
+from Bio.Align import MultipleSeqAlignment
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+
+from .Interfaces import AlignmentIterator
+from .Interfaces import SequentialAlignmentWriter
+
+
+class StockholmWriter(SequentialAlignmentWriter):
+    """Stockholm/PFAM alignment writer."""
+
+    # These dictionaries should be kept in sync with those
+    # defined in the StockholmIterator class.
+    pfam_gr_mapping = {
+        "secondary_structure": "SS",
+        "surface_accessibility": "SA",
+        "transmembrane": "TM",
+        "posterior_probability": "PP",
+        "ligand_binding": "LI",
+        "active_site": "AS",
+        "intron": "IN",
+    }
+    # These GC mappings are in addition to *_cons in GR mapping:
+    pfam_gc_mapping = {"reference_annotation": "RF", "model_mask": "MM"}
+    # Following dictionary deliberately does not cover AC, DE or DR
+    pfam_gs_mapping = {"organism": "OS", "organism_classification": "OC", "look": "LO"}
+
+    def write_alignment(self, alignment):
+        """Use this to write (another) single alignment to an open file.
+
+        Note that sequences and their annotation are recorded
+        together (rather than having a block of annotation followed
+        by a block of aligned sequences).
+        """
+        count = len(alignment)
+
+        self._length_of_sequences = alignment.get_alignment_length()
+        self._ids_written = []
+
+        if count == 0:
+            raise ValueError("Must have at least one sequence")
+        if self._length_of_sequences == 0:
+            raise ValueError("Non-empty sequences are required")
+
+        self.handle.write("# STOCKHOLM 1.0\n")
+        self.handle.write("#=GF SQ %i\n" % count)
+        for record in alignment:
+            self._write_record(record)
+        # This shouldn't be None... but just in case,
+        if alignment.column_annotations:
+            for k, v in sorted(alignment.column_annotations.items()):
+                if k in self.pfam_gc_mapping:
+                    self.handle.write(f"#=GC {self.pfam_gc_mapping[k]} {v}\n")
+                elif k in self.pfam_gr_mapping:
+                    self.handle.write(f"#=GC {self.pfam_gr_mapping[k]}_cons {v}\n")
+                else:
+                    # It doesn't follow the PFAM standards, but should we record
+                    # this data anyway?
+                    pass
+        self.handle.write("//\n")
+
+    def _write_record(self, record):
+        """Write a single SeqRecord to the file (PRIVATE)."""
+        if self._length_of_sequences != len(record.seq):
+            raise ValueError("Sequences must all be the same length")
+
+        # For the case for stockholm to stockholm, try and use record.name
+        seq_name = record.id
+        if record.name is not None:
+            if "accession" in record.annotations:
+                if record.id == record.annotations["accession"]:
+                    seq_name = record.name
+
+        # In the Stockholm file format, spaces are not allowed in the id
+        seq_name = seq_name.replace(" ", "_")
+
+        if "start" in record.annotations and "end" in record.annotations:
+            suffix = f"/{record.annotations['start']}-{record.annotations['end']}"
+            if seq_name[-len(suffix) :] != suffix:
+                seq_name = "%s/%s-%s" % (
+                    seq_name,
+                    record.annotations["start"],
+                    record.annotations["end"],
+                )
+
+        if seq_name in self._ids_written:
+            raise ValueError(f"Duplicate record identifier: {seq_name}")
+        self._ids_written.append(seq_name)
+        self.handle.write(f"{seq_name} {record.seq}\n")
+
+        # The recommended placement for GS lines (per sequence annotation)
+        # is above the alignment (as a header block) or just below the
+        # corresponding sequence.
+        #
+        # The recommended placement for GR lines (per sequence per column
+        # annotation such as secondary structure) is just below the
+        # corresponding sequence.
+        #
+        # We put both just below the corresponding sequence as this allows
+        # us to write the file using a single pass through the records.
+
+        # AC = Accession
+        if "accession" in record.annotations:
+            self.handle.write(
+                f"#=GS {seq_name} AC {self.clean(record.annotations['accession'])}\n"
+            )
+        elif record.id:
+            self.handle.write(f"#=GS {seq_name} AC {self.clean(record.id)}\n")
+
+        # DE = description
+        if record.description:
+            self.handle.write(f"#=GS {seq_name} DE {self.clean(record.description)}\n")
+
+        # DE = database links
+        for xref in record.dbxrefs:
+            self.handle.write(f"#=GS {seq_name} DR {self.clean(xref)}\n")
+
+        # GS = other per sequence annotation
+        for key, value in record.annotations.items():
+            if key in self.pfam_gs_mapping:
+                data = self.clean(str(value))
+                if data:
+                    self.handle.write(
+                        "#=GS %s %s %s\n"
+                        % (seq_name, self.clean(self.pfam_gs_mapping[key]), data)
+                    )
+            else:
+                # It doesn't follow the PFAM standards, but should we record
+                # this data anyway?
+                pass
+
+        # GR = per row per column sequence annotation
+        for key, value in record.letter_annotations.items():
+            if key in self.pfam_gr_mapping and len(str(value)) == len(record.seq):
+                data = self.clean(str(value))
+                if data:
+                    self.handle.write(
+                        "#=GR %s %s %s\n"
+                        % (seq_name, self.clean(self.pfam_gr_mapping[key]), data)
+                    )
+            else:
+                # It doesn't follow the PFAM standards, but should we record
+                # this data anyway?
+                pass
+
+
+class StockholmIterator(AlignmentIterator):
+    """Loads a Stockholm file from PFAM into MultipleSeqAlignment objects.
+
+    The file may contain multiple concatenated alignments, which are loaded
+    and returned incrementally.
+
+    This parser will detect if the Stockholm file follows the PFAM
+    conventions for sequence specific meta-data (lines starting #=GS
+    and #=GR) and populates the SeqRecord fields accordingly.
+
+    Any annotation which does not follow the PFAM conventions is currently
+    ignored.
+
+    If an accession is provided for an entry in the meta data, IT WILL NOT
+    be used as the record.id (it will be recorded in the record's
+    annotations).  This is because some files have (sub) sequences from
+    different parts of the same accession (differentiated by different
+    start-end positions).
+
+    Wrap-around alignments are not supported - each sequences must be on
+    a single line.  However, interlaced sequences should work.
+
+    For more information on the file format, please see:
+    http://sonnhammer.sbc.su.se/Stockholm.html
+    https://en.wikipedia.org/wiki/Stockholm_format
+    http://bioperl.org/formats/alignment_formats/Stockholm_multiple_alignment_format.html
+
+    For consistency with BioPerl and EMBOSS we call this the "stockholm"
+    format.
+    """
+
+    # These dictionaries should be kept in sync with those
+    # defined in the PfamStockholmWriter class.
+    pfam_gr_mapping = {
+        "SS": "secondary_structure",
+        "SA": "surface_accessibility",
+        "TM": "transmembrane",
+        "PP": "posterior_probability",
+        "LI": "ligand_binding",
+        "AS": "active_site",
+        "IN": "intron",
+    }
+    # These GC mappings are in addition to *_cons in GR mapping:
+    pfam_gc_mapping = {"RF": "reference_annotation", "MM": "model_mask"}
+    # Following dictionary deliberately does not cover AC, DE or DR
+    pfam_gs_mapping = {"OS": "organism", "OC": "organism_classification", "LO": "look"}
+
+    _header = None  # for caching lines between __next__ calls
+
+    def __next__(self):
+        """Parse the next alignment from the handle."""
+        handle = self.handle
+
+        if self._header is None:
+            line = handle.readline()
+        else:
+            # Header we saved from when we were parsing
+            # the previous alignment.
+            line = self._header
+            self._header = None
+
+        if not line:
+            # Empty file - just give up.
+            raise StopIteration
+        if line.strip() != "# STOCKHOLM 1.0":
+            raise ValueError("Did not find STOCKHOLM header")
+
+        # Note: If this file follows the PFAM conventions, there should be
+        # a line containing the number of sequences, e.g. "#=GF SQ 67"
+        # We do not check for this - perhaps we should, and verify that
+        # if present it agrees with our parsing.
+
+        seqs = {}
+        ids = {}  # Really only need an OrderedSet, but python lacks this
+        gs = {}
+        gr = {}
+        gf = {}
+        gc = {}
+        passed_end_alignment = False
+        while True:
+            line = handle.readline()
+            if not line:
+                break  # end of file
+            line = line.strip()  # remove trailing \n
+            if line == "# STOCKHOLM 1.0":
+                self._header = line
+                break
+            elif line == "//":
+                # The "//" line indicates the end of the alignment.
+                # There may still be more meta-data
+                passed_end_alignment = True
+            elif line == "":
+                # blank line, ignore
+                pass
+            elif line[0] != "#":
+                # Sequence
+                # Format: "<seqname> <sequence>"
+                assert not passed_end_alignment
+                parts = [x.strip() for x in line.split(" ", 1)]
+                if len(parts) != 2:
+                    # This might be someone attempting to store a zero length sequence?
+                    raise ValueError(
+                        "Could not split line into identifier and sequence:\n" + line
+                    )
+                seq_id, seq = parts
+                if seq_id not in ids:
+                    ids[seq_id] = True
+                seqs.setdefault(seq_id, "")
+                seqs[seq_id] += seq.replace(".", "-")
+            elif len(line) >= 5:
+                # Comment line or meta-data
+                if line[:5] == "#=GF ":
+                    # Generic per-File annotation, free text
+                    # Format: #=GF <feature> <free text>
+                    feature, text = line[5:].strip().split(None, 1)
+                    # Each feature key could be used more than once,
+                    # so store the entries as a list of strings.
+                    if feature not in gf:
+                        gf[feature] = [text]
+                    else:
+                        gf[feature].append(text)
+                elif line[:5] == "#=GC ":
+                    # Generic per-Column annotation, exactly 1 char per column
+                    # Format: "#=GC <feature> <exactly 1 char per column>"
+                    feature, text = line[5:].strip().split(None, 2)
+                    if feature not in gc:
+                        gc[feature] = ""
+                    gc[feature] += text.strip()  # append to any previous entry
+                    # Might be interleaved blocks, so can't check length yet
+                elif line[:5] == "#=GS ":
+                    # Generic per-Sequence annotation, free text
+                    # Format: "#=GS <seqname> <feature> <free text>"
+                    try:
+                        seq_id, feature, text = line[5:].strip().split(None, 2)
+                    except ValueError:
+                        # Free text can sometimes be empty, which a one line split throws an error for.
+                        # See https://github.com/biopython/biopython/issues/2982 for more details
+                        seq_id, feature = line[5:].strip().split(None, 1)
+                        text = ""
+                    # if seq_id not in ids:
+                    #    ids.append(seq_id)
+                    if seq_id not in gs:
+                        gs[seq_id] = {}
+                    if feature not in gs[seq_id]:
+                        gs[seq_id][feature] = [text]
+                    else:
+                        gs[seq_id][feature].append(text)
+                elif line[:5] == "#=GR ":
+                    # Generic per-Sequence AND per-Column markup
+                    # Format: "#=GR <seqname> <feature> <exactly 1 char per column>"
+                    seq_id, feature, text = line[5:].strip().split(None, 2)
+                    # if seq_id not in ids:
+                    #    ids.append(seq_id)
+                    if seq_id not in gr:
+                        gr[seq_id] = {}
+                    if feature not in gr[seq_id]:
+                        gr[seq_id][feature] = ""
+                    gr[seq_id][feature] += text.strip()  # append to any previous entry
+                    # Might be interleaved blocks, so can't check length yet
+            # Next line...
+
+        assert len(seqs) <= len(ids)
+        # assert len(gs)   <= len(ids)
+        # assert len(gr)   <= len(ids)
+
+        self.ids = ids.keys()
+        self.sequences = seqs
+        self.seq_annotation = gs
+        self.seq_col_annotation = gr
+
+        if ids and seqs:
+            if (
+                self.records_per_alignment is not None
+                and self.records_per_alignment != len(ids)
+            ):
+                raise ValueError(
+                    "Found %i records in this alignment, told to expect %i"
+                    % (len(ids), self.records_per_alignment)
+                )
+
+            alignment_length = len(list(seqs.values())[0])
+            records = []  # Alignment obj will put them all in a list anyway
+            for seq_id in ids:
+                seq = seqs[seq_id]
+                if alignment_length != len(seq):
+                    raise ValueError(
+                        "Sequences have different lengths, or repeated identifier"
+                    )
+                name, start, end = self._identifier_split(seq_id)
+                record = SeqRecord(
+                    Seq(seq),
+                    id=seq_id,
+                    name=name,
+                    description=seq_id,
+                    annotations={"accession": name},
+                )
+                # Accession will be overridden by _populate_meta_data if an explicit
+                # accession is provided:
+                record.annotations["accession"] = name
+
+                if start is not None:
+                    record.annotations["start"] = start
+                if end is not None:
+                    record.annotations["end"] = end
+
+                self._populate_meta_data(seq_id, record)
+                records.append(record)
+            for k, v in gc.items():
+                if len(v) != alignment_length:
+                    raise ValueError(
+                        "%s length %i, expected %i" % (k, len(v), alignment_length)
+                    )
+            alignment = MultipleSeqAlignment(records)
+
+            for k, v in sorted(gc.items()):
+                if k in self.pfam_gc_mapping:
+                    alignment.column_annotations[self.pfam_gc_mapping[k]] = v
+                elif k.endswith("_cons") and k[:-5] in self.pfam_gr_mapping:
+                    alignment.column_annotations[self.pfam_gr_mapping[k[:-5]]] = v
+                else:
+                    # Ignore it?
+                    alignment.column_annotations["GC:" + k] = v
+
+            # TODO - Introduce an annotated alignment class?
+            # For now, store the annotation a new private property:
+            alignment._annotations = gr
+
+            return alignment
+        else:
+            raise StopIteration
+
+    def _identifier_split(self, identifier):
+        """Return (name, start, end) string tuple from an identifier (PRIVATE)."""
+        if "/" in identifier:
+            name, start_end = identifier.rsplit("/", 1)
+            if start_end.count("-") == 1:
+                try:
+                    start, end = start_end.split("-")
+                    return name, int(start), int(end)
+                except ValueError:
+                    # Non-integers after final '/' - fall through
+                    pass
+        return identifier, None, None
+
+    def _get_meta_data(self, identifier, meta_dict):
+        """Take an identifier and returns dict of all meta-data matching it (PRIVATE).
+
+        For example, given "Q9PN73_CAMJE/149-220" will return all matches to
+        this or "Q9PN73_CAMJE" which the identifier without its /start-end
+        suffix.
+
+        In the example below, the suffix is required to match the AC, but must
+        be removed to match the OS and OC meta-data::
+
+            # STOCKHOLM 1.0
+            #=GS Q9PN73_CAMJE/149-220  AC Q9PN73
+            ...
+            Q9PN73_CAMJE/149-220               NKA...
+            ...
+            #=GS Q9PN73_CAMJE OS Campylobacter jejuni
+            #=GS Q9PN73_CAMJE OC Bacteria
+
+        This function will return an empty dictionary if no data is found.
+        """
+        name, start, end = self._identifier_split(identifier)
+        if name == identifier:
+            identifier_keys = [identifier]
+        else:
+            identifier_keys = [identifier, name]
+        answer = {}
+        for identifier_key in identifier_keys:
+            try:
+                for feature_key in meta_dict[identifier_key]:
+                    answer[feature_key] = meta_dict[identifier_key][feature_key]
+            except KeyError:
+                pass
+        return answer
+
+    def _populate_meta_data(self, identifier, record):
+        """Add meta-date to a SecRecord's annotations dictionary (PRIVATE).
+
+        This function applies the PFAM conventions.
+        """
+        seq_data = self._get_meta_data(identifier, self.seq_annotation)
+        for feature in seq_data:
+            # Note this dictionary contains lists!
+            if feature == "AC":  # ACcession number
+                assert len(seq_data[feature]) == 1
+                record.annotations["accession"] = seq_data[feature][0]
+            elif feature == "DE":  # DEscription
+                record.description = "\n".join(seq_data[feature])
+            elif feature == "DR":  # Database Reference
+                # Should we try and parse the strings?
+                record.dbxrefs = seq_data[feature]
+            elif feature in self.pfam_gs_mapping:
+                record.annotations[self.pfam_gs_mapping[feature]] = ", ".join(
+                    seq_data[feature]
+                )
+            else:
+                # Ignore it?
+                record.annotations["GS:" + feature] = ", ".join(seq_data[feature])
+
+        # Now record the per-letter-annotations
+        seq_col_data = self._get_meta_data(identifier, self.seq_col_annotation)
+        for feature in seq_col_data:
+            # Note this dictionary contains strings!
+            if feature in self.pfam_gr_mapping:
+                record.letter_annotations[self.pfam_gr_mapping[feature]] = seq_col_data[
+                    feature
+                ]
+            else:
+                # Ignore it?
+                record.letter_annotations["GR:" + feature] = seq_col_data[feature]
+
+
+if __name__ == "__main__":
+    from Bio._utils import run_doctest
+
+    run_doctest()

.venv_haddock/lib/python3.12/site-packages/Bio/AlignIO/__init__.py

@@ -0,0 +1,474 @@
+# Copyright 2008-2018 by Peter Cock.  All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+"""Multiple sequence alignment input/output as alignment objects.
+
+The Bio.AlignIO interface is deliberately very similar to Bio.SeqIO, and in
+fact the two are connected internally.  Both modules use the same set of file
+format names (lower case strings).  From the user's perspective, you can read
+in a PHYLIP file containing one or more alignments using Bio.AlignIO, or you
+can read in the sequences within these alignments using Bio.SeqIO.
+
+Bio.AlignIO is also documented at http://biopython.org/wiki/AlignIO and by
+a whole chapter in our Tutorial_:
+
+.. _Tutorial: https://biopython.org/docs/latest/Tutorial/index.html
+
+Input
+-----
+For the typical special case when your file or handle contains one and only
+one alignment, use the function Bio.AlignIO.read().  This takes an input file
+handle (or in recent versions of Biopython a filename as a string), format
+string and optional number of sequences per alignment.  It will return a single
+MultipleSeqAlignment object (or raise an exception if there isn't just one
+alignment):
+
+>>> from Bio import AlignIO
+>>> align = AlignIO.read("Phylip/interlaced.phy", "phylip")
+>>> print(align)
+Alignment with 3 rows and 384 columns
+-----MKVILLFVLAVFTVFVSS---------------RGIPPE...I-- CYS1_DICDI
+MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTL...VAA ALEU_HORVU
+------MWATLPLLCAGAWLLGV--------PVCGAAELSVNSL...PLV CATH_HUMAN
+
+For the general case, when the handle could contain any number of alignments,
+use the function Bio.AlignIO.parse(...) which takes the same arguments, but
+returns an iterator giving MultipleSeqAlignment objects (typically used in a
+for loop). If you want random access to the alignments by number, turn this
+into a list:
+
+>>> from Bio import AlignIO
+>>> alignments = list(AlignIO.parse("Emboss/needle.txt", "emboss"))
+>>> print(alignments[2])
+Alignment with 2 rows and 120 columns
+-KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKER...--- ref_rec
+LHIVVVDDDPGTCVYIESVFAELGHTCKSFVRPEAAEEYILTHP...HKE gi|94967506|receiver
+
+Most alignment file formats can be concatenated so as to hold as many
+different multiple sequence alignments as possible.  One common example
+is the output of the tool seqboot in the PHLYIP suite.  Sometimes there
+can be a file header and footer, as seen in the EMBOSS alignment output.
+
+Output
+------
+Use the function Bio.AlignIO.write(...), which takes a complete set of
+Alignment objects (either as a list, or an iterator), an output file handle
+(or filename in recent versions of Biopython) and of course the file format::
+
+    from Bio import AlignIO
+    alignments = ...
+    count = SeqIO.write(alignments, "example.faa", "fasta")
+
+If using a handle make sure to close it to flush the data to the disk::
+
+    from Bio import AlignIO
+    alignments = ...
+    with open("example.faa", "w") as handle:
+        count = SeqIO.write(alignments, handle, "fasta")
+
+In general, you are expected to call this function once (with all your
+alignments) and then close the file handle.  However, for file formats
+like PHYLIP where multiple alignments are stored sequentially (with no file
+header and footer), then multiple calls to the write function should work as
+expected when using handles.
+
+If you are using a filename, the repeated calls to the write functions will
+overwrite the existing file each time.
+
+Conversion
+----------
+The Bio.AlignIO.convert(...) function allows an easy interface for simple
+alignment file format conversions. Additionally, it may use file format
+specific optimisations so this should be the fastest way too.
+
+In general however, you can combine the Bio.AlignIO.parse(...) function with
+the Bio.AlignIO.write(...) function for sequence file conversion. Using
+generator expressions provides a memory efficient way to perform filtering or
+other extra operations as part of the process.
+
+File Formats
+------------
+When specifying the file format, use lowercase strings.  The same format
+names are also used in Bio.SeqIO and include the following:
+
+  - clustal -   Output from Clustal W or X.
+  - emboss    - EMBOSS tools' "pairs" and "simple" alignment formats.
+  - fasta     - The generic sequence file format where each record starts with
+    an identifier line starting with a ">" character, followed by
+    lines of sequence.
+  - fasta-m10 - For the pairwise alignments output by Bill Pearson's FASTA
+    tools when used with the -m 10 command line option for machine
+    readable output.
+  - ig        - The IntelliGenetics file format, apparently the same as the
+    MASE alignment format.
+  - msf       - The GCG MSF alignment format, originally from PileUp tool.
+  - nexus     - Output from NEXUS, see also the module Bio.Nexus which can also
+    read any phylogenetic trees in these files.
+  - phylip    - Interlaced PHYLIP, as used by the PHYLIP tools.
+  - phylip-sequential - Sequential PHYLIP.
+  - phylip-relaxed - PHYLIP like format allowing longer names.
+  - stockholm - A richly annotated alignment file format used by PFAM.
+  - mauve - Output from progressiveMauve/Mauve
+
+Note that while Bio.AlignIO can read all the above file formats, it cannot
+write to all of them.
+
+You can also use any file format supported by Bio.SeqIO, such as "fasta" or
+"ig" (which are listed above), PROVIDED the sequences in your file are all the
+same length.
+"""
+
+# TODO
+# - define policy on reading aligned sequences with gaps in
+#   (e.g. - and . characters)
+#
+# - Can we build the to_alignment(...) functionality
+#   into the generic Alignment class instead?
+#
+# - How best to handle unique/non unique record.id when writing.
+#   For most file formats reading such files is fine; The stockholm
+#   parser would fail.
+#
+# - MSF multiple alignment format, aka GCG, aka PileUp format (*.msf)
+#   http://www.bioperl.org/wiki/MSF_multiple_alignment_format
+from Bio.Align import MultipleSeqAlignment
+from Bio.File import as_handle
+
+from . import ClustalIO
+from . import EmbossIO
+from . import FastaIO
+from . import MafIO
+from . import MauveIO
+from . import MsfIO
+from . import NexusIO
+from . import PhylipIO
+from . import StockholmIO
+
+# Convention for format names is "mainname-subtype" in lower case.
+# Please use the same names as BioPerl and EMBOSS where possible.
+
+_FormatToIterator = {  # "fasta" is done via Bio.SeqIO
+    "clustal": ClustalIO.ClustalIterator,
+    "emboss": EmbossIO.EmbossIterator,
+    "fasta-m10": FastaIO.FastaM10Iterator,
+    "maf": MafIO.MafIterator,
+    "mauve": MauveIO.MauveIterator,
+    "msf": MsfIO.MsfIterator,
+    "nexus": NexusIO.NexusIterator,
+    "phylip": PhylipIO.PhylipIterator,
+    "phylip-sequential": PhylipIO.SequentialPhylipIterator,
+    "phylip-relaxed": PhylipIO.RelaxedPhylipIterator,
+    "stockholm": StockholmIO.StockholmIterator,
+}
+
+_FormatToWriter = {  # "fasta" is done via Bio.SeqIO
+    "clustal": ClustalIO.ClustalWriter,
+    "maf": MafIO.MafWriter,
+    "mauve": MauveIO.MauveWriter,
+    "nexus": NexusIO.NexusWriter,
+    "phylip": PhylipIO.PhylipWriter,
+    "phylip-sequential": PhylipIO.SequentialPhylipWriter,
+    "phylip-relaxed": PhylipIO.RelaxedPhylipWriter,
+    "stockholm": StockholmIO.StockholmWriter,
+}
+
+
+def write(alignments, handle, format):
+    """Write complete set of alignments to a file.
+
+    Arguments:
+     - alignments - A list (or iterator) of MultipleSeqAlignment objects,
+       or a single alignment object.
+     - handle    - File handle object to write to, or filename as string
+       (note older versions of Biopython only took a handle).
+     - format    - lower case string describing the file format to write.
+
+    You should close the handle after calling this function.
+
+    Returns the number of alignments written (as an integer).
+    """
+    from Bio import SeqIO
+
+    # Try and give helpful error messages:
+    if not isinstance(format, str):
+        raise TypeError("Need a string for the file format (lower case)")
+    if not format:
+        raise ValueError("Format required (lower case string)")
+    if format != format.lower():
+        raise ValueError(f"Format string '{format}' should be lower case")
+
+    if isinstance(alignments, MultipleSeqAlignment):
+        # This raised an exception in older versions of Biopython
+        alignments = [alignments]
+
+    with as_handle(handle, "w") as fp:
+        # Map the file format to a writer class
+        if format in _FormatToWriter:
+            writer_class = _FormatToWriter[format]
+            count = writer_class(fp).write_file(alignments)
+        elif format in SeqIO._FormatToWriter:
+            # Exploit the existing SeqIO parser to do the dirty work!
+            # TODO - Can we make one call to SeqIO.write() and count the alignments?
+            count = 0
+            for alignment in alignments:
+                if not isinstance(alignment, MultipleSeqAlignment):
+                    raise TypeError(
+                        "Expect a list or iterator of MultipleSeqAlignment "
+                        "objects, got: %r" % alignment
+                    )
+                SeqIO.write(alignment, fp, format)
+                count += 1
+        elif format in _FormatToIterator or format in SeqIO._FormatToIterator:
+            raise ValueError(f"Reading format '{format}' is supported, but not writing")
+        else:
+            raise ValueError(f"Unknown format '{format}'")
+
+    if not isinstance(count, int):
+        raise RuntimeError(
+            "Internal error - the underlying %s "
+            "writer should have returned the alignment count, not %r" % (format, count)
+        )
+
+    return count
+
+
+# This is a generator function!
+def _SeqIO_to_alignment_iterator(handle, format, seq_count=None):
+    """Use Bio.SeqIO to create an MultipleSeqAlignment iterator (PRIVATE).
+
+    Arguments:
+     - handle    - handle to the file.
+     - format    - string describing the file format.
+     - seq_count - Optional integer, number of sequences expected in each
+       alignment.  Recommended for fasta format files.
+
+    If count is omitted (default) then all the sequences in the file are
+    combined into a single MultipleSeqAlignment.
+    """
+    from Bio import SeqIO
+
+    if format not in SeqIO._FormatToIterator:
+        raise ValueError(f"Unknown format '{format}'")
+
+    if seq_count:
+        # Use the count to split the records into batches.
+        seq_record_iterator = SeqIO.parse(handle, format)
+
+        records = []
+        for record in seq_record_iterator:
+            records.append(record)
+            if len(records) == seq_count:
+                yield MultipleSeqAlignment(records)
+                records = []
+        if records:
+            raise ValueError("Check seq_count argument, not enough sequences?")
+    else:
+        # Must assume that there is a single alignment using all
+        # the SeqRecord objects:
+        records = list(SeqIO.parse(handle, format))
+        if records:
+            yield MultipleSeqAlignment(records)
+
+
+def parse(handle, format, seq_count=None):
+    """Iterate over an alignment file as MultipleSeqAlignment objects.
+
+    Arguments:
+     - handle    - handle to the file, or the filename as a string
+       (note older versions of Biopython only took a handle).
+     - format    - string describing the file format.
+     - seq_count - Optional integer, number of sequences expected in each
+       alignment.  Recommended for fasta format files.
+
+    If you have the file name in a string 'filename', use:
+
+    >>> from Bio import AlignIO
+    >>> filename = "Emboss/needle.txt"
+    >>> format = "emboss"
+    >>> for alignment in AlignIO.parse(filename, format):
+    ...     print("Alignment of length %i" % alignment.get_alignment_length())
+    Alignment of length 124
+    Alignment of length 119
+    Alignment of length 120
+    Alignment of length 118
+    Alignment of length 125
+
+    If you have a string 'data' containing the file contents, use::
+
+      from Bio import AlignIO
+      from io import StringIO
+      my_iterator = AlignIO.parse(StringIO(data), format)
+
+    Use the Bio.AlignIO.read() function when you expect a single record only.
+    """
+    from Bio import SeqIO
+
+    # Try and give helpful error messages:
+    if not isinstance(format, str):
+        raise TypeError("Need a string for the file format (lower case)")
+    if not format:
+        raise ValueError("Format required (lower case string)")
+    if format != format.lower():
+        raise ValueError(f"Format string '{format}' should be lower case")
+    if seq_count is not None and not isinstance(seq_count, int):
+        raise TypeError("Need integer for seq_count (sequences per alignment)")
+
+    with as_handle(handle) as fp:
+        # Map the file format to a sequence iterator:
+        if format in _FormatToIterator:
+            iterator_generator = _FormatToIterator[format]
+            i = iterator_generator(fp, seq_count)
+
+        elif format in SeqIO._FormatToIterator:
+            # Exploit the existing SeqIO parser to the dirty work!
+            i = _SeqIO_to_alignment_iterator(fp, format, seq_count=seq_count)
+        else:
+            raise ValueError(f"Unknown format '{format}'")
+
+        yield from i
+
+
+def read(handle, format, seq_count=None):
+    """Turn an alignment file into a single MultipleSeqAlignment object.
+
+    Arguments:
+     - handle    - handle to the file, or the filename as a string
+       (note older versions of Biopython only took a handle).
+     - format    - string describing the file format.
+     - seq_count - Optional integer, number of sequences expected in each
+       alignment.  Recommended for fasta format files.
+
+    If the handle contains no alignments, or more than one alignment,
+    an exception is raised.  For example, using a PFAM/Stockholm file
+    containing one alignment:
+
+    >>> from Bio import AlignIO
+    >>> filename = "Clustalw/protein.aln"
+    >>> format = "clustal"
+    >>> alignment = AlignIO.read(filename, format)
+    >>> print("Alignment of length %i" % alignment.get_alignment_length())
+    Alignment of length 411
+
+    If however you want the first alignment from a file containing
+    multiple alignments this function would raise an exception.
+
+    >>> from Bio import AlignIO
+    >>> filename = "Emboss/needle.txt"
+    >>> format = "emboss"
+    >>> alignment = AlignIO.read(filename, format)
+    Traceback (most recent call last):
+        ...
+    ValueError: More than one record found in handle
+
+    Instead use:
+
+    >>> from Bio import AlignIO
+    >>> filename = "Emboss/needle.txt"
+    >>> format = "emboss"
+    >>> alignment = next(AlignIO.parse(filename, format))
+    >>> print("First alignment has length %i" % alignment.get_alignment_length())
+    First alignment has length 124
+
+    You must use the Bio.AlignIO.parse() function if you want to read multiple
+    records from the handle.
+    """
+    iterator = parse(handle, format, seq_count)
+    try:
+        alignment = next(iterator)
+    except StopIteration:
+        raise ValueError("No records found in handle") from None
+    try:
+        next(iterator)
+        raise ValueError("More than one record found in handle")
+    except StopIteration:
+        pass
+    if seq_count:
+        if len(alignment) != seq_count:
+            raise RuntimeError(
+                "More sequences found in alignment than specified in seq_count: %s."
+                % seq_count
+            )
+    return alignment
+
+
+def convert(in_file, in_format, out_file, out_format, molecule_type=None):
+    """Convert between two alignment files, returns number of alignments.
+
+    Arguments:
+     - in_file - an input handle or filename
+     - in_format - input file format, lower case string
+     - output - an output handle or filename
+     - out_file - output file format, lower case string
+     - molecule_type - optional molecule type to apply, string containing
+       "DNA", "RNA" or "protein".
+
+    **NOTE** - If you provide an output filename, it will be opened which will
+    overwrite any existing file without warning. This may happen if even the
+    conversion is aborted (e.g. an invalid out_format name is given).
+
+    Some output formats require the molecule type be specified where this
+    cannot be determined by the parser. For example, converting to FASTA,
+    Clustal, or PHYLIP format to NEXUS:
+
+    >>> from io import StringIO
+    >>> from Bio import AlignIO
+    >>> handle = StringIO()
+    >>> AlignIO.convert("Phylip/horses.phy", "phylip", handle, "nexus", "DNA")
+    1
+    >>> print(handle.getvalue())
+    #NEXUS
+    begin data;
+    dimensions ntax=10 nchar=40;
+    format datatype=dna missing=? gap=-;
+    matrix
+    Mesohippus   AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+    Hypohippus   AAACCCCCCCAAAAAAAAACAAAAAAAAAAAAAAAAAAAA
+    Archaeohip   CAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAA
+    Parahippus   CAAACAACAACAAAAAAAACAAAAAAAAAAAAAAAAAAAA
+    Merychippu   CCAACCACCACCCCACACCCAAAAAAAAAAAAAAAAAAAA
+    'M. secundu' CCAACCACCACCCACACCCCAAAAAAAAAAAAAAAAAAAA
+    Nannipus     CCAACCACAACCCCACACCCAAAAAAAAAAAAAAAAAAAA
+    Neohippari   CCAACCCCCCCCCCACACCCAAAAAAAAAAAAAAAAAAAA
+    Calippus     CCAACCACAACCCACACCCCAAAAAAAAAAAAAAAAAAAA
+    Pliohippus   CCCACCCCCCCCCACACCCCAAAAAAAAAAAAAAAAAAAA
+    ;
+    end;
+    <BLANKLINE>
+    """
+    if molecule_type:
+        if not isinstance(molecule_type, str):
+            raise TypeError(f"Molecule type should be a string, not {molecule_type!r}")
+        elif (
+            "DNA" in molecule_type
+            or "RNA" in molecule_type
+            or "protein" in molecule_type
+        ):
+            pass
+        else:
+            raise ValueError(f"Unexpected molecule type, {molecule_type!r}")
+
+    # TODO - Add optimised versions of important conversions
+    # For now just off load the work to SeqIO parse/write
+    # Don't open the output file until we've checked the input is OK:
+    alignments = parse(in_file, in_format, None)
+
+    if molecule_type:
+        # Edit the records on the fly to set molecule type
+
+        def over_ride(alignment):
+            """Over-ride molecule in-place."""
+            for record in alignment:
+                record.annotations["molecule_type"] = molecule_type
+            return alignment
+
+        alignments = (over_ride(_) for _ in alignments)
+    return write(alignments, out_file, out_format)
+
+
+if __name__ == "__main__":
+    from Bio._utils import run_doctest
+
+    run_doctest()

.venv_haddock/lib/python3.12/site-packages/Bio/Alphabet/__init__.py

@@ -0,0 +1,22 @@
+# Copyright 2000-2002 by Andrew Dalke.
+# Revisions copyright 2007-2010 by Peter Cock.
+# All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+"""Alphabets were previously used to declare sequence type and letters (OBSOLETE).
+
+The design of Bio.Alphabet included a number of historic design choices
+which, with the benefit of hindsight, were regretable. Bio.Alphabet was
+therefore removed from Biopython in release 1.78. Instead, the molecule type is
+included as an annotation on SeqRecords where appropriate.
+
+Please see https://biopython.org/wiki/Alphabet for examples showing how to
+transition from Bio.Alphabet to molecule type annotations.
+"""
+
+raise ImportError(
+    "Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the ``molecule_type`` as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information."
+)

.venv_haddock/lib/python3.12/site-packages/Bio/Blast/NCBIWWW.py

@@ -0,0 +1,373 @@
+# Copyright 1999 by Jeffrey Chang.  All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+#
+# Patched by Brad Chapman.
+# Chris Wroe added modifications for work in myGrid
+
+"""Code to invoke the NCBI BLAST server over the internet.
+
+This module provides code to work with the WWW version of BLAST
+provided by the NCBI. https://blast.ncbi.nlm.nih.gov/
+
+Variables:
+
+    - email        Set the Blast email parameter (default is None).
+    - tool         Set the Blast tool parameter (default is ``biopython``).
+
+"""
+
+import time
+import warnings
+from io import StringIO
+from urllib.parse import urlencode
+from urllib.request import build_opener
+from urllib.request import HTTPBasicAuthHandler
+from urllib.request import HTTPPasswordMgrWithDefaultRealm
+from urllib.request import install_opener
+from urllib.request import Request
+from urllib.request import urlopen
+
+from Bio import BiopythonWarning
+from Bio._utils import function_with_previous
+
+email = None
+tool = "biopython"
+
+
+NCBI_BLAST_URL = "https://blast.ncbi.nlm.nih.gov/Blast.cgi"
+
+
+@function_with_previous
+def qblast(
+    program,
+    database,
+    sequence,
+    url_base=NCBI_BLAST_URL,
+    auto_format=None,
+    composition_based_statistics=None,
+    db_genetic_code=None,
+    endpoints=None,
+    entrez_query="(none)",
+    expect=10.0,
+    filter=None,
+    gapcosts=None,
+    genetic_code=None,
+    hitlist_size=50,
+    i_thresh=None,
+    layout=None,
+    lcase_mask=None,
+    matrix_name=None,
+    nucl_penalty=None,
+    nucl_reward=None,
+    other_advanced=None,
+    perc_ident=None,
+    phi_pattern=None,
+    query_file=None,
+    query_believe_defline=None,
+    query_from=None,
+    query_to=None,
+    searchsp_eff=None,
+    service=None,
+    threshold=None,
+    ungapped_alignment=None,
+    word_size=None,
+    short_query=None,
+    alignments=500,
+    alignment_view=None,
+    descriptions=500,
+    entrez_links_new_window=None,
+    expect_low=None,
+    expect_high=None,
+    format_entrez_query=None,
+    format_object=None,
+    format_type="XML",
+    ncbi_gi=None,
+    results_file=None,
+    show_overview=None,
+    megablast=None,
+    template_type=None,
+    template_length=None,
+    username="blast",
+    password=None,
+):
+    """BLAST search using NCBI's QBLAST server.
+
+    Supports all parameters of the old qblast API for Put and Get.
+
+    Please note that NCBI uses the new Common URL API for BLAST searches
+    on the internet (https://blast.ncbi.nlm.nih.gov/doc/blast-help/urlapi.html).
+    Thus, some of the parameters used by this function are not (or are no longer)
+    officially supported by NCBI. Although they are still functioning, this
+    may change in the future.
+
+    Some useful parameters:
+
+     - program        blastn, blastp, blastx, tblastn, or tblastx (lower case)
+     - database       Which database to search against (e.g. "nr").
+     - sequence       The sequence to search.
+     - ncbi_gi        TRUE/FALSE whether to give 'gi' identifier.
+     - descriptions   Number of descriptions to show.  Def 500.
+     - alignments     Number of alignments to show.  Def 500.
+     - expect         An expect value cutoff.  Def 10.0.
+     - matrix_name    Specify an alt. matrix (PAM30, PAM70, BLOSUM80, BLOSUM45).
+     - filter         "none" turns off filtering.  Default no filtering
+     - format_type    "HTML", "Text", "ASN.1", or "XML".  Def. "XML".
+     - entrez_query   Entrez query to limit Blast search - only applies when searching nucleotide BLASTDBs
+     - hitlist_size   Number of hits to return. Default 50
+     - megablast      TRUE/FALSE whether to use MEga BLAST algorithm (blastn only)
+     - short_query    TRUE/FALSE whether to adjust the search parameters for a
+                      short query sequence. Note that this will override
+                      manually set parameters like word size and e value. Turns
+                      off when sequence length is > 30 residues. Default: None.
+     - service        plain, psi, phi, rpsblast, megablast (lower case)
+
+    This function does no checking of the validity of the parameters
+    and passes the values to the server as is.  More help is available at:
+    https://blast.ncbi.nlm.nih.gov/doc/blast-help/urlapi.html
+
+    """
+    programs = ["blastn", "blastp", "blastx", "tblastn", "tblastx"]
+    if program not in programs:
+        raise ValueError(
+            f"Program specified is {program}. Expected one of {', '.join(programs)}"
+        )
+
+    # SHORT_QUERY_ADJUST throws an error when using blastn (wrong parameter
+    # assignment from NCBIs side).
+    # Thus we set the (known) parameters directly:
+    if short_query and program == "blastn":
+        short_query = None
+        # We only use the 'short-query' parameters for short sequences:
+        if len(sequence) < 31:
+            expect = 1000
+            word_size = 7
+            nucl_reward = 1
+            filter = None
+            lcase_mask = None
+            warnings.warn(
+                '"SHORT_QUERY_ADJUST" is incorrectly implemented (by NCBI) for blastn.'
+                " We bypass the problem by manually adjusting the search parameters."
+                " Thus, results may slightly differ from web page searches.",
+                BiopythonWarning,
+            )
+
+    # Format the "Put" command, which sends search requests to qblast.
+    # Parameters taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node5.html on 9 July 2007
+    # Additional parameters are taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node9.html on 8 Oct 2010
+    # To perform a PSI-BLAST or PHI-BLAST search the service ("Put" and "Get" commands) must be specified
+    # (e.g. psi_blast = NCBIWWW.qblast("blastp", "refseq_protein", input_sequence, service="psi"))
+    parameters = {
+        "AUTO_FORMAT": auto_format,
+        "COMPOSITION_BASED_STATISTICS": composition_based_statistics,
+        "DATABASE": database,
+        "DB_GENETIC_CODE": db_genetic_code,
+        "ENDPOINTS": endpoints,
+        "ENTREZ_QUERY": entrez_query,
+        "EXPECT": expect,
+        "FILTER": filter,
+        "GAPCOSTS": gapcosts,
+        "GENETIC_CODE": genetic_code,
+        "HITLIST_SIZE": hitlist_size,
+        "I_THRESH": i_thresh,
+        "LAYOUT": layout,
+        "LCASE_MASK": lcase_mask,
+        "MEGABLAST": megablast,
+        "MATRIX_NAME": matrix_name,
+        "NUCL_PENALTY": nucl_penalty,
+        "NUCL_REWARD": nucl_reward,
+        "OTHER_ADVANCED": other_advanced,
+        "PERC_IDENT": perc_ident,
+        "PHI_PATTERN": phi_pattern,
+        "PROGRAM": program,
+        # ('PSSM': pssm: - It is possible to use PSI-BLAST via this API?
+        "QUERY": sequence,
+        "QUERY_FILE": query_file,
+        "QUERY_BELIEVE_DEFLINE": query_believe_defline,
+        "QUERY_FROM": query_from,
+        "QUERY_TO": query_to,
+        # 'RESULTS_FILE': ...: - Can we use this parameter?
+        "SEARCHSP_EFF": searchsp_eff,
+        "SERVICE": service,
+        "SHORT_QUERY_ADJUST": short_query,
+        "TEMPLATE_TYPE": template_type,
+        "TEMPLATE_LENGTH": template_length,
+        "THRESHOLD": threshold,
+        "UNGAPPED_ALIGNMENT": ungapped_alignment,
+        "WORD_SIZE": word_size,
+        "CMD": "Put",
+    }
+
+    if password is not None:
+        # handle authentication for BLAST cloud
+        password_mgr = HTTPPasswordMgrWithDefaultRealm()
+        password_mgr.add_password(None, url_base, username, password)
+        handler = HTTPBasicAuthHandler(password_mgr)
+        opener = build_opener(handler)
+        install_opener(opener)
+
+    if url_base == NCBI_BLAST_URL:
+        parameters.update({"email": email, "tool": tool})
+    parameters = {key: value for key, value in parameters.items() if value is not None}
+    message = urlencode(parameters).encode()
+    request = Request(url_base, message, {"User-Agent": "BiopythonClient"})
+    # Send off the initial query to qblast.
+    # Note the NCBI do not currently impose a rate limit here, other
+    # than the request not to make say 50 queries at once using multiple
+    # threads.
+    handle = urlopen(request)
+
+    # Format the "Get" command, which gets the formatted results from qblast
+    # Parameters taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node6.html on 9 July 2007
+    rid, rtoe = _parse_qblast_ref_page(handle)
+    parameters = {
+        "ALIGNMENTS": alignments,
+        "ALIGNMENT_VIEW": alignment_view,
+        "DESCRIPTIONS": descriptions,
+        "ENTREZ_LINKS_NEW_WINDOW": entrez_links_new_window,
+        "EXPECT_LOW": expect_low,
+        "EXPECT_HIGH": expect_high,
+        "FORMAT_ENTREZ_QUERY": format_entrez_query,
+        "FORMAT_OBJECT": format_object,
+        "FORMAT_TYPE": format_type,
+        "NCBI_GI": ncbi_gi,
+        "RID": rid,
+        "RESULTS_FILE": results_file,
+        "SERVICE": service,
+        "SHOW_OVERVIEW": show_overview,
+        "CMD": "Get",
+    }
+    parameters = {key: value for key, value in parameters.items() if value is not None}
+    message = urlencode(parameters).encode()
+
+    # Poll NCBI until the results are ready.
+    # https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo
+    # 1. Do not contact the server more often than once every 10 seconds.
+    # 2. Do not poll for any single RID more often than once a minute.
+    # 3. Use the URL parameter email and tool, so that the NCBI
+    #    can contact you if there is a problem.
+    # 4. Run scripts weekends or between 9 pm and 5 am Eastern time
+    #    on weekdays if more than 50 searches will be submitted.
+    # --
+    # Could start with a 10s delay, but expect most short queries
+    # will take longer thus at least 70s with delay. Therefore,
+    # start with 20s delay, thereafter once a minute.
+    delay = 20  # seconds
+    start_time = time.time()
+    while True:
+        current = time.time()
+        wait = qblast.previous + delay - current
+        if wait > 0:
+            time.sleep(wait)
+            qblast.previous = current + wait
+        else:
+            qblast.previous = current
+        # delay by at least 60 seconds only if running the request against the public NCBI API
+        if delay < 60 and url_base == NCBI_BLAST_URL:
+            # Wasn't a quick return, must wait at least a minute
+            delay = 60
+        elapsed = time.time() - start_time
+        # Throw a warning if search takes longer than ten minutes
+        if elapsed >= 600:
+            warnings.warn(
+                f"BLAST request {rid} is taking longer than 10 minutes, consider re-issuing it",
+                BiopythonWarning,
+            )
+
+        request = Request(url_base, message, {"User-Agent": "BiopythonClient"})
+        handle = urlopen(request)
+        results = handle.read().decode()
+
+        # Can see an "\n\n" page while results are in progress,
+        # if so just wait a bit longer...
+        if results == "\n\n":
+            continue
+        # XML results don't have the Status tag when finished
+        if "Status=" not in results:
+            break
+        i = results.index("Status=")
+        j = results.index("\n", i)
+        status = results[i + len("Status=") : j].strip()
+        if status.upper() == "READY":
+            break
+    return StringIO(results)
+
+
+qblast.previous = 0
+
+
+def _parse_qblast_ref_page(handle):
+    """Extract a tuple of RID, RTOE from the 'please wait' page (PRIVATE).
+
+    The NCBI FAQ pages use TOE for 'Time of Execution', so RTOE is probably
+    'Request Time of Execution' and RID would be 'Request Identifier'.
+    """
+    s = handle.read().decode()
+    i = s.find("RID =")
+    if i == -1:
+        rid = None
+    else:
+        j = s.find("\n", i)
+        rid = s[i + len("RID =") : j].strip()
+
+    i = s.find("RTOE =")
+    if i == -1:
+        rtoe = None
+    else:
+        j = s.find("\n", i)
+        rtoe = s[i + len("RTOE =") : j].strip()
+
+    if not rid and not rtoe:
+        # Can we reliably extract the error message from the HTML page?
+        # e.g.  "Message ID#24 Error: Failed to read the Blast query:
+        #       Nucleotide FASTA provided for protein sequence"
+        # or    "Message ID#32 Error: Query contains no data: Query
+        #       contains no sequence data"
+        #
+        # This used to occur inside a <div class="error msInf"> entry:
+        i = s.find('<div class="error msInf">')
+        if i != -1:
+            msg = s[i + len('<div class="error msInf">') :].strip()
+            msg = msg.split("</div>", 1)[0].split("\n", 1)[0].strip()
+            if msg:
+                raise ValueError(f"Error message from NCBI: {msg}")
+        # In spring 2010 the markup was like this:
+        i = s.find('<p class="error">')
+        if i != -1:
+            msg = s[i + len('<p class="error">') :].strip()
+            msg = msg.split("</p>", 1)[0].split("\n", 1)[0].strip()
+            if msg:
+                raise ValueError(f"Error message from NCBI: {msg}")
+        # Generic search based on the way the error messages start:
+        i = s.find("Message ID#")
+        if i != -1:
+            # Break the message at the first HTML tag
+            msg = s[i:].split("<", 1)[0].split("\n", 1)[0].strip()
+            raise ValueError(f"Error message from NCBI: {msg}")
+        # We didn't recognise the error layout :(
+        # print(s)
+        raise ValueError(
+            "No RID and no RTOE found in the 'please wait' page, "
+            "there was probably an error in your request but we "
+            "could not extract a helpful error message."
+        )
+    elif not rid:
+        # Can this happen?
+        raise ValueError(
+            f"No RID found in the 'please wait' page. (although RTOE = {rtoe!r})"
+        )
+    elif not rtoe:
+        # Can this happen?
+        raise ValueError(
+            f"No RTOE found in the 'please wait' page. (although RID = {rid!r})"
+        )
+
+    try:
+        return rid, int(rtoe)
+    except ValueError:
+        raise ValueError(
+            f"A non-integer RTOE found in the 'please wait' page, {rtoe!r}"
+        ) from None

.venv_haddock/lib/python3.12/site-packages/Bio/Blast/NCBIXML.py

@@ -0,0 +1,1331 @@
+# Copyright 1999-2000 by Jeffrey Chang.  All rights reserved.
+# Copyright 2000 by Bertrand Frottier.  All rights reserved.
+# Revisions 2005-2006 copyright Michiel de Hoon
+# Revisions 2006-2009 copyright Peter Cock
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+"""Code to work with the BLAST XML output.
+
+The BLAST XML DTD file is available on the NCBI site at:
+https://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd
+
+Record classes to hold BLAST output are:
+
+Classes:
+Blast              Holds all the information from a blast search.
+PSIBlast           Holds all the information from a psi-blast search.
+
+Header             Holds information from the header.
+Description        Holds information about one hit description.
+Alignment          Holds information about one alignment hit.
+HSP                Holds information about one HSP.
+MultipleAlignment  Holds information about a multiple alignment.
+DatabaseReport     Holds information from the database report.
+Parameters         Holds information from the parameters.
+
+"""
+# XXX finish printable BLAST output
+
+import sys
+import warnings
+import xml.sax
+from xml.sax.handler import ContentHandler
+
+from Bio import BiopythonParserWarning
+
+from Bio.Align import MultipleSeqAlignment
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+
+
+def fmt_(value, format_spec="%s", default_str="<unknown>"):
+    """Ensure the given value formats to a string correctly."""
+    if value is None:
+        return default_str
+    return format_spec % value
+
+
+class Header:
+    """Saves information from a blast header.
+
+    Members:
+    application         The name of the BLAST flavor that generated this data.
+    version             Version of blast used.
+    date                Date this data was generated.
+    reference           Reference for blast.
+
+    query               Name of query sequence.
+    query_letters       Number of letters in the query sequence.  (int)
+
+    database            Name of the database.
+    database_sequences  Number of sequences in the database.  (int)
+    database_letters    Number of letters in the database.  (int)
+
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        self.application = ""
+        self.version = ""
+        self.date = ""
+        self.reference = ""
+
+        self.query = ""
+        self.query_letters = None
+
+        self.database = ""
+        self.database_sequences = None
+        self.database_letters = None
+
+
+class Description:
+    """Stores information about one hit in the descriptions section.
+
+    Members:
+    title           Title of the hit.
+    score           Number of bits.  (int)
+    bits            Bit score. (float)
+    e               E value.  (float)
+    num_alignments  Number of alignments for the same subject.  (int)
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        self.title = ""
+        self.score = None
+        self.bits = None
+        self.e = None
+        self.num_alignments = None
+
+    def __str__(self):
+        """Return the description as a string."""
+        return f"{self.title:<66} {self.score:>5}  {self.e}"
+
+
+class DescriptionExt(Description):
+    """Extended description record for BLASTXML version 2.
+
+    Members:
+    items           List of DescriptionExtItem
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        super().__init__()
+
+        self.items = []
+
+    def append_item(self, item):
+        """Add a description extended record."""
+        if len(self.items) == 0:
+            self.title = str(item)
+        self.items.append(item)
+
+
+class DescriptionExtItem:
+    """Stores information about one record in hit description for BLASTXML version 2.
+
+    Members:
+    id              Database identifier
+    title           Title of the hit.
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        self.id = None
+        self.title = None
+        self.accession = None
+        self.taxid = None
+        self.sciname = None
+
+    def __str__(self):
+        """Return the description identifier and title as a string."""
+        return f"{self.id} {self.title}"
+
+
+class Alignment:
+    """Stores information about one hit in the alignments section.
+
+    Members:
+    title      Name.
+    hit_id     Hit identifier. (str)
+    hit_def    Hit definition. (str)
+    length     Length.  (int)
+    hsps       A list of HSP objects.
+
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        self.title = ""
+        self.hit_id = ""
+        self.hit_def = ""
+        self.length = None
+        self.hsps = []
+
+    def __str__(self):
+        """Return the BLAST alignment as a formatted string."""
+        lines = self.title.split("\n")
+        lines.append(f"Length = {self.length}\n")
+        return "\n           ".join(lines)
+
+
+class HSP:
+    """Stores information about one hsp in an alignment hit.
+
+    Members:
+        - score           BLAST score of hit.  (float)
+        - bits            Number of bits for that score.  (float)
+        - expect          Expect value.  (float)
+        - num_alignments  Number of alignments for same subject.  (int)
+        - identities      Number of identities (int) if using the XML parser.
+          Tuple of number of identities/total aligned (int, int)
+          if using the (obsolete) plain text parser.
+        - positives       Number of positives (int) if using the XML parser.
+          Tuple of number of positives/total aligned (int, int)
+          if using the (obsolete) plain text parser.
+        - gaps            Number of gaps (int) if using the XML parser.
+          Tuple of number of gaps/total aligned (int, int) if
+          using the (obsolete) plain text parser.
+        - align_length    Length of the alignment. (int)
+        - strand          Tuple of (query, target) strand.
+        - frame           Tuple of 1 or 2 frame shifts, depending on the flavor.
+
+        - query           The query sequence.
+        - query_start     The start residue for the query sequence.  (1-based)
+        - query_end       The end residue for the query sequence.  (1-based)
+        - match           The match sequence.
+        - sbjct           The sbjct sequence.
+        - sbjct_start     The start residue for the sbjct sequence.  (1-based)
+        - sbjct_end       The end residue for the sbjct sequence.  (1-based)
+
+    Not all flavors of BLAST return values for every attribute::
+
+                  score     expect     identities   positives    strand  frame
+        BLASTP     X          X            X            X
+        BLASTN     X          X            X            X          X
+        BLASTX     X          X            X            X                  X
+        TBLASTN    X          X            X            X                  X
+        TBLASTX    X          X            X            X                 X/X
+
+    Note: for BLASTX, the query sequence is shown as a protein sequence,
+    but the numbering is based on the nucleotides.  Thus, the numbering
+    is 3x larger than the number of amino acid residues.  A similar effect
+    can be seen for the sbjct sequence in TBLASTN, and for both sequences
+    in TBLASTX.
+
+    Also, for negative frames, the sequence numbering starts from
+    query_start and counts down.
+
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        self.score = None
+        self.bits = None
+        self.expect = None
+        self.num_alignments = None
+        self.identities = (None, None)
+        self.positives = (None, None)
+        self.gaps = (None, None)
+        self.align_length = None
+        self.strand = (None, None)
+        self.frame = ()
+
+        self.query = ""
+        self.query_start = None
+        self.query_end = None
+        self.match = ""
+        self.sbjct = ""
+        self.sbjct_start = None
+        self.sbjct_end = None
+
+    def __str__(self):
+        """Return the BLAST HSP as a formatted string."""
+        lines = [
+            "Score %s (%s bits), expectation %s, alignment length %s"
+            % (
+                fmt_(self.score, "%i"),
+                fmt_(self.bits, "%i"),
+                fmt_(self.expect, "%0.1e"),
+                fmt_(self.align_length, "%i"),
+            )
+        ]
+        if self.align_length is None:
+            return "\n".join(lines)
+        if self.align_length < 50:
+            lines.append(
+                "Query:%8s %s %s" % (self.query_start, self.query, self.query_end)
+            )
+            lines.append(f"               {self.match}")
+            lines.append(
+                "Sbjct:%8s %s %s" % (self.sbjct_start, self.sbjct, self.sbjct_end)
+            )
+        else:
+            lines.append(
+                "Query:%8s %s...%s %s"
+                % (self.query_start, self.query[:45], self.query[-3:], self.query_end)
+            )
+            lines.append(f"               {self.match[:45]}...{self.match[-3:]}")
+            lines.append(
+                "Sbjct:%8s %s...%s %s"
+                % (self.sbjct_start, self.sbjct[:45], self.sbjct[-3:], self.sbjct_end)
+            )
+        return "\n".join(lines)
+
+
+class MultipleAlignment:
+    """Holds information about a multiple alignment.
+
+    Members:
+    alignment  A list of tuples (name, start residue, sequence, end residue).
+
+    The start residue is 1-based.  It may be blank, if that sequence is
+    not aligned in the multiple alignment.
+
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        self.alignment = []
+
+    def to_generic(self):
+        """Retrieve generic alignment object for the given alignment.
+
+        Instead of the tuples, this returns a MultipleSeqAlignment object
+        from Bio.Align, through which you can manipulate and query
+        the object.
+
+        Thanks to James Casbon for the code.
+        """
+        seq_parts = []
+        seq_names = []
+        parse_number = 0
+        n = 0
+        for name, start, seq, end in self.alignment:
+            if name == "QUERY":  # QUERY is the first in each alignment block
+                parse_number += 1
+                n = 0
+
+            if parse_number == 1:  # create on first_parse, append on all others
+                seq_parts.append(seq)
+                seq_names.append(name)
+            else:
+                seq_parts[n] += seq
+                n += 1
+
+        records = (
+            SeqRecord(Seq(seq), name) for (name, seq) in zip(seq_names, seq_parts)
+        )
+        return MultipleSeqAlignment(records)
+
+
+class Round:
+    """Holds information from a PSI-BLAST round.
+
+    Members:
+    number       Round number.  (int)
+    reused_seqs  Sequences in model, found again.  List of Description objects.
+    new_seqs     Sequences not found, or below threshold.  List of Description.
+    alignments          A list of Alignment objects.
+    multiple_alignment  A MultipleAlignment object.
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        self.number = None
+        self.reused_seqs = []
+        self.new_seqs = []
+        self.alignments = []
+        self.multiple_alignment = None
+
+
+class DatabaseReport:
+    """Holds information about a database report.
+
+    Members:
+    database_name              List of database names.  (can have multiple dbs)
+    num_letters_in_database    Number of letters in the database.  (int)
+    num_sequences_in_database  List of number of sequences in the database.
+    posted_date                List of the dates the databases were posted.
+    ka_params                  A tuple of (lambda, k, h) values.  (floats)
+    gapped                     # XXX this isn't set right!
+    ka_params_gap              A tuple of (lambda, k, h) values.  (floats)
+
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        self.database_name = []
+        self.posted_date = []
+        self.num_letters_in_database = []
+        self.num_sequences_in_database = []
+        self.ka_params = (None, None, None)
+        self.gapped = 0
+        self.ka_params_gap = (None, None, None)
+
+
+class Parameters:
+    """Holds information about the parameters.
+
+    Members:
+    matrix              Name of the matrix.
+    gap_penalties       Tuple of (open, extend) penalties.  (floats)
+    sc_match            Match score for nucleotide-nucleotide comparison
+    sc_mismatch         Mismatch penalty for nucleotide-nucleotide comparison
+    num_hits            Number of hits to the database.  (int)
+    num_sequences       Number of sequences.  (int)
+    num_good_extends    Number of extensions.  (int)
+    num_seqs_better_e   Number of sequences better than e-value.  (int)
+    hsps_no_gap         Number of HSP's better, without gapping.  (int)
+    hsps_prelim_gapped  Number of HSP's gapped in prelim test.  (int)
+    hsps_prelim_gapped_attemped  Number of HSP's attempted in prelim.  (int)
+    hsps_gapped         Total number of HSP's gapped.  (int)
+    query_length        Length of the query.  (int)
+    query_id            Identifier of the query sequence. (str)
+    database_length     Number of letters in the database.  (int)
+    effective_hsp_length         Effective HSP length.  (int)
+    effective_query_length       Effective length of query.  (int)
+    effective_database_length    Effective length of database.  (int)
+    effective_search_space       Effective search space.  (int)
+    effective_search_space_used  Effective search space used.  (int)
+    frameshift          Frameshift window.  Tuple of (int, float)
+    threshold           Threshold.  (int)
+    window_size         Window size.  (int)
+    dropoff_1st_pass    Tuple of (score, bits).  (int, float)
+    gap_x_dropoff       Tuple of (score, bits).  (int, float)
+    gap_x_dropoff_final Tuple of (score, bits).  (int, float)
+    gap_trigger         Tuple of (score, bits).  (int, float)
+    blast_cutoff        Tuple of (score, bits).  (int, float)
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        self.matrix = ""
+        self.gap_penalties = (None, None)
+        self.sc_match = None
+        self.sc_mismatch = None
+        self.num_hits = None
+        self.num_sequences = None
+        self.num_good_extends = None
+        self.num_seqs_better_e = None
+        self.hsps_no_gap = None
+        self.hsps_prelim_gapped = None
+        self.hsps_prelim_gapped_attemped = None
+        self.hsps_gapped = None
+        self.query_id = None
+        self.query_length = None
+        self.database_length = None
+        self.effective_hsp_length = None
+        self.effective_query_length = None
+        self.effective_database_length = None
+        self.effective_search_space = None
+        self.effective_search_space_used = None
+        self.frameshift = (None, None)
+        self.threshold = None
+        self.window_size = None
+        self.dropoff_1st_pass = (None, None)
+        self.gap_x_dropoff = (None, None)
+        self.gap_x_dropoff_final = (None, None)
+        self.gap_trigger = (None, None)
+        self.blast_cutoff = (None, None)
+
+
+# TODO - Add a friendly __str__ method to BLAST results
+class Blast(Header, DatabaseReport, Parameters):
+    """Saves the results from a blast search.
+
+    Members:
+    descriptions        A list of Description objects.
+    alignments          A list of Alignment objects.
+    multiple_alignment  A MultipleAlignment object.
+    + members inherited from base classes
+
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        Header.__init__(self)
+        DatabaseReport.__init__(self)
+        Parameters.__init__(self)
+        self.descriptions = []
+        self.alignments = []
+        self.multiple_alignment = None
+
+
+class PSIBlast(Header, DatabaseReport, Parameters):
+    """Saves the results from a blastpgp search.
+
+    Members:
+    rounds       A list of Round objects.
+    converged    Whether the search converged.
+    + members inherited from base classes
+
+    """
+
+    def __init__(self):
+        """Initialize the class."""
+        Header.__init__(self)
+        DatabaseReport.__init__(self)
+        Parameters.__init__(self)
+        self.rounds = []
+        self.converged = 0
+
+
+class _XMLparser(ContentHandler):
+    """Generic SAX Parser (PRIVATE).
+
+    Just a very basic SAX parser.
+
+    Redefine the methods startElement, characters and endElement.
+    """
+
+    def __init__(self, debug=0):
+        """Initialize the parser.
+
+        Arguments:
+         - debug - integer, amount of debug information to print
+
+        """
+        self._tag = []
+        self._value = ""
+        self._debug = debug
+        self._debug_ignore_list = []
+        self._method_name_level = 1
+        self._method_map = None
+
+    def startElement(self, name, attr):
+        """Found XML start tag.
+
+        No real need of attr, BLAST DTD doesn't use them
+
+        Arguments:
+         - name -- name of the tag
+         - attr -- tag attributes
+
+        """
+        self._tag.append(name)
+
+        if len(self._tag) == 1:
+            # root node
+            self._on_root_node(name)
+            return
+
+        # Try to call a method (defined in subclasses)
+        method = "start_" + self._node_method_name(name)
+
+        # Note could use try / except AttributeError
+        # BUT I found often triggered by nested errors...
+        if method in self._method_map:
+            self._method_map[method]()
+            if self._debug > 4:
+                sys.stderr.write("NCBIXML: Parsed: " + method + "\n")
+        elif self._debug > 3:
+            # Doesn't exist (yet) and may want to warn about it
+            if method not in self._debug_ignore_list:
+                sys.stderr.write("NCBIXML: Ignored: " + method + "\n")
+                self._debug_ignore_list.append(method)
+
+        # We don't care about white space in parent tags like Hsp,
+        # but that white space doesn't belong to child tags like Hsp_midline
+        if self._value.strip():
+            raise ValueError(
+                f"What should we do with {self._value} before the {name!r} tag?"
+            )
+        self._value = ""
+
+    def characters(self, ch):
+        """Found some text.
+
+        Arguments:
+         - ch -- characters read
+
+        """
+        self._value += ch  # You don't ever get the whole string
+
+    def endElement(self, name):
+        """Found XML end tag.
+
+        Arguments:
+         - name -- tag name
+
+        """
+        # DON'T strip any white space, we may need it e.g. the hsp-midline
+
+        # Try to call a method (defined in subclasses)
+        method = "end_" + self._node_method_name(name)
+
+        # Note could use try / except AttributeError
+        # BUT I found often triggered by nested errors...
+        if method in self._method_map:
+            self._method_map[method]()
+            if self._debug > 2:
+                sys.stderr.write(f"NCBIXML: Parsed: {method} {self._value}\n")
+        elif self._debug > 1:
+            # Doesn't exist (yet) and may want to warn about it
+            if method not in self._debug_ignore_list:
+                sys.stderr.write(f"NCBIXML: Ignored: {method} {self._value}\n")
+                self._debug_ignore_list.append(method)
+
+        # Reset character buffer
+        self._value = ""
+
+        self._tag.pop()
+
+    def _node_method_name(self, name):
+        if self._method_name_level == 1:
+            return name
+        return "/".join(self._tag[-self._method_name_level :])
+
+
+class BlastParser(_XMLparser):
+    """Parse XML BLAST data into a Blast object.
+
+    Parses XML output from BLAST (direct use discouraged).
+    This (now) returns a list of Blast records.
+    Historically it returned a single Blast record.
+    You are expected to use this via the parse or read functions.
+
+    All XML 'action' methods are private methods and may be:
+
+    - ``_start_TAG`` called when the start tag is found
+    - ``_end_TAG`` called when the end tag is found
+
+    """
+
+    def __init__(self, debug=0):
+        """Initialize the parser.
+
+        Arguments:
+         - debug - integer, amount of debug information to print
+
+        """
+        # Calling superclass method
+        _XMLparser.__init__(self, debug)
+
+        self._parser = xml.sax.make_parser()
+        self._parser.setContentHandler(self)
+
+        # To avoid ValueError: unknown url type: NCBI_BlastOutput.dtd
+        self._parser.setFeature(xml.sax.handler.feature_validation, 0)
+        self._parser.setFeature(xml.sax.handler.feature_namespaces, 0)
+        self._parser.setFeature(xml.sax.handler.feature_external_pes, 0)
+        self._parser.setFeature(xml.sax.handler.feature_external_ges, 0)
+
+        self._xml_version = 1
+
+        self.reset()
+
+    def reset(self):
+        """Reset all the data allowing reuse of the BlastParser() object."""
+        self._records = []
+        self._header = Header()
+        self._parameters = Parameters()
+        self._parameters.filter = None  # Maybe I should update the class?
+
+    def _on_root_node(self, name):
+        if name == "BlastOutput":
+            self._setup_blast_v1()
+        elif name == "BlastXML2":
+            self._setup_blast_v2()
+        else:
+            raise ValueError(
+                "Invalid root node name: %s. Root node should be either"
+                " BlastOutput or BlastXML2" % name
+            )
+
+    def _setup_blast_v1(self):
+        self._method_map = {
+            "start_Iteration": self._start_blast_record,
+            "end_Iteration": self._end_blast_record,
+            "end_BlastOutput_program": self._set_header_application,
+            "end_BlastOutput_version": self._set_header_version,
+            "end_BlastOutput_reference": self._set_header_reference,
+            "end_BlastOutput_db": self._set_header_database,
+            "end_BlastOutput_query-ID": self._set_header_query_id,
+            "end_BlastOutput_query-def": self._set_header_query,
+            "end_BlastOutput_query-len": self._set_header_query_letters,
+            "end_Iteration_query-ID": self._set_record_query_id,
+            "end_Iteration_query-def": self._set_record_query_def,
+            "end_Iteration_query-len": self._set_record_query_letters,
+            "end_BlastOutput_hits": self._set_record_hits,
+            "end_Parameters_matrix": self._set_parameters_matrix,
+            "end_Parameters_expect": self._set_parameters_expect,
+            "end_Parameters_sc-match": self._set_parameters_sc_match,
+            "end_Parameters_sc-mismatch": self._set_parameters_sc_mismatch,
+            "end_Parameters_gap-open": self._set_parameters_gap_penalties,
+            "end_Parameters_gap-extend": self._set_parameters_gap_extend,
+            "end_Parameters_filter": self._set_parameters_filter,
+            "start_Hit": self._start_hit,
+            "end_Hit": self._end_hit,
+            "end_Hit_id": self.set_hit_id,
+            "end_Hit_def": self.set_hit_def,
+            "end_Hit_accession": self.set_hit_accession,
+            "end_Hit_len": self.set_hit_len,
+            "start_Hsp": self._start_hsp,
+            "end_Hsp_score": self._set_hsp_score,
+            "end_Hsp_bit-score": self._set_hsp_bit_score,
+            "end_Hsp_evalue": self._set_hsp_e_value,
+            "end_Hsp_query-from": self._set_hsp_query_start,
+            "end_Hsp_query-to": self._set_hsp_query_end,
+            "end_Hsp_hit-from": self._set_hsp_hit_from,
+            "end_Hsp_hit-to": self._set_hsp_hit_to,
+            "end_Hsp_query-frame": self._set_hsp_query_frame,
+            "end_Hsp_hit-frame": self._set_hsp_hit_frame,
+            "end_Hsp_identity": self._set_hsp_identity,
+            "end_Hsp_positive": self._set_hsp_positive,
+            "end_Hsp_gaps": self._set_hsp_gaps,
+            "end_Hsp_align-len": self._set_hsp_align_len,
+            "end_Hsp_qseq": self._set_hsp_query_seq,
+            "end_Hsp_hseq": self._set_hsp_subject_seq,
+            "end_Hsp_midline": self._set_hsp_midline,
+            "end_Statistics_db-num": self._set_statistics_db_num,
+            "end_Statistics_db-len": self._set_statistics_db_len,
+            "end_Statistics_hsp-len": self._set_statistics_hsp_len,
+            "end_Statistics_eff-space": self._set_statistics_eff_space,
+            "end_Statistics_kappa": self._set_statistics_kappa,
+            "end_Statistics_lambda": self._set_statistics_lambda,
+            "end_Statistics_entropy": self._set_statistics_entropy,
+        }
+
+    def _setup_blast_v2(self):
+        self._method_name_level = 2
+        self._xml_version = 2
+        self._method_map = {
+            "start_report/Report": self._start_blast_record,
+            "end_report/Report": self._end_blast_record,
+            "end_Report/program": self._set_header_application,
+            "end_Report/version": self._set_header_version,
+            "end_Report/reference": self._set_header_reference,
+            "end_Target/db": self._set_header_database,
+            "end_Search/query-id": self._set_record_query_id,
+            "end_Search/query-title": self._set_record_query_def,
+            "end_Search/query-len": self._set_record_query_letters,
+            "end_BlastOutput_hits": self._set_record_hits,
+            "end_Parameters/matrix": self._set_parameters_matrix,
+            "end_Parameters/expect": self._set_parameters_expect,
+            "end_Parameters/sc-match": self._set_parameters_sc_match,
+            "end_Parameters/sc-mismatch": self._set_parameters_sc_mismatch,
+            "end_Parameters/gap-open": self._set_parameters_gap_penalties,
+            "end_Parameters/gap-extend": self._set_parameters_gap_extend,
+            "end_Parameters/filter": self._set_parameters_filter,
+            "start_hits/Hit": self._start_hit,
+            "end_hits/Hit": self._end_hit,
+            "start_description/HitDescr": self._start_hit_descr_item,
+            "end_description/HitDescr": self._end_hit_descr_item,
+            "end_HitDescr/id": self._end_description_id,
+            "end_HitDescr/accession": self._end_description_accession,
+            "end_HitDescr/title": self._end_description_title,
+            "end_HitDescr/taxid": self._end_description_taxid,
+            "end_HitDescr/sciname": self._end_description_sciname,
+            "end_Hit/len": self.set_hit_len,
+            "start_hsps/Hsp": self._start_hsp,
+            "end_hsps/Hsp": self._end_hsp,
+            "end_Hsp/score": self._set_hsp_score,
+            "end_Hsp/bit-score": self._set_hsp_bit_score,
+            "end_Hsp/evalue": self._set_hsp_e_value,
+            "end_Hsp/query-from": self._set_hsp_query_start,
+            "end_Hsp/query-to": self._set_hsp_query_end,
+            "end_Hsp/hit-from": self._set_hsp_hit_from,
+            "end_Hsp/hit-to": self._set_hsp_hit_to,
+            "end_Hsp/query-frame": self._set_hsp_query_frame,
+            "end_Hsp/hit-frame": self._set_hsp_hit_frame,
+            "end_Hsp/query-strand": self._set_hsp_query_strand,
+            "end_Hsp/hit-strand": self._set_hsp_hit_strand,
+            "end_Hsp/identity": self._set_hsp_identity,
+            "end_Hsp/positive": self._set_hsp_positive,
+            "end_Hsp/gaps": self._set_hsp_gaps,
+            "end_Hsp/align-len": self._set_hsp_align_len,
+            "end_Hsp/qseq": self._set_hsp_query_seq,
+            "end_Hsp/hseq": self._set_hsp_subject_seq,
+            "end_Hsp/midline": self._set_hsp_midline,
+            "end_Statistics/db-num": self._set_statistics_db_num,
+            "end_Statistics/db-len": self._set_statistics_db_len,
+            "end_Statistics/hsp-len": self._set_statistics_hsp_len,
+            "end_Statistics/eff-space": self._set_statistics_eff_space,
+            "end_Statistics/kappa": self._set_statistics_kappa,
+            "end_Statistics/lambda": self._set_statistics_lambda,
+            "end_Statistics/entropy": self._set_statistics_entropy,
+        }
+
+    def _start_blast_record(self):
+        """Start interaction (PRIVATE)."""
+        self._blast = Blast()
+
+    def _end_blast_record(self):
+        """End interaction (PRIVATE)."""
+        # We stored a lot of generic "top level" information
+        # in self._header (an object of type Header)
+        self._blast.reference = self._header.reference
+        self._blast.date = self._header.date
+        self._blast.version = self._header.version
+        self._blast.database = self._header.database
+        self._blast.application = self._header.application
+
+        # These are required for "old" pre 2.2.14 files
+        # where only <BlastOutput_query-ID>, <BlastOutput_query-def>
+        # and <BlastOutput_query-len> were used.  Now they
+        # are supplemented/replaced by <Iteration_query-ID>,
+        # <Iteration_query-def> and <Iteration_query-len>
+        if not hasattr(self._blast, "query") or not self._blast.query:
+            self._blast.query = self._header.query
+        if not hasattr(self._blast, "query_id") or not self._blast.query_id:
+            self._blast.query_id = self._header.query_id
+        if not hasattr(self._blast, "query_letters") or not self._blast.query_letters:
+            self._blast.query_letters = self._header.query_letters
+
+        # Hack to record the query length as both the query_letters and
+        # query_length properties (as in the plain text parser, see
+        # Bug 2176 comment 12):
+        self._blast.query_length = self._blast.query_letters
+        # Perhaps in the long term we should deprecate one, but I would
+        # prefer to drop query_letters - so we need a transition period
+        # with both.
+
+        # Hack to record the claimed database size as database_length
+        # (as well as in num_letters_in_database, see Bug 2176 comment 13):
+        self._blast.database_length = self._blast.num_letters_in_database
+        # TODO? Deprecate database_letters next?
+
+        # Hack to record the claimed database sequence count as database_sequences
+        self._blast.database_sequences = self._blast.num_sequences_in_database
+
+        # Apply the "top level" parameter information
+        self._blast.matrix = self._parameters.matrix
+        self._blast.num_seqs_better_e = self._parameters.num_seqs_better_e
+        self._blast.gap_penalties = self._parameters.gap_penalties
+        self._blast.filter = self._parameters.filter
+        self._blast.expect = self._parameters.expect
+        self._blast.sc_match = self._parameters.sc_match
+        self._blast.sc_mismatch = self._parameters.sc_mismatch
+
+        # Add to the list
+        self._records.append(self._blast)
+        # Clear the object (a new empty one is create in _start_Iteration)
+        self._blast = None
+
+        if self._debug:
+            sys.stderr.write("NCBIXML: Added Blast record to results\n")
+
+    # Header
+    def _set_header_application(self):
+        """BLAST program, e.g., blastp, blastn, etc. (PRIVATE).
+
+        Save this to put on each blast record object
+        """
+        self._header.application = self._value.upper()
+
+    def _set_header_version(self):
+        """Version number and date of the BLAST engine (PRIVATE).
+
+        e.g. "BLASTX 2.2.12 [Aug-07-2005]" but there can also be
+        variants like "BLASTP 2.2.18+" without the date.
+
+        Save this to put on each blast record object
+        """
+        parts = self._value.split()
+        # TODO - Check the first word starts with BLAST?
+
+        # The version is the second word (field one)
+        self._header.version = parts[1]
+
+        # Check there is a third word (the date)
+        if len(parts) >= 3:
+            if parts[2][0] == "[" and parts[2][-1] == "]":
+                self._header.date = parts[2][1:-1]
+            else:
+                # Assume this is still a date, but without the
+                # square brackets
+                self._header.date = parts[2]
+
+    def _set_header_reference(self):
+        """Record any article reference describing the algorithm (PRIVATE).
+
+        Save this to put on each blast record object
+        """
+        self._header.reference = self._value
+
+    def _set_header_database(self):
+        """Record the database(s) searched (PRIVATE).
+
+        Save this to put on each blast record object
+        """
+        self._header.database = self._value
+
+    def _set_header_query_id(self):
+        """Record the identifier of the query (PRIVATE).
+
+        Important in old pre 2.2.14 BLAST, for recent versions
+        <Iteration_query-ID> is enough
+        """
+        self._header.query_id = self._value
+
+    def _set_header_query(self):
+        """Record the definition line of the query (PRIVATE).
+
+        Important in old pre 2.2.14 BLAST, for recent versions
+        <Iteration_query-def> is enough
+        """
+        self._header.query = self._value
+
+    def _set_header_query_letters(self):
+        """Record the length of the query (PRIVATE).
+
+        Important in old pre 2.2.14 BLAST, for recent versions
+        <Iteration_query-len> is enough
+        """
+        self._header.query_letters = int(self._value)
+
+    def _set_record_query_id(self):
+        """Record the identifier of the query (PRIVATE)."""
+        self._blast.query_id = self._value
+
+    def _set_record_query_def(self):
+        """Record the definition line of the query (PRIVATE)."""
+        self._blast.query = self._value
+
+    def _set_record_query_letters(self):
+        """Record the length of the query (PRIVATE)."""
+        self._blast.query_letters = int(self._value)
+
+    # def _end_BlastOutput_query_seq(self):
+    #     """The query sequence (PRIVATE)."""
+    #     pass # XXX Missing in Blast ?
+
+    # def _end_BlastOutput_iter_num(self):
+    #     """The psi-blast iteration number (PRIVATE)."""
+    #     pass # XXX TODO PSI
+
+    def _set_record_hits(self):
+        """Hits to the database sequences, one for every sequence (PRIVATE)."""
+        self._blast.num_hits = int(self._value)
+
+    # def _end_BlastOutput_message(self):
+    #     """error messages (PRIVATE)."""
+    #     pass # XXX What to do ?
+
+    # Parameters
+    def _set_parameters_matrix(self):
+        """Matrix used (-M on legacy BLAST) (PRIVATE)."""
+        self._parameters.matrix = self._value
+
+    def _set_parameters_expect(self):
+        """Expect values cutoff (PRIVATE)."""
+        # NOTE: In old text output there was a line:
+        # Number of sequences better than 1.0e-004: 1
+        # As far as I can see, parameters.num_seqs_better_e
+        # would take the value of 1, and the expectation
+        # value was not recorded.
+        #
+        # Anyway we should NOT record this against num_seqs_better_e
+        self._parameters.expect = self._value
+
+    # def _end_Parameters_include(self):
+    #     """Inclusion threshold for a psi-blast iteration (-h) (PRIVATE)."""
+    #     pass # XXX TODO PSI
+
+    def _set_parameters_sc_match(self):
+        """Match score for nucleotide-nucleotide comparison (-r) (PRIVATE)."""
+        self._parameters.sc_match = int(self._value)
+
+    def _set_parameters_sc_mismatch(self):
+        """Mismatch penalty for nucleotide-nucleotide comparison (-r) (PRIVATE)."""
+        self._parameters.sc_mismatch = int(self._value)
+
+    def _set_parameters_gap_penalties(self):
+        """Gap existence cost (-G) (PRIVATE)."""
+        self._parameters.gap_penalties = int(self._value)
+
+    def _set_parameters_gap_extend(self):
+        """Gap extension cose (-E) (PRIVATE)."""
+        self._parameters.gap_penalties = (
+            self._parameters.gap_penalties,
+            int(self._value),
+        )
+
+    def _set_parameters_filter(self):
+        """Record filtering options (-F) (PRIVATE)."""
+        self._parameters.filter = self._value
+
+    # def _end_Parameters_pattern(self):
+    #     """Pattern used for phi-blast search (PRIVATE).
+    #     """
+    #     pass # XXX TODO PSI
+
+    # def _end_Parameters_entrez_query(self):
+    #     """Entrez query used to limit search (PRIVATE).
+    #     """
+    #     pass # XXX TODO PSI
+
+    # Hits
+    def _start_hit(self):
+        """Start filling records (PRIVATE)."""
+        self._blast.alignments.append(Alignment())
+        self._descr = Description() if self._xml_version == 1 else DescriptionExt()
+        self._blast.descriptions.append(self._descr)
+        self._blast.multiple_alignment = []
+        self._hit = self._blast.alignments[-1]
+
+        self._descr.num_alignments = 0
+        # Specifically ignore CREATE_VIEW statements that sometimes
+        # exist between <Hit> tags, as a result of very large remote
+        # BLAST searches.
+        if self._value.strip() == "CREATE_VIEW":
+            warnings.warn(
+                f"NCBIXML: Ignored: {self._value!r}",
+                BiopythonParserWarning,
+            )
+            self._value = ""
+
+    def _end_hit(self):
+        """Clear variables (PRIVATE)."""
+        # Cleanup
+        self._blast.multiple_alignment = None
+        self._hit = None
+        self._descr = None
+
+    def set_hit_id(self):
+        """Record the identifier of the database sequence (PRIVATE)."""
+        self._hit.hit_id = self._value
+        self._hit.title = self._value + " "
+
+    def set_hit_def(self):
+        """Record the definition line of the database sequence (PRIVATE)."""
+        self._hit.hit_def = self._value
+        self._hit.title += self._value
+        self._descr.title = self._hit.title
+
+    def set_hit_accession(self):
+        """Record the accession value of the database sequence (PRIVATE)."""
+        self._hit.accession = self._value
+        self._descr.accession = self._value
+
+    def set_hit_len(self):
+        """Record the length of the hit."""
+        self._hit.length = int(self._value)
+
+    # HSPs
+    def _start_hsp(self):
+        # Note that self._start_Hit() should have been called
+        # to setup things like self._blast.multiple_alignment
+        self._hsp = HSP()
+        self._hsp.positives = None
+        self._hit.hsps.append(self._hsp)
+        self._descr.num_alignments += 1
+        self._blast.multiple_alignment.append(MultipleAlignment())
+        self._mult_al = self._blast.multiple_alignment[-1]
+
+    def _end_hsp(self):
+        if self._hsp.frame and len(self._hsp.frame) == 1:
+            self._hsp.frame += (0,)
+
+    # Hsp_num is useless
+    def _set_hsp_score(self):
+        """Record the raw score of HSP (PRIVATE)."""
+        self._hsp.score = float(self._value)
+        if self._descr.score is None:
+            self._descr.score = float(self._value)
+
+    def _set_hsp_bit_score(self):
+        """Record the Bit score of HSP (PRIVATE)."""
+        self._hsp.bits = float(self._value)
+        if self._descr.bits is None:
+            self._descr.bits = float(self._value)
+
+    def _set_hsp_e_value(self):
+        """Record the expect value of the HSP (PRIVATE)."""
+        self._hsp.expect = float(self._value)
+        if self._descr.e is None:
+            self._descr.e = float(self._value)
+
+    def _set_hsp_query_start(self):
+        """Offset of query at the start of the alignment (one-offset) (PRIVATE)."""
+        self._hsp.query_start = int(self._value)
+
+    def _set_hsp_query_end(self):
+        """Offset of query at the end of the alignment (one-offset) (PRIVATE)."""
+        self._hsp.query_end = int(self._value)
+
+    def _set_hsp_hit_from(self):
+        """Offset of the database at the start of the alignment (one-offset) (PRIVATE)."""
+        self._hsp.sbjct_start = int(self._value)
+
+    def _set_hsp_hit_to(self):
+        """Offset of the database at the end of the alignment (one-offset) (PRIVATE)."""
+        self._hsp.sbjct_end = int(self._value)
+
+    # def _end_Hsp_pattern_from(self):
+    #     """Start of phi-blast pattern on the query (one-offset) (PRIVATE)."""
+    #     pass # XXX TODO PSI
+
+    # def _end_Hsp_pattern_to(self):
+    #     """End of phi-blast pattern on the query (one-offset) (PRIVATE)."""
+    #     pass # XXX TODO PSI
+
+    def _set_hsp_query_frame(self):
+        """Frame of the query if applicable (PRIVATE)."""
+        v = int(self._value)
+        self._hsp.frame = (v,)
+        if self._header.application == "BLASTN":
+            self._hsp.strand = ("Plus" if v > 0 else "Minus",)
+
+    def _set_hsp_hit_frame(self):
+        """Frame of the database sequence if applicable (PRIVATE)."""
+        v = int(self._value)
+        if len(self._hsp.frame) == 0:
+            self._hsp.frame = (0, v)
+        else:
+            self._hsp.frame += (v,)
+        if self._header.application == "BLASTN":
+            self._hsp.strand += ("Plus" if v > 0 else "Minus",)
+
+    def _set_hsp_query_strand(self):
+        """Frame of the query if applicable (PRIVATE)."""
+        self._hsp.strand = (self._value,)
+        if self._header.application == "BLASTN":
+            self._hsp.frame = (1 if self._value == "Plus" else -1,)
+
+    def _set_hsp_hit_strand(self):
+        """Frame of the database sequence if applicable (PRIVATE)."""
+        self._hsp.strand += (self._value,)
+        if self._header.application == "BLASTN":
+            self._hsp.frame += (1 if self._value == "Plus" else -1,)
+
+    def _set_hsp_identity(self):
+        """Record the number of identities in the alignment (PRIVATE)."""
+        v = int(self._value)
+        self._hsp.identities = v
+        if self._hsp.positives is None:
+            self._hsp.positives = v
+
+    def _set_hsp_positive(self):
+        """Record the number of positive (conservative) substitutions in the alignment (PRIVATE)."""
+        self._hsp.positives = int(self._value)
+
+    def _set_hsp_gaps(self):
+        """Record the number of gaps in the alignment (PRIVATE)."""
+        self._hsp.gaps = int(self._value)
+
+    def _set_hsp_align_len(self):
+        """Record the length of the alignment (PRIVATE)."""
+        self._hsp.align_length = int(self._value)
+
+    # def _en_Hsp_density(self):
+    #     """Score density (PRIVATE)."""
+    #     pass # XXX ???
+
+    def _set_hsp_query_seq(self):
+        """Record the alignment string for the query (PRIVATE)."""
+        self._hsp.query = self._value
+
+    def _set_hsp_subject_seq(self):
+        """Record the alignment string for the database (PRIVATE)."""
+        self._hsp.sbjct = self._value
+
+    def _set_hsp_midline(self):
+        """Record the middle line as normally seen in BLAST report (PRIVATE)."""
+        self._hsp.match = self._value  # do NOT strip spaces!
+        assert len(self._hsp.match) == len(self._hsp.query)
+        assert len(self._hsp.match) == len(self._hsp.sbjct)
+
+    # Statistics
+    def _set_statistics_db_num(self):
+        """Record the number of sequences in the database (PRIVATE)."""
+        self._blast.num_sequences_in_database = int(self._value)
+
+    def _set_statistics_db_len(self):
+        """Record the number of letters in the database (PRIVATE)."""
+        self._blast.num_letters_in_database = int(self._value)
+
+    def _set_statistics_hsp_len(self):
+        """Record the effective HSP length (PRIVATE)."""
+        self._blast.effective_hsp_length = int(self._value)
+
+    def _set_statistics_eff_space(self):
+        """Record the effective search space (PRIVATE)."""
+        self._blast.effective_search_space = float(self._value)
+
+    def _set_statistics_kappa(self):
+        """Karlin-Altschul parameter K (PRIVATE)."""
+        self._blast.ka_params = float(self._value)
+
+    def _set_statistics_lambda(self):
+        """Karlin-Altschul parameter Lambda (PRIVATE)."""
+        self._blast.ka_params = (float(self._value), self._blast.ka_params)
+
+    def _set_statistics_entropy(self):
+        """Karlin-Altschul parameter H (PRIVATE)."""
+        self._blast.ka_params = self._blast.ka_params + (float(self._value),)
+
+    def _start_hit_descr_item(self):
+        """XML v2. Start hit description item."""
+        self._hit_descr_item = DescriptionExtItem()
+
+    def _end_hit_descr_item(self):
+        """XML v2. Start hit description item."""
+        self._descr.append_item(self._hit_descr_item)
+        if not self._hit.title:
+            self._hit.title = str(self._hit_descr_item)
+        self._hit_descr_item = None
+
+    def _end_description_id(self):
+        """XML v2. The identifier of the database sequence(PRIVATE)."""
+        self._hit_descr_item.id = self._value
+        if not self._hit.hit_id:
+            self._hit.hit_id = self._value
+
+    def _end_description_accession(self):
+        """XML v2. The accession value of the database sequence (PRIVATE)."""
+        self._hit_descr_item.accession = self._value
+        if not getattr(self._hit, "accession", None):
+            self._hit.accession = self._value
+
+    def _end_description_title(self):
+        """XML v2. The hit description title (PRIVATE)."""
+        self._hit_descr_item.title = self._value
+
+    def _end_description_taxid(self):
+        try:
+            self._hit_descr_item.taxid = int(self._value)
+        except ValueError:
+            pass
+
+    def _end_description_sciname(self):
+        self._hit_descr_item.sciname = self._value
+
+
+def read(handle, debug=0):
+    """Return a single Blast record (assumes just one query).
+
+    Uses the BlastParser internally.
+
+    This function is for use when there is one and only one BLAST
+    result in your XML file.
+
+    Use the Bio.Blast.NCBIXML.parse() function if you expect more than
+    one BLAST record (i.e. if you have more than one query sequence).
+    """
+    iterator = parse(handle, debug)
+    try:
+        record = next(iterator)
+    except StopIteration:
+        raise ValueError("No records found in handle") from None
+    try:
+        next(iterator)
+        raise ValueError("More than one record found in handle")
+    except StopIteration:
+        pass
+    return record
+
+
+def parse(handle, debug=0):
+    """Return an iterator a Blast record for each query.
+
+    Incremental parser, this is an iterator that returns
+    Blast records.  It uses the BlastParser internally.
+
+    handle - file handle to and XML file to parse
+    debug - integer, amount of debug information to print
+
+    This is a generator function that returns multiple Blast records
+    objects - one for each query sequence given to blast.  The file
+    is read incrementally, returning complete records as they are read
+    in.
+
+    Should cope with new BLAST 2.2.14+ which gives a single XML file
+    for multiple query records.
+
+    Should also cope with XML output from older versions BLAST which
+    gave multiple XML files concatenated together (giving a single file
+    which strictly speaking wasn't valid XML).
+    """
+    from xml.parsers import expat
+
+    BLOCK = 1024
+    MARGIN = 10  # must be at least length of newline + XML start
+    XML_START = "<?xml"
+    NEW_LINE = "\n"
+    NULL = ""
+
+    pending = ""
+    text = handle.read(BLOCK)
+    if isinstance(text, bytes):
+        # Not a text handle, raw bytes mode
+        XML_START = b"<?xml"
+        NEW_LINE = b"\n"
+        NULL = b""
+        pending = b""
+
+    if not text:
+        # NO DATA FOUND!
+        raise ValueError("Your XML file was empty")
+
+    try:
+        while text:
+            # We are now starting a new XML file
+            if not text.startswith(XML_START):
+                raise ValueError(
+                    "Your XML file did not start with %r... but instead %r"
+                    % (XML_START, text[:20])
+                )
+
+            expat_parser = expat.ParserCreate()
+            blast_parser = BlastParser(debug)
+            expat_parser.StartElementHandler = blast_parser.startElement
+            expat_parser.EndElementHandler = blast_parser.endElement
+            expat_parser.CharacterDataHandler = blast_parser.characters
+
+            expat_parser.Parse(text, False)
+            while blast_parser._records:
+                record = blast_parser._records[0]
+                blast_parser._records = blast_parser._records[1:]
+                yield record
+
+            while True:
+                # Read in another block of the file...
+                text, pending = pending + handle.read(BLOCK), ""
+                if not text:
+                    # End of the file!
+                    break
+
+                # Now read a little bit more so we can check for the
+                # start of another XML file...
+                pending = handle.read(MARGIN)
+
+                if (NEW_LINE + XML_START) not in (text + pending):
+                    # Good - still dealing with the same XML file
+                    expat_parser.Parse(text, False)
+                    while blast_parser._records:
+                        yield blast_parser._records.pop(0)
+                else:
+                    # This is output from pre 2.2.14 BLAST,
+                    # one XML file for each query!
+
+                    # Finish the old file:
+                    text, pending = (text + pending).split(NEW_LINE + XML_START, 1)
+                    pending = XML_START + pending
+
+                    expat_parser.Parse(text, True)  # End of XML record
+                    while blast_parser._records:
+                        yield blast_parser._records.pop(0)
+
+                    # Now we are going to re-loop, reset the
+                    # parsers and start reading the next XML file
+                    text, pending = pending, NULL
+                    break
+
+            # At this point we have finished the first XML record.
+            # If the file is from an old version of blast, it may
+            # contain more XML records (check if text=="").
+            assert not pending, pending
+            assert len(blast_parser._records) == 0, len(blast_parser._records)
+    finally:
+        expat_parser.Parse(NULL, True)
+
+    # We should have finished the file!
+    assert not text, text
+    assert not pending, pending
+    assert len(blast_parser._records) == 0, len(blast_parser._records)

.venv_haddock/lib/python3.12/site-packages/Bio/Blast/__init__.py

@@ -0,0 +1,1352 @@
+# Copyright 1999 by Jeffrey Chang.  All rights reserved.
+# Revisions 2023 by Michiel de Hoon.  All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+
+"""Code to parse and store BLAST XML output, and to invoke the NCBI BLAST web server.
+
+This module provides code to parse and store BLAST XML output, following its
+definition in the associated BLAST XML DTD file:
+https://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd
+
+This module also provides code to invoke the BLAST web server provided by NCBI.
+https://blast.ncbi.nlm.nih.gov/
+
+Variables:
+
+    - email        Set the Blast email parameter (default is None).
+    - tool         Set the Blast tool parameter (default is ``biopython``).
+
+"""
+
+import io
+import textwrap
+import time
+import warnings
+from collections import UserList
+from urllib.parse import urlencode
+from urllib.request import build_opener
+from urllib.request import HTTPBasicAuthHandler
+from urllib.request import HTTPPasswordMgrWithDefaultRealm
+from urllib.request import install_opener
+from urllib.request import Request
+from urllib.request import urlopen
+from xml.parsers import expat
+
+import numpy as np
+
+from Bio import BiopythonWarning
+from Bio import StreamModeError
+from Bio._utils import function_with_previous
+from Bio.Align import Alignment
+from Bio.Align import Alignments
+from Bio.Blast import _writers
+
+email = None
+tool = "biopython"
+
+
+NCBI_BLAST_URL = "https://blast.ncbi.nlm.nih.gov/Blast.cgi"
+
+BLOCK = 2048  # default block size from expat
+
+
+class NotXMLError(ValueError):
+    """Failed to parse file as XML."""
+
+    def __init__(self, message):
+        """Initialize the class."""
+        self.msg = message
+
+    def __str__(self):
+        """Return a string summary of the exception."""
+        return (
+            "Failed to parse the XML data (%s). Please make sure that the input data "
+            "are in XML format." % self.msg
+        )
+
+
+class CorruptedXMLError(ValueError):
+    """Corrupted XML."""
+
+    def __init__(self, message):
+        """Initialize the class."""
+        self.msg = message
+
+    def __str__(self):
+        """Return a string summary of the exception."""
+        return (
+            "Failed to parse the XML data (%s). Please make sure that the input data "
+            "are not corrupted." % self.msg
+        )
+
+
+class HSP(Alignment):
+    """Stores an alignment of one query sequence against a target sequence.
+
+    An HSP (High-scoring Segment Pair) stores the alignment of one query
+    sequence segment against one target (hit) sequence segment. The
+    ``Bio.Blast.HSP`` class inherits from the ``Bio.Align.Alignment`` class.
+
+    In addition to the ``target`` and ``query`` attributes of a
+    ``Bio.Align.Alignment``, a ``Bio.Blast.HSP`` object has the following
+    attributes:
+
+     - score:       score of HSP;
+     - annotations: a dictionary that may contain the following keys:
+                     - 'bit score': score (in bits) of HSP (float);
+                     - 'evalue':    e-value of HSP (float);
+                     - 'identity':  number of identities in HSP (integer);
+                     - 'positive':  number of positives in HSP (integer);
+                     - 'gaps':      number of gaps in HSP (integer);
+                     - 'midline':   formatting middle line.
+
+    A ``Bio.Blast.HSP`` object behaves the same as a `Bio.Align.Alignment``
+    object and can be used as such. However, when printing a ``Bio.Blast.HSP``
+    object, the BLAST e-value and bit score are included in the output (in
+    addition to the alignment itself).
+
+    See the documentation of ``Bio.Blast.Record`` for a more detailed
+    explanation of how the information in BLAST records is stored in
+    Biopython.
+    """
+
+    def __repr__(self):
+        query = self.query
+        target = self.target
+        n, m = self.shape
+        return f"<Bio.Blast.HSP target.id={target.id!r} query.id={query.id!r}; {n} rows x {m} columns>"
+
+    def __str__(self):
+        alignment_text = super().__str__()
+        query = self.query
+        target = self.target
+        query_strand = (
+            "Plus" if self.coordinates[1, 0] <= self.coordinates[1, -1] else "Minus"
+        )
+        target_strand = (
+            "Plus" if self.coordinates[0, 0] <= self.coordinates[0, -1] else "Minus"
+        )
+        indent = " " * 8
+        query_description = textwrap.fill(
+            query.description,
+            width=80,
+            initial_indent=indent,
+            subsequent_indent=indent,
+        )
+        target_description = textwrap.fill(
+            target.description,
+            width=80,
+            initial_indent=indent,
+            subsequent_indent=indent,
+        )
+        evalue = self.annotations["evalue"]
+        bitscore = self.annotations["bit score"]
+        score = self.score
+        steps = np.diff(self.coordinates, 1)
+        aln_span = sum(abs(steps).max(0))
+        terms = []
+        identity = self.annotations["identity"]
+        identity_percentage = round(100.0 * identity / aln_span)
+        identity_text = "Identities:%d/%d(%d%%)" % (
+            identity,
+            aln_span,
+            identity_percentage,
+        )
+        terms.append(identity_text)
+        positive = self.annotations.get("positive")
+        if positive is not None:
+            positive_percentage = round(100.0 * positive / aln_span)
+            positive_text = "Positives:%d/%d(%d%%)" % (
+                positive,
+                aln_span,
+                positive_percentage,
+            )
+            terms.append(positive_text)
+        try:
+            gaps = self.annotations["gaps"]
+        except KeyError:
+            pass
+        else:
+            gaps_percentage = round(100.0 * gaps / aln_span)
+            gaps_text = "Gaps:%d.%d(%d%%)" % (gaps, aln_span, gaps_percentage)
+            terms.append(gaps_text)
+        counts_line = ",  ".join(terms)
+        return """\
+Query : %s Length: %d Strand: %s
+%s
+Target: %s Length: %d Strand: %s
+%s
+
+Score:%d bits(%d), Expect:%.1g,
+%s
+
+%s
+""" % (
+            query.id,
+            len(query),
+            query_strand,
+            query_description,
+            target.id,
+            len(target),
+            target_strand,
+            target_description,
+            bitscore,
+            score,
+            evalue,
+            counts_line,
+            alignment_text,
+        )
+
+
+class Hit(Alignments):
+    """Stores a single BLAST hit of one single query against one target.
+
+    The ``Bio.Blast.Hit`` class inherits from the ``Bio.Align.Alignments``
+    class, which is a subclass of a Python list. The ``Bio.Blast.Hit`` class
+    stores ``Bio.Blast.HSP`` objwcts, which inherit from
+    ``Bio.Align.Alignment``. A ``Bio.Blast.Hit`` object is therefore
+    effectively a list of ``Bio.Align.Alignment`` objects. Most hits consist of
+    only 1 or a few Alignment objects.
+
+    Each ``Bio.Blast.Hit`` object has a ``target`` attribute containing the
+    following information:
+
+     - target.id:          seqId of subject;
+     - target.description: definition line of subject;
+     - target.name:        accession of subject;
+     - len(target.seq):    sequence length of subject.
+
+    See the documentation of ``Bio.Blast.Record`` for a more detailed
+    explanation of the information stored in the alignments contained in the
+    ``Bio.Blast.Hit`` object.
+    """
+
+    def __getitem__(self, key):
+        try:
+            value = super().__getitem__(key)
+        except IndexError:
+            raise IndexError("index out of range") from None
+        if isinstance(key, slice):
+            hit = Hit(value)
+            hit.target = self.target
+            return hit
+        else:
+            return value
+
+    def __repr__(self):
+        target = self.target
+        try:
+            alignment = self[0]
+        except IndexError:
+            return f"<Bio.Blast.Hit target.id={target.id!r}; no hits>"
+        query = alignment.query
+        nhsps = len(self)
+        if nhsps == 1:
+            unit = "HSP"
+        else:  # nhsps > 1
+            unit = "HSPs"
+        return f"<Bio.Blast.Hit target.id={target.id!r} query.id={query.id!r}; {nhsps} {unit}>"
+
+    def __str__(self):
+        """Return a human readable summary of the Hit object."""
+        lines = []
+
+        # set query id line
+        query = self[0].query
+        qid_line = "Query: %s" % query.id
+        lines.append(qid_line)
+        indent = " " * 7
+        description_lines = textwrap.wrap(
+            query.description,
+            width=80,
+            initial_indent=indent,
+            subsequent_indent=indent,
+        )
+        lines.extend(description_lines)
+
+        # set hit id line
+        target = self.target
+        hid_line = "  Hit: %s (length=%i)" % (target.id, len(target))
+        lines.append(hid_line)
+        description_lines = textwrap.wrap(
+            target.description,
+            width=80,
+            initial_indent=indent,
+            subsequent_indent=indent,
+        )
+        lines.extend(description_lines)
+
+        # set hsp line and table
+        lines.append(
+            " HSPs: %s  %s  %s  %s  %s  %s"
+            % ("-" * 4, "-" * 8, "-" * 9, "-" * 6, "-" * 15, "-" * 21)
+        )
+        pattern = "%11s  %8s  %9s  %6s  %15s  %21s"
+        lines.append(
+            pattern % ("#", "E-value", "Bit score", "Span", "Query range", "Hit range")
+        )
+        lines.append(pattern % ("-" * 4, "-" * 8, "-" * 9, "-" * 6, "-" * 15, "-" * 21))
+        for idx, hsp in enumerate(self):
+            # evalue
+            evalue = format(hsp.annotations["evalue"], ".2g")
+            # bit score
+            bitscore = format(hsp.annotations["bit score"], ".2f")
+            # alignment length
+            steps = np.diff(hsp.coordinates, 1)
+            aln_span = sum(abs(steps).max(0))
+            # query region
+            query_start = hsp.coordinates[1, 0]
+            query_end = hsp.coordinates[1, -1]
+            query_range = f"[{query_start}:{query_end}]"
+            # max column length is 18
+            query_range = (
+                query_range[:13] + "~]" if len(query_range) > 15 else query_range
+            )
+            # hit region
+            hit_start = hsp.coordinates[0, 0]
+            hit_end = hsp.coordinates[0, -1]
+            hit_range = f"[{hit_start}:{hit_end}]"
+            hit_range = hit_range[:19] + "~]" if len(hit_range) > 21 else hit_range
+            # append the hsp row
+            lines.append(
+                pattern % (idx, evalue, bitscore, aln_span, query_range, hit_range)
+            )
+
+        return "\n".join(lines)
+
+
+class Record(list):
+    """Stores the BLAST results for a single query.
+
+    A ``Bio.Blast.Record`` object is a list of ``Bio.Blast.Hit`` objects, each
+    corresponding to one hit for the query in the BLAST output.
+
+    The ``Bio.Blast.Record`` object may have the following attributes:
+     - query:   A ``SeqRecord`` object which may contain some or all of the
+                following information:
+                 - query.id:          SeqId of query;
+                 - query.description: Definition line of query;
+                 - len(query.seq):    Length of the query sequence.
+     - stat:    A dictionary with summary statistics of the BLAST run. It may
+                contain the following keys:
+                 - 'db-num':    number of sequences in BLAST db (integer);
+                 - 'db-len':    length of BLAST db (integer);
+                 - 'hsp-len':   effective HSP length (integer);
+                 - 'eff-space': effective search space (float);
+                 - 'kappa':     Karlin-Altschul parameter K (float);
+                 - 'lambda':    Karlin-Altschul parameter Lambda (float);
+                 - 'entropy':   Karlin-Altschul parameter H (float).
+     - message: Some (error?) information.
+
+    Each ``Bio.Blast.Hit`` object has a ``target`` attribute containing the
+    following information:
+
+     - target.id:          seqId of subject;
+     - target.description: definition line of subject;
+     - target.name:        accession of subject;
+     - len(target.seq):    sequence length of subject.
+
+    The ``Bio.Blast.Hit`` class inherits from the ``Bio.Align.Alignments``
+    class, which inherits from a Python list. In this list, the
+    ``Bio.Blast.Hit`` object stores ``Bio.Blast.HSP`` objects, which inherit
+    from the ``Bio.Align.Alignment`` class.  A ``Bio.Blast.Hit`` object is
+    therefore effectively a list of alignment objects.
+
+    Each HSP in a ``Bio.Blast.Hit`` object has the attributes ``target`` and
+    ``query`` attributes, as usual for of a ``Bio.Align.Alignment`` object
+    storing a pairwise alignment, pointing to a ``SeqRecord`` object
+    representing the target and query, respectively.  For translated BLAST
+    searches, the ``features`` attribute of the target or query may contain a
+    ``SeqFeature`` of type CDS that stores the amino acid sequence region.  The
+    ``qualifiers`` attribute of such a feature is a dictionary with  a single
+    key 'coded_by'; the corresponding value specifies the nucleotide sequence
+    region, in a GenBank-style string with 1-based coordinates, that encodes
+    the amino acid sequence.
+
+    Each ``Bio.Blast.HSP`` object has the following additional attributes:
+
+     - score:       score of HSP;
+     - annotations: a dictionary that may contain the following keys:
+                     - 'bit score': score (in bits) of HSP (float);
+                     - 'evalue':    e-value of HSP (float);
+                     - 'identity':  number of identities in HSP (integer);
+                     - 'positive':  number of positives in HSP (integer);
+                     - 'gaps':      number of gaps in HSP (integer);
+                     - 'midline':   formatting middle line.
+
+    >>> from Bio import Blast
+    >>> record = Blast.read("Blast/xml_2212L_blastx_001.xml")
+    >>> record.query
+    SeqRecord(seq=Seq(None, length=556), id='gi|1347369|gb|G25137.1|G25137', name='<unknown name>', description='human STS EST48004, sequence tagged site', dbxrefs=[])
+    >>> record.stat
+    {'db-num': 2934173, 'db-len': 1011751523, 'hsp-len': 0, 'eff-space': 0, 'kappa': 0.041, 'lambda': 0.267, 'entropy': 0.14}
+    >>> len(record)
+    78
+    >>> hit = record[0]
+    >>> type(hit)
+    <class 'Bio.Blast.Hit'>
+    >>> from Bio.Align import Alignments
+    >>> isinstance(hit, Alignments)
+    True
+    >>> hit.target
+    SeqRecord(seq=Seq(None, length=319), id='gi|12654095|gb|AAH00859.1|', name='AAH00859', description='Unknown (protein for IMAGE:3459481) [Homo sapiens]', dbxrefs=[])
+
+    Most hits consist of only 1 or a few Alignment objects:
+
+    >>> len(hit)
+    1
+    >>> alignment = hit[0]
+    >>> type(alignment)
+    <class 'Bio.Blast.HSP'>
+    >>> alignment.score
+    630.0
+    >>> alignment.annotations
+    {'bit score': 247.284, 'evalue': 1.69599e-64, 'identity': 122, 'positive': 123, 'gaps': 0, 'midline': 'DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERF GPYTDFTP TTE QKL EQAL TYPVNT ERW  IA AVPGR K+'}
+
+    Target and query information are stored in the respective attributes of the
+    alignment:
+
+    >>> alignment.target
+    SeqRecord(seq=Seq({155: 'DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDP...TKK'}, length=319), id='gi|12654095|gb|AAH00859.1|', name='AAH00859', description='Unknown (protein for IMAGE:3459481) [Homo sapiens]', dbxrefs=[])
+    >>> alignment.query
+    SeqRecord(seq=Seq('DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDP...XKE'), id='gi|1347369|gb|G25137.1|G25137', name='<unknown name>', description='human STS EST48004, sequence tagged site', dbxrefs=[])
+
+    This was a BLASTX run, so the query sequence was translated:
+
+    >>> len(alignment.target.features)
+    0
+    >>> len(alignment.query.features)
+    1
+    >>> feature = alignment.query.features[0]
+    >>> feature
+    SeqFeature(SimpleLocation(ExactPosition(0), ExactPosition(133)), type='CDS', qualifiers=...)
+    >>> feature.qualifiers
+    {'coded_by': 'gi|1347369|gb|G25137.1|G25137:1..399'}
+
+    i.e., nucleotides 0:399 (in zero-based coordinates) encode the amino acids
+    of the query in the alignment.
+
+    For an alignment against the reverse strand, the location in the qualifier
+    is shown as in this example:
+
+    >>> record[72][0].query.features[0].qualifiers
+    {'coded_by': 'complement(gi|1347369|gb|G25137.1|G25137:345..530)'}
+
+    """
+
+    def __init__(self):
+        """Initialize the Record object."""
+        self.query = None
+
+    def __repr__(self):
+        query = self.query
+        try:
+            query_id = query.id
+        except AttributeError:
+            query_id = "unknown"
+        nhits = len(self)
+        if nhits == 0:
+            return f"<Bio.Blast.Record query.id={query_id!r}; no hits>"
+        elif nhits == 1:
+            return f"<Bio.Blast.Record query.id={query_id!r}; 1 hit>"
+        else:
+            return f"<Bio.Blast.Record query.id={query_id!r}; {nhits} hits>"
+
+    def __str__(self):
+        lines = []
+        try:
+            version = self.version
+        except AttributeError:
+            pass
+        else:
+            lines.append(f"Program: {version}")
+        try:
+            db = self.db
+        except AttributeError:
+            pass
+        else:
+            lines.append(f"     db: {db}")
+        if self.query is not None:
+            # self.query may be None with legacy Blast if there are no hits
+            lines.append("  Query: %s (length=%d)" % (self.query.id, len(self.query)))
+            indent = " " * 9
+            description_lines = textwrap.wrap(
+                self.query.description,
+                width=80,
+                initial_indent=indent,
+                subsequent_indent=indent,
+            )
+            lines.extend(description_lines)
+        if len(self) == 0:
+            lines.append("   Hits: No hits found")
+        else:
+            lines.append("   Hits: %s  %s  %s" % ("-" * 4, "-" * 5, "-" * 58))
+            pattern = "%13s  %5s  %s"
+            lines.append(pattern % ("#", "# HSP", "ID + description"))
+            lines.append(pattern % ("-" * 4, "-" * 5, "-" * 58))
+            for idx, hit in enumerate(self):
+                n = len(hit)  # Number of HSPs
+                if idx < 30:
+                    hid_line = "%s  %s" % (hit.target.id, hit.target.description)
+                    if len(hid_line) > 58:
+                        hid_line = hid_line[:55] + "..."
+                    lines.append(pattern % (idx, len(hit), hid_line))
+                elif idx > len(self) - 4:
+                    hid_line = "%s  %s" % (hit.target.id, hit.target.description)
+                    if len(hid_line) > 58:
+                        hid_line = hid_line[:55] + "..."
+                    lines.append(pattern % (idx, len(hit), hid_line))
+                elif idx == 30:
+                    lines.append("%14s" % "~~~")
+        return "\n".join(lines)
+
+    def __getitem__(self, key):
+        try:
+            value = super().__getitem__(key)
+        except IndexError:
+            raise IndexError("index out of range") from None
+        except TypeError:
+            if not isinstance(key, str):
+                raise TypeError("key must be an integer, slice, or str") from None
+            for hit in self:
+                if hit.target.id == key:
+                    return hit
+            raise KeyError(key)
+        else:
+            if isinstance(key, slice):
+                record = Record()
+                record.extend(value)
+                # Only store the query attribute, as the other attributes
+                # pertain to the complete Blast record:
+                try:
+                    query = self.query
+                except AttributeError:
+                    pass
+                else:
+                    record.query = query
+                # The following keys may be present if the record was created
+                # by Blast.read:
+                keys = (
+                    "source",
+                    "program",
+                    "version",
+                    "reference",
+                    "db",
+                    "param",
+                    "mbstat",
+                )
+                for key in keys:
+                    try:
+                        value = getattr(self, key)
+                    except AttributeError:
+                        pass
+                    else:
+                        setattr(record, key, value)
+                return record
+            return value
+
+    def keys(self):
+        """Return a list of the target.id of each hit."""
+        return [hit.target.id for hit in self]
+
+    def __contains__(self, key):
+        for hit in self:
+            if hit.target.id == key:
+                return True
+        return False
+
+    def index(self, key):
+        """Return the index of the hit for which the target.id is equal to the key."""
+        for i, hit in enumerate(self):
+            if hit.target.id == key:
+                return i
+        raise ValueError(f"'{key}' not found")
+
+
+class Records(UserList):
+    """Stores the BLAST results of a single BLAST run.
+
+    A ``Bio.Blast.Records`` object is an iterator. Iterating over it returns
+    returns ``Bio.Blast.Record`` objects, each of which corresponds to one
+    BLAST query.
+
+    Common attributes of a ``Bio.Blast.Records`` object are
+
+     - source:     The input data from which the ``Bio.Blast.Records`` object
+                   was constructed.
+     - program:    The specific BLAST program that was used (e.g., 'blastn').
+     - version:    The version of the BLAST program (e.g., 'BLASTN 2.2.27+').
+     - reference:  The literature reference to the BLAST publication.
+     - db:         The BLAST database against which the query was run
+                   (e.g., 'nr').
+     - query:      A ``SeqRecord`` object which may contain some or all of the
+                   following information:
+                    - query.id:          SeqId of the query;
+                    - query.description: Definition line of the query;
+                    - query.seq:         The query sequence. The query sequence.
+                                         The query sequence.
+     - param:      A dictionary with the parameters used for the BLAST run.
+                   You may find the following keys in this dictionary:
+                    - 'matrix':       the scoring matrix used in the BLAST run
+                                      (e.g., 'BLOSUM62') (string);
+                    - 'expect':       threshold on the expected number of chance
+                                      matches (float);
+                    - 'include':      e-value threshold for inclusion in
+                                      multipass model in psiblast (float);
+                    - 'sc-match':     score for matching nucleotides (integer);
+                    - 'sc-mismatch':  score for mismatched nucleotides
+                                      (integer);
+                    - 'gap-open':     gap opening cost (integer);
+                    - 'gap-extend':   gap extension cost (integer);
+                    - 'filter':       filtering options applied in the BLAST
+                                      run (string);
+                    - 'pattern':      PHI-BLAST pattern (string);
+                    - 'entrez-query': Limit of request to Entrez query (string).
+     - mbstat:     A dictionary with Mega BLAST search statistics.  As this
+                   information is stored near the end of the XML file, this
+                   attribute can only be accessed after the file has been read
+                   completely (by iterating over the records until a
+                   ``StopIteration`` is issued. This dictionary can contain the
+                   same keys as the dictionary stored under the ``stat``
+                   attribute of a ``Record`` object.
+
+    >>> from Bio import Blast
+    >>> path = "Blast/xml_2218_blastp_002.xml"
+
+    In a script, you would use a ``with`` block, as in
+
+    >>> with Blast.parse(path) as records:
+    ...     print(records.source)
+    ...
+    Blast/xml_2218_blastp_002.xml
+
+    to ensure that the file is closed at the end of the block.
+    Here, we will simply do
+
+    >>> records = Blast.parse("Blast/xml_2218_blastp_002.xml")
+
+    so we can see the output of each command right away.
+
+    >>> type(records)
+    <class 'Bio.Blast.Records'>
+    >>> records.source
+    'Blast/xml_2218_blastp_002.xml'
+    >>> records.program
+    'blastp'
+    >>> records.version
+    'BLASTP 2.2.18+'
+    >>> records.reference
+    'Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.'
+    >>> records.db
+    'gpipe/9606/Previous/protein'
+    >>> records.param
+    {'matrix': 'BLOSUM62', 'expect': 0.01, 'gap-open': 11, 'gap-extend': 1, 'filter': 'm L; R -d repeat/repeat_9606;'}
+
+    Iterating over the records returns Bio.Blast.Record objects:
+
+    >>> record = next(records)
+    >>> type(record)
+    <class 'Bio.Blast.Record'>
+    >>> record.query.id
+    'gi|585505|sp|Q08386|MOPB_RHOCA'
+    >>> record = next(records)
+    >>> type(record)
+    <class 'Bio.Blast.Record'>
+    >>> record.query.id
+    'gi|129628|sp|P07175.1|PARA_AGRTU'
+    >>> record = next(records)  # doctest:+ELLIPSIS
+    Traceback (most recent call last):
+    ...
+    StopIteration
+
+    You can also use the records as a list, for example by extracting a record
+    by index, or by calling ``len`` or ``print`` on the records. The parser
+    will then automatically iterate over the records and store them:
+
+    >>> records = Blast.parse("Blast/wnts.xml")
+    >>> record = records[3]  # this causes all records to be read in and stored
+    >>> record.query.id
+    'Query_4'
+    >>> len(records)
+    5
+
+    After the records have been read in, you can still iterate over them:
+
+    >>> for i, record in enumerate(records):
+    ...     print(i, record.query.id)
+    ...
+    0 Query_1
+    1 Query_2
+    2 Query_3
+    3 Query_4
+    4 Query_5
+
+    """  # noqa: RST201, RST203, RST301
+
+    def __init__(self, source):
+        """Initialize the Records object."""
+        if isinstance(source, list):  # UserList API requirement
+            self._records = source
+            self._loaded = True
+            self._index = 0
+            return
+
+        self.source = source
+        try:
+            stream = open(source, "rb")
+        except TypeError:  # not a path, assume we received a stream
+            if source.read(0) != b"":
+                raise StreamModeError(
+                    "BLAST output files must be opened in binary mode."
+                ) from None
+            stream = source
+        self._stream = stream
+        self._read_header()
+        self._records = []  # for when we want to use Records as a list
+        self._loaded = False
+
+    def _read_header(self):
+        from Bio.Blast._parser import XMLHandler
+
+        stream = self._stream
+        source = self.source
+        try:  # context manager won't kick in until after parse returns
+            parser = expat.ParserCreate(namespace_separator=" ")
+            self._parser = parser
+
+            handler = XMLHandler(parser)
+            handler._records = self
+
+            while True:
+                data = stream.read(BLOCK)
+                if data == b"":
+                    try:
+                        handler._parser
+                    except AttributeError:
+                        break
+                    else:
+                        try:
+                            parser.Parse(b"", True)
+                        except expat.ExpatError as e:
+                            if parser.StartElementHandler is not None:
+                                raise ValueError(
+                                    f"premature end of XML file: line {e.lineno}, column {e.offset}"
+                                )
+                            raise e
+                try:
+                    parser.Parse(data, False)
+                except expat.ExpatError as e:
+                    try:
+                        parser.Parse(b"", True)
+                    except expat.ExpatError:
+                        pass
+                    if parser.StartElementHandler:
+                        # We saw the initial <!xml declaration, so we can be
+                        # sure that we are parsing XML data. Most likely, the
+                        # XML file is corrupted.
+                        raise CorruptedXMLError(e) from None
+                    else:
+                        # We have not seen the initial <!xml declaration, so
+                        # probably the input data is not in XML format.
+                        raise NotXMLError(e) from None
+                try:
+                    self._cache
+                except AttributeError:
+                    pass
+                else:
+                    # We have finished reading the header
+                    break
+        except Exception:
+            if stream is not source:
+                stream.close()
+            raise
+        self._index = 0
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, exc_type, exc_value, exc_traceback):
+        try:
+            self._parser.Parse(b"", True)
+            del self._parser
+        except (AttributeError, expat.ExpatError):
+            pass
+
+        try:
+            del self._cache
+        except AttributeError:
+            pass
+
+        try:
+            stream = self._stream
+        except AttributeError:
+            return
+        if stream is not self.source:
+            stream.close()
+        del self._stream
+
+    def __iter__(self):
+        return self
+
+    def __next__(self):
+        if self._loaded is True:
+            try:
+                record = self._records[self._index]
+            except IndexError:
+                raise StopIteration from None
+            self._index += 1
+            return record
+        try:
+            cache = self._cache
+        except AttributeError:
+            raise StopIteration from None
+        parser = self._parser
+        stream = self._stream
+        while True:
+            try:
+                record = self._cache.popleft()
+            except IndexError:  # no record ready to be returned
+                pass
+            else:
+                self._index += 1
+                return record
+            # Read in another block of data from the file.
+            data = stream.read(BLOCK)
+            if data == b"":
+                try:
+                    del self._parser
+                    try:
+                        parser.Parse(b"", True)
+                    except expat.ExpatError as e:
+                        if parser.StartElementHandler is not None:
+                            raise ValueError(
+                                f"premature end of XML file: line {e.lineno}, column {e.offset}"
+                            )
+                        raise e
+                except AttributeError:
+                    pass
+                raise StopIteration
+            try:
+                parser.Parse(data, False)
+            except expat.ExpatError as e:
+                raise CorruptedXMLError(e) from None
+
+    def __getitem__(self, index):
+        item = super().__getitem__(index)
+        if index == slice(None, None, None):
+            for key, value in self.__dict__.items():
+                if key not in ("_stream", "_parser", "_cache"):
+                    item.__dict__[key] = value
+        return item
+
+    @property
+    def data(self):
+        """Overrides the data attribute of UserList."""
+        if self._loaded is False:
+            # Read all records and store them
+            index = self._index
+            if index > 0:
+                try:
+                    self._stream.seek(0)
+                except io.UnsupportedOperation:
+                    raise ValueError(
+                        "list-like access after iterating is supported only if the input data is seekable."
+                    )
+                self._read_header()
+                self._index = 0
+            for record in self:
+                self._records.append(record)
+            stream = self._stream
+            if stream is not self.source:
+                stream.close()
+            del self._stream
+            self._loaded = True
+            self._index = index
+        return self._records
+
+    def __repr__(self):
+        return f"<Bio.Blast.Records source={self.source!r} program={self.program!r} version={self.version!r} db={self.db!r}>"
+
+    def __str__(self):
+        text = """\
+Program: %s
+     db: %s""" % (
+            self.version,
+            self.db,
+        )
+        records = self[:]  # to ensure that the records are read in
+        for record in self._records:
+            text += "\n\n" + str(record)
+        return text
+
+
+def parse(source):
+    """Parse an XML file containing BLAST output and return a Bio.Blast.Records object.
+
+    This returns an iterator object; iterating over it returns Bio.Blast.Record
+    objects one by one.
+
+    The source can be a file stream or the path to an XML file containing the
+    BLAST output. If a file stream, source  must be in binary mode. This allows
+    the parser to detect the encoding from the XML file,and to use it to convert
+    any text in the XML to the correct Unicode string. The qblast function in
+    Bio.Blast returns a file stream in binary mode. For files, please use mode
+    "rb" when opening the file, as in
+
+    >>> from Bio import Blast
+    >>> stream = open("Blast/wnts.xml", "rb")  # opened in binary mode
+    >>> records = Blast.parse(stream)
+    >>> for record in records:
+    ...     print(record.query.id, record.query.description)
+    ...
+    Query_1 gi|195230749:301-1383 Homo sapiens wingless-type MMTV integration site family member 2 (WNT2), transcript variant 1, mRNA
+    Query_2 gi|325053704:108-1166 Homo sapiens wingless-type MMTV integration site family, member 3A (WNT3A), mRNA
+    Query_3 gi|156630997:105-1160 Homo sapiens wingless-type MMTV integration site family, member 4 (WNT4), mRNA
+    Query_4 gi|371502086:108-1205 Homo sapiens wingless-type MMTV integration site family, member 5A (WNT5A), transcript variant 2, mRNA
+    Query_5 gi|53729353:216-1313 Homo sapiens wingless-type MMTV integration site family, member 6 (WNT6), mRNA
+    >>> stream.close()
+
+    """
+    return Records(source)
+
+
+def read(source):
+    """Parse an XML file containing BLAST output for a single query and return it.
+
+    Internally, this function uses Bio.Blast.parse to obtain an iterator over
+    BLAST records.  The function then reads one record from the iterator,
+    ensures that there are no further records, and returns the record it found
+    as a Bio.Blast.Record object. An exception is raised if no records are
+    found, or more than one record is found.
+
+    The source can be a file stream or the path to an XML file containing the
+    BLAST output. If a file stream, source  must be in binary mode. This allows
+    the parser to detect the encoding from the XML file,and to use it to convert
+    any text in the XML to the correct Unicode string. The qblast function in
+    Bio.Blast returns a file stream in binary mode. For files, please use mode
+    "rb" when opening the file, as in
+
+    >>> from Bio import Blast
+    >>> stream = open("Blast/xml_21500_blastn_001.xml", "rb")  # opened in binary mode
+    >>> record = Blast.read(stream)
+    >>> record.query.id
+    'Query_78041'
+    >>> record.query.description
+    'G26684.1 human STS STS_D11570, sequence tagged site'
+    >>> len(record)
+    11
+    >>> stream.close()
+
+    Use the Bio.Blast.parse function if you want to read a file containing
+    BLAST output for more than one query.
+    """
+    with parse(source) as records:
+        try:
+            record = next(records)
+        except StopIteration:
+            raise ValueError("No BLAST output found.") from None
+        try:
+            next(records)
+            raise ValueError("BLAST output for more than one query found.")
+        except StopIteration:
+            pass
+    for key in ("source", "program", "version", "reference", "db", "param", "mbstat"):
+        try:
+            value = getattr(records, key)
+        except AttributeError:
+            pass
+        else:
+            setattr(record, key, value)
+    return record
+
+
+def write(records, destination, fmt="XML"):
+    """Write BLAST records as an XML file, and return the number of records.
+
+    Arguments:
+     - records     - A ``Bio.Blast.Records`` object.
+     - destination - File or file-like object to write to, or filename as
+                     string.
+                     The File object must have been opened for writing in
+                     binary mode, and must be closed (or flushed) by the caller
+                     after this function returns to ensure that all records are
+                     written.
+     - fmt         - string describing the file format to write
+                     (case-insensitive).
+                     Currently, only "XML" and "XML2" are accepted.
+
+    Returns the number of records written (as an integer).
+    """
+    fmt = fmt.upper()
+    if fmt == "XML":
+        Writer = _writers.XMLWriter
+    elif fmt == "XML2":
+        Writer = _writers.XML2Writer
+    else:
+        raise ValueError(f"Unknown format {fmt}; expected 'XML' or 'XML2'")
+    try:
+        stream = open(destination, "wb")
+    except TypeError:  # not a path, assume we received a stream
+        try:
+            destination.write(b"")
+        except TypeError:
+            # destination was opened in text mode
+            raise StreamModeError(
+                "File must be opened in binary mode for writing."
+            ) from None
+        stream = destination
+    writer = Writer(stream)
+    try:
+        count = writer.write(records)
+    finally:
+        if stream is not destination:
+            stream.close()
+    return count
+
+
+@function_with_previous
+def qblast(
+    program,
+    database,
+    sequence,
+    url_base=NCBI_BLAST_URL,
+    auto_format=None,
+    composition_based_statistics=None,
+    db_genetic_code=None,
+    endpoints=None,
+    entrez_query="(none)",
+    expect=10.0,
+    filter=None,
+    gapcosts=None,
+    genetic_code=None,
+    hitlist_size=50,
+    i_thresh=None,
+    layout=None,
+    lcase_mask=None,
+    matrix_name=None,
+    nucl_penalty=None,
+    nucl_reward=None,
+    other_advanced=None,
+    perc_ident=None,
+    phi_pattern=None,
+    query_file=None,
+    query_believe_defline=None,
+    query_from=None,
+    query_to=None,
+    searchsp_eff=None,
+    service=None,
+    threshold=None,
+    ungapped_alignment=None,
+    word_size=None,
+    short_query=None,
+    alignments=500,
+    alignment_view=None,
+    descriptions=500,
+    entrez_links_new_window=None,
+    expect_low=None,
+    expect_high=None,
+    format_entrez_query=None,
+    format_object=None,
+    format_type="XML",
+    ncbi_gi=None,
+    results_file=None,
+    show_overview=None,
+    megablast=None,
+    template_type=None,
+    template_length=None,
+    username="blast",
+    password=None,
+):
+    """BLAST search using NCBI's QBLAST server.
+
+    Supports all parameters of the old qblast API for Put and Get.
+
+    Please note that NCBI uses the new Common URL API for BLAST searches on
+    the internet (https://blast.ncbi.nlm.nih.gov/doc/blast-help/urlapi.html).
+    Thus, some of the parameters used by this function are not (or are no
+    longer) officially supported by NCBI. Although they are still functioning,
+    this may change in the future.
+
+    Some useful parameters:
+
+     - program        blastn, blastp, blastx, tblastn, or tblastx (lower case)
+     - database       Which database to search against (e.g. "nr").
+     - sequence       The sequence to search.
+     - ncbi_gi        TRUE/FALSE whether to give 'gi' identifier.
+     - descriptions   Number of descriptions to show.  Def 500.
+     - alignments     Number of alignments to show.  Def 500.
+     - expect         An expect value cutoff.  Def 10.0.
+     - matrix_name    Specify an alt. matrix (PAM30, PAM70, BLOSUM80, BLOSUM45).
+     - filter         "none" turns off filtering.  Default no filtering
+     - format_type    "XML" (default), "HTML", "Text", "XML2", "JSON2",
+                      or "Tabular".
+     - entrez_query   Entrez query to limit Blast search - only applies when searching nucleotide BLASTDBs
+     - hitlist_size   Number of hits to return. Default 50
+     - megablast      TRUE/FALSE whether to use MEga BLAST algorithm (blastn only)
+     - short_query    TRUE/FALSE whether to adjust the search parameters for a
+                      short query sequence. Note that this will override
+                      manually set parameters like word size and e value. Turns
+                      off when sequence length is > 30 residues. Default: None.
+     - service        plain, psi, phi, rpsblast, megablast (lower case)
+
+    This function does no checking of the validity of the parameters
+    and passes the values to the server as is.  More help is available at:
+    https://blast.ncbi.nlm.nih.gov/doc/blast-help/urlapi.html
+
+    The http.client.HTTPResponse object returned by this function has the
+    additional attributes rid and rtoe with the Request ID and Request Time Of
+    Execution for this BLAST search.
+
+    """
+    programs = ["blastn", "blastp", "blastx", "tblastn", "tblastx"]
+    if program not in programs:
+        raise ValueError(
+            f"Program specified is {program}. Expected one of {', '.join(programs)}"
+        )
+
+    # SHORT_QUERY_ADJUST throws an error when using blastn (wrong parameter
+    # assignment from NCBIs side).
+    # Thus we set the (known) parameters directly:
+    if short_query and program == "blastn":
+        short_query = None
+        # We only use the 'short-query' parameters for short sequences:
+        if len(sequence) < 31:
+            expect = 1000
+            word_size = 7
+            nucl_reward = 1
+            filter = None
+            lcase_mask = None
+            warnings.warn(
+                '"SHORT_QUERY_ADJUST" is incorrectly implemented (by NCBI) for blastn.'
+                " We bypass the problem by manually adjusting the search parameters."
+                " Thus, results may slightly differ from web page searches.",
+                BiopythonWarning,
+            )
+
+    # Format the "Put" command, which sends search requests to qblast.
+    # Parameters taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node5.html on 9 July 2007
+    # Additional parameters are taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node9.html on 8 Oct 2010
+    # To perform a PSI-BLAST or PHI-BLAST search the service ("Put" and "Get" commands) must be specified
+    # (e.g. psi_blast = NCBIWWW.qblast("blastp", "refseq_protein", input_sequence, service="psi"))
+    parameters = {
+        "AUTO_FORMAT": auto_format,
+        "COMPOSITION_BASED_STATISTICS": composition_based_statistics,
+        "DATABASE": database,
+        "DB_GENETIC_CODE": db_genetic_code,
+        "ENDPOINTS": endpoints,
+        "ENTREZ_QUERY": entrez_query,
+        "EXPECT": expect,
+        "FILTER": filter,
+        "GAPCOSTS": gapcosts,
+        "GENETIC_CODE": genetic_code,
+        "HITLIST_SIZE": hitlist_size,
+        "I_THRESH": i_thresh,
+        "LAYOUT": layout,
+        "LCASE_MASK": lcase_mask,
+        "MEGABLAST": megablast,
+        "MATRIX_NAME": matrix_name,
+        "NUCL_PENALTY": nucl_penalty,
+        "NUCL_REWARD": nucl_reward,
+        "OTHER_ADVANCED": other_advanced,
+        "PERC_IDENT": perc_ident,
+        "PHI_PATTERN": phi_pattern,
+        "PROGRAM": program,
+        # ('PSSM': pssm: - It is possible to use PSI-BLAST via this API?
+        "QUERY": sequence,
+        "QUERY_FILE": query_file,
+        "QUERY_BELIEVE_DEFLINE": query_believe_defline,
+        "QUERY_FROM": query_from,
+        "QUERY_TO": query_to,
+        # 'RESULTS_FILE': ...: - Can we use this parameter?
+        "SEARCHSP_EFF": searchsp_eff,
+        "SERVICE": service,
+        "SHORT_QUERY_ADJUST": short_query,
+        "TEMPLATE_TYPE": template_type,
+        "TEMPLATE_LENGTH": template_length,
+        "THRESHOLD": threshold,
+        "UNGAPPED_ALIGNMENT": ungapped_alignment,
+        "WORD_SIZE": word_size,
+        "CMD": "Put",
+    }
+
+    if password is not None:
+        # handle authentication for BLAST cloud
+        password_mgr = HTTPPasswordMgrWithDefaultRealm()
+        password_mgr.add_password(None, url_base, username, password)
+        handler = HTTPBasicAuthHandler(password_mgr)
+        opener = build_opener(handler)
+        install_opener(opener)
+
+    if url_base == NCBI_BLAST_URL:
+        parameters.update({"email": email, "tool": tool})
+    parameters = {key: value for key, value in parameters.items() if value is not None}
+    message = urlencode(parameters).encode()
+    request = Request(url_base, message, {"User-Agent": "BiopythonClient"})
+    # Send off the initial query to qblast.
+    # Note the NCBI do not currently impose a rate limit here, other
+    # than the request not to make say 50 queries at once using multiple
+    # threads.
+    stream = urlopen(request)
+
+    # Format the "Get" command, which gets the formatted results from qblast
+    # Parameters taken from http://www.ncbi.nlm.nih.gov/BLAST/Doc/node6.html on 9 July 2007
+    rid, rtoe = _parse_qblast_ref_page(stream)
+    parameters = {
+        "ALIGNMENTS": alignments,
+        "ALIGNMENT_VIEW": alignment_view,
+        "DESCRIPTIONS": descriptions,
+        "ENTREZ_LINKS_NEW_WINDOW": entrez_links_new_window,
+        "EXPECT_LOW": expect_low,
+        "EXPECT_HIGH": expect_high,
+        "FORMAT_ENTREZ_QUERY": format_entrez_query,
+        "FORMAT_OBJECT": format_object,
+        "FORMAT_TYPE": format_type,
+        "NCBI_GI": ncbi_gi,
+        "RID": rid,
+        "RESULTS_FILE": results_file,
+        "SERVICE": service,
+        "SHOW_OVERVIEW": show_overview,
+        "CMD": "Get",
+    }
+    parameters = {key: value for key, value in parameters.items() if value is not None}
+    message = urlencode(parameters).encode()
+
+    # Poll NCBI until the results are ready.
+    # https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo
+    # 1. Do not contact the server more often than once every 10 seconds.
+    # 2. Do not poll for any single RID more often than once a minute.
+    # 3. Use the URL parameter email and tool, so that the NCBI
+    #    can contact you if there is a problem.
+    # 4. Run scripts weekends or between 9 pm and 5 am Eastern time
+    #    on weekdays if more than 50 searches will be submitted.
+    # --
+    # Could start with a 10s delay, but expect most short queries
+    # will take longer thus at least 70s with delay. Therefore,
+    # start with 20s delay, thereafter once a minute.
+    delay = 20  # seconds
+    start_time = time.time()
+    while True:
+        current = time.time()
+        wait = qblast.previous + delay - current
+        if wait > 0:
+            time.sleep(wait)
+            qblast.previous = current + wait
+        else:
+            qblast.previous = current
+        # delay by at least 60 seconds only if running the request against the public NCBI API
+        if delay < 60 and url_base == NCBI_BLAST_URL:
+            # Wasn't a quick return, must wait at least a minute
+            delay = 60
+        elapsed = time.time() - start_time
+        if elapsed >= 600:
+            warnings.warn(
+                f"BLAST request {rid} is taking longer than 10 minutes, consider re-issuing it",
+                BiopythonWarning,
+            )
+        request = Request(url_base, message, {"User-Agent": "BiopythonClient"})
+        stream = urlopen(request)
+        data = stream.peek()
+        if format_type == "HTML" and b"<title>NCBI Blast:</title>" in data:
+            continue
+        elif data.startswith(b"<!DOCTYPE html"):
+            continue
+        else:
+            break
+    if format_type == "XML":
+        assert data.startswith(b"<?xml ")
+    elif format_type == "HTML":
+        assert data.startswith(b"<!DOCTYPE html ")
+    elif format_type in ("Text", "Tabular"):
+        assert data.startswith(b"<p><!--\nQBlastInfoBegin")
+    elif format_type in ("XML2", "JSON2"):
+        assert data.startswith(b"PK\x03\x04")  # zipped file
+    stream.rid = rid
+    stream.rtoe = rtoe
+    return stream
+
+
+qblast.previous = 0
+
+
+def _parse_qblast_ref_page(handle):
+    """Extract a tuple of RID, RTOE from the 'please wait' page (PRIVATE).
+
+    The NCBI FAQ pages use TOE for 'Time of Execution', so RTOE is probably
+    'Request Time of Execution' and RID would be 'Request Identifier'.
+    """
+    s = handle.read().decode()
+    i = s.find("RID =")
+    if i == -1:
+        rid = None
+    else:
+        j = s.find("\n", i)
+        rid = s[i + len("RID =") : j].strip()
+
+    i = s.find("RTOE =")
+    if i == -1:
+        rtoe = None
+    else:
+        j = s.find("\n", i)
+        rtoe = s[i + len("RTOE =") : j].strip()
+
+    if not rid and not rtoe:
+        # Can we reliably extract the error message from the HTML page?
+        # e.g.  "Message ID#24 Error: Failed to read the Blast query:
+        #       Nucleotide FASTA provided for protein sequence"
+        # or    "Message ID#32 Error: Query contains no data: Query
+        #       contains no sequence data"
+        #
+        # This used to occur inside a <div class="error msInf"> entry:
+        i = s.find('<div class="error msInf">')
+        if i != -1:
+            msg = s[i + len('<div class="error msInf">') :].strip()
+            msg = msg.split("</div>", 1)[0].split("\n", 1)[0].strip()
+            if msg:
+                raise ValueError(f"Error message from NCBI: {msg}")
+        # In spring 2010 the markup was like this:
+        i = s.find('<p class="error">')
+        if i != -1:
+            msg = s[i + len('<p class="error">') :].strip()
+            msg = msg.split("</p>", 1)[0].split("\n", 1)[0].strip()
+            if msg:
+                raise ValueError(f"Error message from NCBI: {msg}")
+        # Generic search based on the way the error messages start:
+        i = s.find("Message ID#")
+        if i != -1:
+            # Break the message at the first HTML tag
+            msg = s[i:].split("<", 1)[0].split("\n", 1)[0].strip()
+            raise ValueError(f"Error message from NCBI: {msg}")
+        # We didn't recognise the error layout :(
+        # print(s)
+        raise ValueError(
+            "No RID and no RTOE found in the 'please wait' page, "
+            "there was probably an error in your request but we "
+            "could not extract a helpful error message."
+        )
+    elif not rid:
+        # Can this happen?
+        raise ValueError(
+            f"No RID found in the 'please wait' page. (although RTOE = {rtoe!r})"
+        )
+    elif not rtoe:
+        # Can this happen?
+        raise ValueError(
+            f"No RTOE found in the 'please wait' page. (although RID = {rid!r})"
+        )
+
+    try:
+        return rid, int(rtoe)
+    except ValueError:
+        raise ValueError(
+            f"A non-integer RTOE found in the 'please wait' page, {rtoe!r}"
+        ) from None
+
+
+if __name__ == "__main__":
+    from Bio._utils import run_doctest
+
+    run_doctest()

.venv_haddock/lib/python3.12/site-packages/Bio/Blast/_parser.py

@@ -0,0 +1,1226 @@
+# Copyright 1999 by Jeffrey Chang.  All rights reserved.
+# Copyright 2000 by Bertrand Frottier.  All rights reserved.
+# Revisions 2005-2006 copyright Michiel de Hoon
+# Revisions 2006-2009 copyright Peter Cock
+# Revisions 2023 by Michiel de Hoon.  All rights reserved.
+#
+# This file is part of the Biopython distribution and governed by your
+# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
+# Please see the LICENSE file that should have been included as part of this
+# package.
+"""Code to parse BLAST XML output, and to parse the BLAST DTD file defining the XML.
+
+The BLAST XML DTD file is available on the NCBI site at:
+https://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd
+"""
+
+import html
+import os.path
+from collections import deque
+from xml.parsers import expat
+
+from Bio import Entrez
+from Bio.Align import Alignment
+from Bio.Blast import Hit
+from Bio.Blast import HSP
+from Bio.Blast import Record
+from Bio.Seq import reverse_complement
+from Bio.Seq import Seq
+from Bio.SeqFeature import SeqFeature
+from Bio.SeqFeature import SimpleLocation
+from Bio.SeqRecord import SeqRecord
+
+import numpy as np
+
+
+class DTDHandler:
+    """Parser for the BLAST XML DTD file."""
+
+    def __init__(self):
+        """Initialize the parser and parse the BLAST XML DTD file."""
+        parser = expat.ParserCreate()
+        parser.SetParamEntityParsing(expat.XML_PARAM_ENTITY_PARSING_ALWAYS)
+        parser.ExternalEntityRefHandler = self._externalEntityRefHandler
+        self.parser = parser
+        self.start_methods = {}
+        self.end_methods = {}
+        XMLHandler._dtd_methods = self.start_methods, self.end_methods
+
+    def _elementDeclHandler(self, name, model):
+        method_name = name
+        if name not in (
+            "BlastOutput_query-ID",
+            "BlastOutput_query-def",
+            "BlastOutput_query-len",
+        ):
+            # Note that NCBI_BlastOutput.dtd defines both BlastOutput_query-ID
+            # and Iteration_query-ID, while NCBI_BlastOutput2.xsd defines
+            # query-id only, which corresponds to Iteration_query-ID.
+            # Same for BlastOutput_query-def and BlastOutput_query-len.
+            for prefix in (
+                "BlastOutput_",
+                "Iteration_",
+                "Parameters_",
+                "Statistics_",
+                "Hit_",
+                "Hsp_",
+            ):
+                method_name = method_name.replace(prefix, "")
+        method_name = method_name.lower().replace("-", "_")
+        start_method = "_start_" + method_name
+        end_method = "_end_" + method_name
+        self.start_methods[name] = getattr(XMLHandler, start_method)
+        self.end_methods[name] = getattr(XMLHandler, end_method)
+
+    def _externalEntityRefHandler(self, context, base, systemId, publicId):
+        assert context is None
+        assert base is None
+        self.parseFile(systemId)
+        return 1
+
+    def parseFile(self, filename):
+        """Parse a DTD file."""
+        directory = Entrez.__path__[0]
+        path = os.path.join(directory, "DTDs", filename)
+        parser = self.parser.ExternalEntityParserCreate(None)
+        parser.ElementDeclHandler = self._elementDeclHandler
+        with open(path, "rb") as stream:
+            parser.ParseFile(stream)
+
+
+class SchemaHandler:
+    """XML Schema parser used to parse NCBI_BlastOutput2.xsd.
+
+    The XML Schema for Blast XML2 is available from
+    https://www.ncbi.nlm.nih.gov/data_specs/schema_alt/NCBI_BlastOutput2.xsd
+    """
+
+    def __init__(self, parser):
+        """Initialize the XML Schema parser."""
+        self.parser = parser
+        self.start_methods = {}
+        self.end_methods = {}
+        XMLHandler._schema_methods = self.start_methods, self.end_methods
+
+    def _startElementHandler(self, name, attributes):
+        """Found XML start tag.
+
+        Arguments:
+         - name       -- name of the tag
+         - attributes -- tag attributes
+
+        """
+        if name == "http://www.w3.org/2001/XMLSchema include":
+            filename = attributes["schemaLocation"]
+            directory = Entrez.__path__[0]
+            path = os.path.join(directory, "XSDs", filename)
+            parser = expat.ParserCreate(namespace_separator=" ")
+            parser.StartElementHandler = self._startElementHandler
+            with open(path, "rb") as stream:
+                parser.ParseFile(stream)
+        elif name == "http://www.w3.org/2001/XMLSchema element":
+            tag = attributes.get("name")
+            if tag is None:
+                return
+            namespace = "http://www.ncbi.nlm.nih.gov"
+            key = f"{namespace} {tag}"
+            if tag == "BlastOutput2":
+                self.start_methods[key] = XMLHandler._start_blastoutput
+                self.end_methods[key] = XMLHandler._end_blastoutput_xml2
+            elif tag in (
+                "error",
+                "Err",
+                "code",
+                "message",
+                "subjects",
+                "bl2seq",
+            ):
+                pass  # TBD
+            else:
+                if tag == "params":
+                    tag = "param"
+                elif tag == "search":
+                    tag = "iterations"
+                elif tag == "Search":
+                    tag = "Iteration"
+                elif tag == "query-title":
+                    tag = "query-def"
+                elif tag == "title":
+                    tag = "def"
+                method_name = tag.lower().replace("-", "_")
+                start_method = "_start_" + method_name
+                end_method = "_end_" + method_name
+                if tag == "eff-space":
+                    end_method += "_xml2"
+                self.start_methods[key] = getattr(XMLHandler, start_method)
+                self.end_methods[key] = getattr(XMLHandler, end_method)
+
+
+class _HSP_cache:
+    __slots__ = (
+        "num",
+        "bit_score",
+        "score",
+        "evalue",
+        "identity",
+        "positive",
+        "query_from",
+        "query_to",
+        "query_frame",
+        "query_strand",
+        "hit_from",
+        "hit_to",
+        "hit_frame",
+        "hit_strand",
+        "qseq",
+        "hseq",
+        "gaps",
+        "align_len",
+        "density",
+        "midline",
+    )
+
+
+class XMLHandler:
+    """Handler for BLAST XML data."""
+
+    schema_namespace = "http://www.w3.org/2001/XMLSchema-instance"
+    _schema_methods = None
+    _dtd_methods = None
+
+    def __init__(self, parser):
+        """Initialize the expat parser."""
+        parser.XmlDeclHandler = self._xmlDeclHandler
+        parser.SetParamEntityParsing(expat.XML_PARAM_ENTITY_PARSING_ALWAYS)
+        self._parser = parser
+
+    def _startNamespaceDeclHandler(self, prefix, uri):
+        parser = self._parser
+        if uri == XMLHandler.schema_namespace:
+            # This is an xml schema
+            parser.StartElementHandler = self._start_blastxml2
+
+    def _endNamespaceDeclHandler(self, prefix):
+        return
+
+    def _start_blastxml2(self, name, attributes):
+        """Process the XML schema (before processing the element)."""
+        uri, localname = name.split(" ")
+        assert uri == "http://www.ncbi.nlm.nih.gov"
+        assert localname in ("BlastXML2", "BlastOutput2")
+        key = "%s schemaLocation" % XMLHandler.schema_namespace
+        domain, url = attributes[key].split()
+        assert domain == "http://www.ncbi.nlm.nih.gov"
+        if XMLHandler._schema_methods is None:
+            filename = os.path.basename(url)
+            directory = Entrez.__path__[0]
+            path = os.path.join(directory, "XSDs", filename)
+            parser = expat.ParserCreate(namespace_separator=" ")
+            handler = SchemaHandler(parser)
+            parser.StartElementHandler = handler._startElementHandler
+            with open(path, "rb") as stream:
+                parser.ParseFile(stream)
+        self._start_methods, self._end_methods = XMLHandler._schema_methods
+        parser = self._parser
+        parser.StartElementHandler = self._startElementHandler
+        parser.EndElementHandler = self._endElementHandler
+        parser.CharacterDataHandler = self._characterDataHandler
+        self._characters = ""
+
+    def _start_blastoutput(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_program(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_version(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_reference(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_db(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_blastoutput_query_id(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_blastoutput_query_def(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_mbstat(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_param(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_parameters(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+        self._records.param = {}
+
+    def _start_matrix(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_expect(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_sc_match(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_sc_mismatch(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_include(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_gap_open(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_gap_extend(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_filter(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_cbs(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_db_gencode(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_query_gencode(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_bl2seq_mode(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_query_masking(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_range(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_from(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_to(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_pattern(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_entrez_query(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_iterations(self, name, attributes):
+        self._records._cache = deque()
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_blastoutput_query_len(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_query_seq(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_iteration(self, name, attributes):
+        if self._program == "psiblast" and name == "http://www.ncbi.nlm.nih.gov Search":
+            # PSIBLAST XML2 uses both <Iteration> and <Search>; ignore one
+            return
+        record = Record()
+        self._record = record
+
+    def _start_iter_num(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_query_id(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_query_def(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_query_len(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_hits(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_hit(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+        self._alignments = Hit()
+
+    def _start_num(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_description(self, name, attributes):
+        self._alignments.targets = []
+
+    def _start_hitdescr(self, name, attributes):
+        return
+
+    def _start_id(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_def(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_taxid(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_sciname(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_hsps(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_len(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_accession(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_hsp(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+        self._hsp = _HSP_cache()
+
+    def _start_bit_score(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_score(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_evalue(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_query_from(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_query_to(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_query_strand(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_hit_from(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_hit_to(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_hit_strand(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_pattern_from(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_pattern_to(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_query_frame(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_hit_frame(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_identity(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_positive(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_gaps(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_align_len(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_density(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_qseq(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_hseq(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_midline(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_stat(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_message(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_statistics(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+        self._stat = {}
+
+    def _start_db_num(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_db_len(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_hsp_len(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_eff_space(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_kappa(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_lambda(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_entropy(self, name, attributes):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _start_report(self, name, attributes):
+        return
+
+    def _start_search_target(self, name, attributes):
+        return
+
+    def _start_target(self, name, attributes):
+        return
+
+    def _start_results(self, name, attributes):
+        return
+
+    def _end_blastoutput(self, name):
+        assert self._characters.strip() == ""
+        parser = self._parser
+        parser.StartElementHandler = None
+        parser.EndElementHandler = None
+        parser.CharacterDataHandler = None
+        del self._characters
+        del self._records
+        del self._parser
+
+    def _end_blastoutput_xml2(self, name):
+        assert self._characters.strip() == ""
+
+    def _end_blastxml2(self, name):
+        self._end_blastoutput(name)
+
+    def _end_program(self, name):
+        program = self._characters
+        self._program = program
+        self._records.program = program
+        self._characters = ""
+
+    def _end_version(self, name):
+        self._records.version = self._characters
+        self._characters = ""
+
+    def _end_reference(self, name):
+        self._records.reference = html.unescape(self._characters)
+        self._characters = ""
+
+    def _end_db(self, name):
+        self._records.db = self._characters
+        self._characters = ""
+
+    def _end_blastoutput_query_id(self, name):
+        query_id = self._characters
+        self._records.query = SeqRecord(None, query_id)
+        self._characters = ""
+
+    def _end_blastoutput_query_def(self, name):
+        query_def = self._characters
+        self._records.query.description = query_def
+        self._characters = ""
+
+    def _end_blastoutput_query_len(self, name):
+        length = int(self._characters)
+        self._records.query.seq = Seq(None, length=length)
+        self._characters = ""
+
+    def _end_query_seq(self, name):
+        seq = Seq(self._characters)
+        self._characters = ""
+        assert len(seq) == len(self._records.query.seq)
+        self._records.query.seq = seq
+
+    def _end_mbstat(self, name):
+        assert self._characters.strip() == ""
+        self._characters = ""
+        self._records.mbstat = self._stat
+        del self._stat
+
+    def _end_param(self, name):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _end_parameters(self, name):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _end_matrix(self, name):
+        self._records.param["matrix"] = self._characters
+        self._characters = ""
+
+    def _end_expect(self, name):
+        self._records.param["expect"] = float(self._characters)
+        self._characters = ""
+
+    def _end_sc_match(self, name):
+        self._records.param["sc-match"] = int(self._characters)
+        self._characters = ""
+
+    def _end_sc_mismatch(self, name):
+        self._records.param["sc-mismatch"] = int(self._characters)
+        self._characters = ""
+
+    def _end_include(self, name):
+        self._records.param["include"] = float(self._characters)
+        self._characters = ""
+
+    def _end_gap_open(self, name):
+        self._records.param["gap-open"] = int(self._characters)
+        self._characters = ""
+
+    def _end_gap_extend(self, name):
+        self._records.param["gap-extend"] = int(self._characters)
+        self._characters = ""
+
+    def _end_filter(self, name):
+        self._records.param["filter"] = self._characters
+        self._characters = ""
+
+    def _end_cbs(self, name):
+        self._records.param["cbs"] = int(self._characters)
+        self._characters = ""
+
+    def _end_db_gencode(self, name):
+        self._records.param["db-gencode"] = int(self._characters)
+        self._characters = ""
+
+    def _end_bl2seq_mode(self, name):
+        self._records.param["bl2seq-mode"] = int(self._characters)
+        self._characters = ""
+
+    def _end_query_masking(self, name):
+        assert self._characters.strip() == ""
+        self._characters = ""
+        location = self._location
+        del self._location
+        feature = SeqFeature(location, type="masking")
+        self._record.query.features.append(feature)
+
+    def _end_range(self, name):
+        start = self._from - 1
+        del self._from
+        end = self._to
+        del self._to
+        self._location = SimpleLocation(start, end)
+
+    def _end_from(self, name):
+        self._from = int(self._characters)
+        self._characters = ""
+
+    def _end_to(self, name):
+        self._to = int(self._characters)
+        self._characters = ""
+
+    def _end_query_gencode(self, name):
+        self._records.param["query-gencode"] = int(self._characters)
+        self._characters = ""
+
+    def _end_pattern(self, name):
+        self._records.param["pattern"] = self._characters
+        self._characters = ""
+
+    def _end_entrez_query(self, name):
+        self._records.param["entrez-query"] = self._characters
+        self._characters = ""
+
+    def _end_iterations(self, name):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _end_iteration(self, name):
+        assert self._characters.strip() == ""
+        self._characters = ""
+        if self._program == "psiblast" and name == "http://www.ncbi.nlm.nih.gov Search":
+            # PSIBLAST XML2 uses both <Iteration> and <Search>; ignore one
+            return
+        self._records._cache.append(self._record)
+        del self._record
+
+    def _end_iter_num(self, name):
+        self._record.num = int(self._characters)
+        self._characters = ""
+
+    def _end_query_id(self, name):
+        query_id = self._characters
+        self._record.query = SeqRecord(None, query_id)
+        self._characters = ""
+
+    def _end_query_def(self, name):
+        query_def = self._characters
+        self._record.query.description = query_def
+        self._characters = ""
+
+    def _end_query_len(self, name):
+        length = int(self._characters)
+        self._record.query.seq = Seq(None, length=length)
+        self._characters = ""
+
+    def _end_hits(self, name):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _end_hit(self, name):
+        assert self._characters.strip() == ""
+        self._characters = ""
+        hit = self._alignments
+        del self._alignments
+        self._record.append(hit)
+
+    def _end_description(self, name):
+        self._alignments.target = self._alignments.targets[0]
+
+    def _end_hitdescr(self, name):
+        self._alignments.targets.append(self._alignments.target)
+
+    def _end_id(self, name):
+        hit_id = self._characters
+        self._alignments.target = SeqRecord(None, hit_id)
+        self._characters = ""
+
+    def _end_def(self, name):
+        description = self._characters
+        self._alignments.target.description = description
+        self._characters = ""
+
+    def _end_taxid(self, name):
+        taxid = self._characters
+        self._alignments.target.annotations["taxid"] = int(taxid)
+        self._characters = ""
+
+    def _end_sciname(self, name):
+        sciname = self._characters
+        self._alignments.target.annotations["sciname"] = sciname
+        self._characters = ""
+
+    def _end_accession(self, name):
+        accession = self._characters
+        self._alignments.target.name = accession
+        self._characters = ""
+
+    def _end_len(self, name):
+        length = int(self._characters)
+        seq = Seq(None, length=length)
+        alignments = self._alignments
+        try:
+            targets = alignments.targets
+        except AttributeError:
+            # XML
+            alignments.target.seq = seq
+        else:
+            # XML2
+            for target in alignments.targets:
+                target.seq = seq
+        self._characters = ""
+
+    def _end_hsps(self, name):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _end_num(self, name):
+        try:
+            element = self._hsp
+        except AttributeError:
+            element = self._alignments
+        element.num = int(self._characters)
+        self._characters = ""
+
+    def _end_bit_score(self, name):
+        self._hsp.bit_score = float(self._characters)
+        self._characters = ""
+
+    def _end_score(self, name):
+        self._hsp.score = float(self._characters)
+        self._characters = ""
+
+    def _end_evalue(self, name):
+        self._hsp.evalue = float(self._characters)
+        self._characters = ""
+
+    def _end_query_from(self, name):
+        self._hsp.query_from = int(self._characters)
+        self._characters = ""
+
+    def _end_query_to(self, name):
+        self._hsp.query_to = int(self._characters)
+        self._characters = ""
+
+    def _end_query_strand(self, name):
+        query_strand = self._characters
+        assert query_strand == "Plus"
+        self._hsp.query_strand = query_strand
+        self._characters = ""
+
+    def _end_hit_from(self, name):
+        self._hsp.hit_from = int(self._characters)
+        self._characters = ""
+
+    def _end_hit_to(self, name):
+        self._hsp.hit_to = int(self._characters)
+        self._characters = ""
+
+    def _end_hit_strand(self, name):
+        hit_strand = self._characters
+        assert hit_strand in ("Plus", "Minus")
+        self._hsp.hit_strand = hit_strand
+        self._characters = ""
+
+    def _end_pattern_from(self, name):
+        self._hsp.pattern_from = int(self._characters)
+        self._characters = ""
+
+    def _end_pattern_to(self, name):
+        self._hsp.pattern_to = int(self._characters)
+        self._characters = ""
+
+    def _end_query_frame(self, name):
+        query_frame = int(self._characters)
+        program = self._program
+        if program in ("blastn", "megablast") and query_frame == 1:
+            pass
+        elif program in ("blastx", "tblastx") and query_frame in (-3, -2, -1, 1, 2, 3):
+            pass
+        elif (
+            program in ("blastp", "tblastn", "rpsblast", "psiblast")
+            and query_frame == 0
+        ):
+            pass
+        else:
+            raise ValueError(
+                f"unexpected value {query_frame} in tag <Hsp_query-frame> for program {program}"
+            )
+        self._hsp.query_frame = query_frame
+        self._characters = ""
+
+    def _end_hit_frame(self, name):
+        hit_frame = int(self._characters)
+        program = self._program
+        if program in ("blastn", "megablast") and hit_frame in (-1, 1):
+            pass
+        elif program in ("blastp", "blastx", "rpsblast", "psiblast") and hit_frame == 0:
+            pass
+        elif program in ("tblastn", "tblastx") and hit_frame in (-3, -2, -1, 1, 2, 3):
+            pass
+        else:
+            raise ValueError(
+                f"unexpected value {hit_frame} in tag <Hsp_hit-frame> for program {program}"
+            )
+        self._hsp.hit_frame = hit_frame
+        self._characters = ""
+
+    def _end_identity(self, name):
+        self._hsp.identity = int(self._characters)
+        self._characters = ""
+
+    def _end_positive(self, name):
+        self._hsp.positive = int(self._characters)
+        self._characters = ""
+
+    def _end_gaps(self, name):
+        self._hsp.gaps = int(self._characters)
+        self._characters = ""
+
+    def _end_align_len(self, name):
+        self._hsp.align_len = int(self._characters)
+        self._characters = ""
+
+    def _end_density(self, name):
+        self._hsp.density = int(self._characters)
+        self._characters = ""
+
+    def _end_qseq(self, name):
+        self._hsp.qseq = self._characters
+        self._characters = ""
+
+    def _end_hseq(self, name):
+        self._hsp.hseq = self._characters
+        self._characters = ""
+
+    def _end_midline(self, name):
+        self._hsp.midline = self._characters
+        self._characters = ""
+
+    def _end_hsp(self, name):
+        assert self._characters.strip() == ""
+        self._characters = ""
+        hsp = self._hsp
+        del self._hsp
+        program = self._program
+        query = self._record.query
+        if query is None:
+            query = self._records.query
+        query_id = query.id
+        query_description = query.description
+        query_length = len(query.seq)
+        query = SeqRecord(None, query_id, description=query_description)
+        target = self._alignments.target
+        target_id = target.id
+        target_name = target.name
+        target_description = target.description
+        target_length = len(target.seq)
+        target = SeqRecord(None, target_id, target_name, description=target_description)
+        query_seq_aligned = hsp.qseq.encode()
+        target_seq_aligned = hsp.hseq.encode()
+        try:
+            align_len = hsp.align_len
+        except AttributeError:  # PSIBLAST XML2
+            assert len(query_seq_aligned) == 0
+            assert len(target_seq_aligned) == 0
+            query_seq_data = None
+            target.seq = Seq(None, target_length)
+            coordinates = np.empty((2, 0), dtype=int)
+        else:
+            assert len(query_seq_aligned) == align_len
+            assert len(target_seq_aligned) == align_len
+            (
+                (
+                    target_seq_data,
+                    query_seq_data,
+                ),
+                coordinates,
+            ) = Alignment.parse_printed_alignment(
+                [target_seq_aligned, query_seq_aligned]
+            )
+            query_start = hsp.query_from - 1
+            query_end = hsp.query_to
+            if program in ("blastx", "tblastx"):
+                assert query_end - query_start == 3 * len(query_seq_data)
+                location = SimpleLocation(0, len(query_seq_data))
+                coded_by = f"{query_id}:{hsp.query_from}..{hsp.query_to}"
+                query_frame = hsp.query_frame
+                if query_frame > 0:
+                    assert query_start % 3 == query_frame - 1
+                elif query_frame < 0:
+                    assert (query_length - query_end) % 3 == -query_frame - 1
+                    coded_by = f"complement({coded_by})"
+                qualifiers = {"coded_by": coded_by}
+                feature = SeqFeature(location, type="CDS", qualifiers=qualifiers)
+                query.features.append(feature)
+            else:
+                coordinates[1, :] += query_start
+                assert query_end - query_start == len(query_seq_data)
+                query_seq_data = {query_start: query_seq_data}
+                if program == "blastn":
+                    try:
+                        query_strand = hsp.query_strand
+                    except AttributeError:
+                        # v1 XML
+                        pass
+                    else:
+                        # v2 XML
+                        assert query_strand == "Plus"
+            if program in ("blastn", "megablast"):
+                try:
+                    target_strand = hsp.hit_strand
+                except AttributeError:
+                    # v1 XML
+                    target_frame = hsp.hit_frame
+                    if target_frame == +1:
+                        target_strand = "Plus"
+                    elif target_frame == -1:
+                        target_strand = "Minus"
+                if target_strand == "Plus":
+                    target_start = hsp.hit_from - 1
+                    target_end = hsp.hit_to
+                    coordinates[0, :] += target_start
+                    assert target_end - target_start == len(target_seq_data)
+                    target_seq_data = {target_start: target_seq_data}
+                    target.seq = Seq(target_seq_data, target_length)
+                elif target_strand == "Minus":
+                    target_start = hsp.hit_to - 1
+                    target_end = hsp.hit_from
+                    coordinates[0, :] = target_end - coordinates[0, :]
+                    assert target_end - target_start == len(target_seq_data)
+                    target_seq_data = {target_length - target_end: target_seq_data}
+                    seq = Seq(target_seq_data, target_length)
+                    target.seq = seq.reverse_complement()
+            elif program in ("blastp", "blastx", "rpsblast", "psiblast"):
+                target_start = hsp.hit_from - 1
+                target_end = hsp.hit_to
+                coordinates[0, :] += target_start
+                assert target_end - target_start == len(target_seq_data)
+                target_seq_data = {target_start: target_seq_data}
+                target.seq = Seq(target_seq_data, target_length)
+            elif program in ("tblastn", "tblastx"):
+                target_start = hsp.hit_from - 1
+                target_end = hsp.hit_to
+                assert target_end - target_start == 3 * len(target_seq_data)
+                location = SimpleLocation(0, target_length)
+                coded_by = f"{target_id}:{hsp.hit_from}..{hsp.hit_to}"
+                target_frame = hsp.hit_frame
+                if target_frame >= 0:
+                    assert target_start % 3 == target_frame - 1
+                elif target_frame < 0:
+                    assert (target_length - target_end) % 3 == -target_frame - 1
+                    coded_by = f"complement({coded_by})"
+                qualifiers = {"coded_by": coded_by}
+                feature = SeqFeature(location, type="CDS", qualifiers=qualifiers)
+                target.features.append(feature)
+                target.seq = Seq(target_seq_data, target_length)
+            else:
+                raise RuntimeError("Unexpected program name '%s'" % program)
+        query.seq = Seq(query_seq_data, query_length)
+        sequences = [target, query]
+        alignment = HSP(sequences, coordinates)
+        alignment.num = hsp.num
+        alignment.score = hsp.score
+        annotations = {}
+        annotations["bit score"] = hsp.bit_score
+        annotations["evalue"] = hsp.evalue
+        annotations["identity"] = hsp.identity
+        try:
+            annotations["positive"] = hsp.positive
+        except AttributeError:
+            # missing in blastn for XML1
+            pass
+        try:
+            annotations["gaps"] = hsp.gaps
+        except AttributeError:
+            # missing in legacy megablast
+            pass
+        try:
+            annotations["midline"] = hsp.midline
+        except AttributeError:
+            # missing in psiblast for XML2
+            pass
+        alignment.annotations = annotations
+        self._alignments.append(alignment)
+
+    def _end_stat(self, name):
+        assert self._characters.strip() == ""
+        self._characters = ""
+        self._record.stat = self._stat
+        del self._stat
+
+    def _end_message(self, name):
+        self._record.message = self._characters
+        self._characters = ""
+
+    def _end_statistics(self, name):
+        assert self._characters.strip() == ""
+        self._characters = ""
+
+    def _end_db_num(self, name):
+        self._stat["db-num"] = int(self._characters)
+        self._characters = ""
+
+    def _end_db_len(self, name):
+        self._stat["db-len"] = int(self._characters)
+        self._characters = ""
+
+    def _end_hsp_len(self, name):
+        self._stat["hsp-len"] = int(self._characters)
+        self._characters = ""
+
+    def _end_eff_space(self, name):
+        characters = self._characters
+        if characters.isdigit():
+            value = int(characters)
+        else:
+            value = float(characters)
+        self._stat["eff-space"] = value
+        self._characters = ""
+
+    def _end_eff_space_xml2(self, name):
+        self._stat["eff-space"] = int(self._characters)
+        self._characters = ""
+
+    def _end_kappa(self, name):
+        self._stat["kappa"] = float(self._characters)
+        self._characters = ""
+
+    def _end_lambda(self, name):
+        self._stat["lambda"] = float(self._characters)
+        self._characters = ""
+
+    def _end_entropy(self, name):
+        self._stat["entropy"] = float(self._characters)
+        self._characters = ""
+
+    def _end_report(self, name):
+        return
+
+    def _end_search_target(self, name):
+        return
+
+    def _end_target(self, name):
+        return
+
+    def _end_results(self, name):
+        return
+
+    def _xmlDeclHandler(self, version, encoding, standalone):
+        parser = self._parser
+        parser.ExternalEntityRefHandler = self._externalEntityRefHandler
+        parser.StartNamespaceDeclHandler = self._startNamespaceDeclHandler
+        parser.EndNamespaceDeclHandler = self._endNamespaceDeclHandler
+        parser.StartElementHandler = self._startElementHandler
+        parser.EndElementHandler = self._endElementHandler
+        parser.CharacterDataHandler = self._characterDataHandler
+        self._characters = ""
+        parser.XmlDeclHandler = None
+
+    def _externalEntityRefHandler(self, context, base, systemId, publicId):
+        """Handle the DTD declaration."""
+        assert context is None
+        assert base is None
+        if systemId not in (
+            "NCBI_BlastOutput.dtd",
+            "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd",
+            "https://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd",
+        ):
+            raise ValueError("output from legacy BLAST program")
+        assert publicId == "-//NCBI//NCBI BlastOutput/EN"
+        if XMLHandler._dtd_methods is None:
+            handler = DTDHandler()
+            handler.parseFile("NCBI_BlastOutput.dtd")
+            self._parser.ExternalEntityRefHandler = None
+        self._start_methods, self._end_methods = XMLHandler._dtd_methods
+        return 1
+
+    def _startElementHandler(self, name, attributes):
+        """Found XML start tag.
+
+        Arguments:
+         - name       -- name of the tag
+         - attributes -- tag attributes
+
+        """
+        method = self._start_methods.get(name)
+        if method is None:
+            raise ValueError(
+                "Failed to find method for %s (%s)" % (name, self._start_methods.keys())
+            )
+        method(self, name, attributes)
+
+    def _endElementHandler(self, name):
+        """Found XML end tag.
+
+        Arguments:
+         - name -- tag name
+
+        """
+        method = self._end_methods.get(name)
+        if method is None:
+            raise ValueError("Failed to find method for %s" % name)
+        method(self, name)
+
+    def _characterDataHandler(self, characters):
+        """Found some text.
+
+        Arguments:
+         - characters -- characters read
+
+        """
+        self._characters += characters
+
+    def __iter__(self):
+        return self
+
+    def __repr__(self):
+        try:
+            stream = self._stream
+        except AttributeError:
+            stream = None
+        try:
+            parser = self._parser
+        except AttributeError:
+            parser = None
+        address = hex(id(self))
+        if stream is None and parser is None:
+            return f"<Bio.Blast._parser.XMLHandler object at {address} with no stream or parser>"
+        elif stream is None:
+            return f"<Bio.Blast._parser.XMLHandler object at {address} with parser {parser} and no stream>"
+        elif parser is None:
+            return f"<Bio.Blast._parser.XMLHandler object at {address} with stream {stream} and no parser>"
+        else:
+            return f"<Bio.Blast._parser.XMLHandler object at {address} with stream {stream} and parser {parser}>"

.venv_haddock/lib/python3.12/site-packages/Bio/Blast/_writers.py

@@ -0,0 +1,1520 @@
+import codecs
+import html
+from abc import ABC
+from abc import abstractmethod
+
+from Bio.Seq import UndefinedSequenceError
+
+
+def _html_entity_replace(error):
+    start = error.start
+    end = error.end
+    character = error.object[start:end]
+    codepoint = ord(character)
+    entity = f"&{html.entities.codepoint2name[codepoint]};"
+    return entity, end
+
+
+codecs.register_error("htmlentityreplace", _html_entity_replace)
+
+
+class BaseXMLWriter(ABC):
+    """XML Writer, abstract base class."""
+
+    def __init__(self, stream):
+        """Init the stuff."""
+        self.stream = stream
+
+    def write(self, records):
+        """Write the records."""
+        stream = self.stream
+        program = records.program
+        self._program = program
+        self._write_xml_declaration()
+        self._write_definition()
+        self._start_blastoutput()
+        self._write_program(program.encode())
+        self._write_version(records.version.encode())
+        reference = html.escape(records.reference).encode("ASCII", "htmlentityreplace")
+        self._write_reference(reference)
+        self._write_db(records.db.encode())
+        try:
+            query = records.query
+        except AttributeError:  # XML2
+            pass
+        else:
+            self._write_query_id(query.id.encode())
+            self._write_query_def(query.description.encode())
+            self._write_query_len(len(query))
+            try:
+                query_seq = bytes(query.seq)
+            except UndefinedSequenceError:
+                pass
+            else:
+                self._write_query_seq(query_seq)
+        self._write_params(records.param)
+        count = self._write_records(records)
+        try:
+            mbstat = records.mbstat
+        except AttributeError:
+            pass
+        else:
+            self._start_mbstat()
+            self._write_statistics(mbstat)
+            self._end_mbstat()
+        self._end_blastoutput()
+        return count
+
+    def _write_xml_declaration(self):
+        self.stream.write(b'<?xml version="1.0"?>\n')
+
+    def _write_params(self, param):
+        self._start_param()
+        value = param.get("matrix")
+        if value is not None:
+            self._write_parameters_matrix(value.encode())
+        self._write_parameters_expect(param["expect"])
+        value = param.get("include")
+        if value is not None:
+            self._write_parameters_include(value)
+        value = param.get("sc-match")
+        if value is not None:
+            self._write_parameters_sc_match(value)
+        value = param.get("sc-mismatch")
+        if value is not None:
+            self._write_parameters_sc_mismatch(value)
+        value = param.get("gap-open")
+        if value is not None:
+            self._write_parameters_gap_open(value)
+        value = param.get("gap-extend")
+        if value is not None:
+            self._write_parameters_gap_extend(value)
+        value = param.get("filter")
+        if value is not None:
+            self._write_parameters_filter(value.encode())
+        value = param.get("pattern")
+        if value is not None:
+            self._write_parameters_pattern(value.encode())
+        value = param.get("entrez-query")
+        if value is not None:
+            self._write_parameters_entrez_query(value.encode())
+        value = param.get("cbs")
+        if value is not None:
+            self._write_parameters_cbs(value)
+        value = param.get("query-gencode")
+        if value is not None:
+            self._write_parameters_query_gencode(value)
+        value = param.get("db-gencode")
+        if value is not None:
+            self._write_parameters_db_gencode(value)
+        value = param.get("bl2seq-mode")
+        if value is not None:
+            self._write_parameters_bl2seq_mode(value.encode())
+        self._end_param()
+
+    def _write_records(self, records):
+        count = 0
+        self._start_iterations()
+        for record in records:
+            self._write_record(record)
+            count += 1
+        self._end_iterations()
+        return count
+
+    def _write_record(self, record):
+        stream = self.stream
+        self._start_iteration(record)
+        query = record.query
+        if query is None:
+            query_length = None
+        else:
+            query_length = len(query.seq)
+            self._write_iteration_query_id(query.id.encode())
+            description = query.description
+            if description != "<unknown description>":
+                self._write_iteration_query_def(description.encode())
+            self._write_iteration_query_len(query_length)
+            for feature in query.features:
+                if feature.type == "masking":
+                    self._write_iteration_query_masking(feature.location)
+        self._start_iteration_hits()
+        for hit in record:
+            self._write_hit(hit, query_length)
+        self._end_iteration_hits()
+        try:
+            stat = record.stat
+        except AttributeError:
+            pass
+        else:
+            self._start_iteration_stat()
+            self._write_statistics(stat)
+            self._end_iteration_stat()
+        self._end_iteration()
+
+    def _write_hit(self, hit, query_length):
+        stream = self.stream
+        program = self._program
+        target = hit.target
+        target_length = len(target.seq)
+        self._start_iteration_hit()
+        self._write_hit_num(hit.num)
+        try:
+            targets = hit.targets
+        except AttributeError:  # XML
+            self._write_hit_id(target.id.encode())
+            self._write_hit_def(target.description.encode())
+            self._write_hit_accession(target.name.encode())
+        else:  # XML2
+            self._start_hit_targets()
+            for target in targets:
+                self._start_hitdescr()
+                self._write_hit_id(target.id.encode())
+                self._write_hit_accession(target.name.encode())
+                self._write_hit_def(target.description.encode())
+                taxid = target.annotations.get("taxid")
+                if taxid is not None:
+                    self._write_hit_taxid(taxid)
+                sciname = target.annotations.get("sciname")
+                if sciname is not None:
+                    self._write_hit_sciname(sciname.encode())
+                self._end_hitdescr()
+            self._end_hit_targets()
+        self._write_hit_len(target_length)
+        self._start_hit_hsps()
+        for hsp in hit:
+            self._write_hsp(hsp, query_length, target_length)
+        self._end_hit_hsps()
+        self._end_iteration_hit()
+
+    def _write_hsp(self, hsp, query_length, target_length):
+        stream = self.stream
+        program = self._program
+        query = hsp.query
+        target = hsp.target
+        coordinates = hsp.coordinates
+        if coordinates.shape[1] > 0:
+            hit_from, query_from = coordinates[:, 0]
+            hit_to, query_to = coordinates[:, -1]
+            if program in ("blastn", "megablast"):
+                if hit_from <= hit_to:
+                    hit_frame = 1
+                    hit_from += 1
+                else:
+                    hit_frame = -1
+                    hit_to += 1
+            elif program in ("blastp", "blastx", "rpsblast", "psiblast"):
+                hit_from += 1
+                hit_frame = 0
+            elif program in ("tblastn", "tblastx"):
+                feature = target.features[0]
+                coded_by = feature.qualifiers["coded_by"]
+                if coded_by.startswith("complement("):
+                    assert coded_by.endswith(")")
+                    coded_by = coded_by[11:-1]
+                    strand = -1
+                else:
+                    strand = +1
+                hit_id, hit_from_to = coded_by.split(":")
+                hit_from, hit_to = hit_from_to.split("..")
+                hit_from = int(hit_from)
+                hit_to = int(hit_to)
+                hit_start = hit_from - 1
+                hit_end = hit_to
+                if strand == +1:
+                    hit_frame = hit_start % 3 + 1
+                else:
+                    hit_frame = (hit_end - target_length) % -3 - 1
+            if program in ("blastn", "megablast"):
+                if query_from <= query_to:
+                    query_from += 1
+                    query_frame = 1
+                else:
+                    query_to += 1
+                    query_frame = -1
+            elif program in ("blastp", "tblastn", "rpsblast", "psiblast"):
+                query_from += 1
+                query_frame = 0
+            elif program in ("blastx", "tblastx"):
+                feature = query.features[0]
+                coded_by = feature.qualifiers["coded_by"]
+                if coded_by.startswith("complement("):
+                    assert coded_by.endswith(")")
+                    coded_by = coded_by[11:-1]
+                    strand = -1
+                else:
+                    strand = +1
+                query_id, query_from_to = coded_by.split(":")
+                query_from, query_to = query_from_to.split("..")
+                query_from = int(query_from)
+                query_to = int(query_to)
+                query_start = query_from - 1
+                query_end = query_to
+                if strand == +1:
+                    query_frame = query_start % 3 + 1
+                else:
+                    query_frame = (query_end - query_length) % -3 - 1
+            hseq = hsp[0]
+            qseq = hsp[1]
+            align_len = len(hseq)
+        else:
+            # PSIBLAST XML2
+            query_from = 0
+            query_to = 0
+            hit_from = 0
+            hit_to = 0
+            hseq = ""
+            qseq = ""
+            query_frame = None
+            hit_frame = None
+            align_len = None
+        annotations = hsp.annotations
+        bit_score = annotations["bit score"]
+        evalue = annotations["evalue"]
+        identity = annotations["identity"]
+        positive = annotations.get("positive")
+        gaps = annotations.get("gaps")
+        midline = annotations.get("midline")
+        self._start_hsp()
+        self._write_hsp_num(hsp.num)
+        self._write_hsp_bit_score(str(bit_score).encode())
+        self._write_hsp_score(hsp.score)
+        self._write_hsp_evalue(str(evalue).encode())
+        self._write_hsp_query_from(query_from)
+        self._write_hsp_query_to(query_to)
+        self._write_hsp_hit_from(hit_from)
+        self._write_hsp_hit_to(hit_to)
+        if query_frame is not None:
+            self._write_hsp_query_frame(query_frame)
+        if hit_frame is not None:
+            self._write_hsp_hit_frame(hit_frame)
+        self._write_hsp_identity(identity)
+        if positive is not None:
+            self._write_hsp_positive(positive)
+        if gaps is not None:
+            self._write_hsp_gaps(gaps)
+        if align_len is not None:
+            self._write_hsp_align_len(align_len)
+        self._write_hsp_qseq(qseq.encode())
+        self._write_hsp_hseq(hseq.encode())
+        if midline is not None:
+            self._write_hsp_midline(midline.encode())
+        self._end_hsp()
+
+    def _write_statistics(self, stat):
+        self.stream.write(b"    <Statistics>\n")
+        self._write_statistics_db_num(stat["db-num"])
+        self._write_statistics_db_len(stat["db-len"])
+        self._write_statistics_hsp_len(stat["hsp-len"])
+        self._write_statistics_eff_space(str(stat["eff-space"]).encode())
+        self._write_statistics_kappa(stat["kappa"])
+        self._write_statistics_lambda(stat["lambda"])
+        self._write_statistics_entropy(stat["entropy"])
+        self.stream.write(b"    </Statistics>\n")
+
+    def _write_definition(self):
+        return
+
+    @abstractmethod
+    def _start_blastoutput(self):
+        return
+
+    @abstractmethod
+    def _end_blastoutput(self):
+        return
+
+    @abstractmethod
+    def _write_program(self, program):
+        return
+
+    @abstractmethod
+    def _write_version(self, version):
+        return
+
+    @abstractmethod
+    def _write_reference(self, reference):
+        return
+
+    @abstractmethod
+    def _write_db(self, db):
+        return
+
+    @abstractmethod
+    def _start_param(self):
+        return
+
+    @abstractmethod
+    def _end_param(self):
+        return
+
+    @abstractmethod
+    def _start_iterations(self):
+        return
+
+    @abstractmethod
+    def _end_iterations(self):
+        return
+
+    @abstractmethod
+    def _start_iteration(self):
+        return
+
+    @abstractmethod
+    def _end_iteration(self):
+        return
+
+    @abstractmethod
+    def _write_iteration_query_id(self, query_id):
+        return
+
+    @abstractmethod
+    def _write_iteration_query_def(self, query_def):
+        return
+
+    @abstractmethod
+    def _write_iteration_query_len(self, query_len):
+        return
+
+    def _write_iteration_query_masking(self, location):
+        return
+
+    @abstractmethod
+    def _start_iteration_hits(self):
+        return
+
+    @abstractmethod
+    def _end_iteration_hits(self):
+        return
+
+    @abstractmethod
+    def _start_iteration_stat(self):
+        return
+
+    @abstractmethod
+    def _end_iteration_stat(self):
+        return
+
+    @abstractmethod
+    def _write_parameters_matrix(self, value):
+        return
+
+    @abstractmethod
+    def _write_parameters_expect(self, value):
+        return
+
+    @abstractmethod
+    def _write_parameters_include(self, value):
+        return
+
+    @abstractmethod
+    def _write_parameters_sc_match(self, value):
+        return
+
+    @abstractmethod
+    def _write_parameters_sc_mismatch(self, value):
+        return
+
+    @abstractmethod
+    def _write_parameters_gap_open(self, value):
+        return
+
+    @abstractmethod
+    def _write_parameters_gap_extend(self, value):
+        return
+
+    @abstractmethod
+    def _write_parameters_filter(self, value):
+        return
+
+    @abstractmethod
+    def _write_parameters_pattern(self, value):
+        return
+
+    @abstractmethod
+    def _write_parameters_entrez_query(self, value):
+        return
+
+    def _write_parameters_cbs(self, value):
+        return
+
+    def _write_parameters_query_gencode(self, value):
+        return
+
+    def _write_parameters_db_gencode(self, value):
+        return
+
+    def _write_parameters_bl2seq_mode(self, value):
+        return
+
+    @abstractmethod
+    def _write_statistics_db_num(self, db_num):
+        return
+
+    @abstractmethod
+    def _write_statistics_db_len(self, db_len):
+        return
+
+    @abstractmethod
+    def _write_statistics_hsp_len(self, hsp_len):
+        return
+
+    @abstractmethod
+    def _write_statistics_eff_space(self, value):
+        return
+
+    @abstractmethod
+    def _write_statistics_kappa(self, value):
+        return
+
+    @abstractmethod
+    def _write_statistics_lambda(self, value):
+        return
+
+    @abstractmethod
+    def _write_statistics_entropy(self, value):
+        return
+
+    @abstractmethod
+    def _start_iteration_hit(self):
+        return
+
+    @abstractmethod
+    def _end_iteration_hit(self):
+        return
+
+    @abstractmethod
+    def _write_hit_num(self, num):
+        return
+
+    @abstractmethod
+    def _write_hit_id(self, hit_id):
+        return
+
+    @abstractmethod
+    def _write_hit_def(self, hit_def):
+        return
+
+    @abstractmethod
+    def _write_hit_accession(self, hit_accession):
+        return
+
+    def _write_hit_taxid(self, taxid):
+        return
+
+    def _write_hit_sciname(self, sciname):
+        return
+
+    @abstractmethod
+    def _write_hit_len(self, hit_length):
+        return
+
+    @abstractmethod
+    def _start_hit_hsps(self):
+        return
+
+    @abstractmethod
+    def _end_hit_hsps(self):
+        return
+
+    @abstractmethod
+    def _start_hsp(self):
+        return
+
+    @abstractmethod
+    def _end_hsp(self):
+        return
+
+    @abstractmethod
+    def _write_hsp_num(self, num):
+        return
+
+    @abstractmethod
+    def _write_hsp_bit_score(self, bit_score):
+        return
+
+    @abstractmethod
+    def _write_hsp_score(self, score):
+        return
+
+    @abstractmethod
+    def _write_hsp_evalue(self, evalue):
+        return
+
+    @abstractmethod
+    def _write_hsp_query_from(self, query_from):
+        return
+
+    @abstractmethod
+    def _write_hsp_query_to(self, query_to):
+        return
+
+    @abstractmethod
+    def _write_hsp_hit_from(self, hit_from):
+        return
+
+    @abstractmethod
+    def _write_hsp_hit_to(self, hit_to):
+        return
+
+    @abstractmethod
+    def _write_hsp_pattern_from(self, hit_from):
+        return
+
+    @abstractmethod
+    def _write_hsp_pattern_to(self, hit_to):
+        return
+
+    @abstractmethod
+    def _write_hsp_query_frame(self, query_frame):
+        return
+
+    @abstractmethod
+    def _write_hsp_hit_frame(self, hit_frame):
+        return
+
+    @abstractmethod
+    def _write_hsp_identity(self, identity):
+        return
+
+    @abstractmethod
+    def _write_hsp_positive(self, positive):
+        return
+
+    @abstractmethod
+    def _write_hsp_gaps(self, gaps):
+        return
+
+    @abstractmethod
+    def _write_hsp_align_len(self, align_len):
+        return
+
+    @abstractmethod
+    def _write_hsp_density(self, density):
+        return
+
+    @abstractmethod
+    def _write_hsp_qseq(self, qseq):
+        return
+
+    @abstractmethod
+    def _write_hsp_hseq(self, hseq):
+        return
+
+    @abstractmethod
+    def _write_hsp_midline(self, midline):
+        return
+
+
+class XMLWriter(BaseXMLWriter):
+    """XML Writer."""
+
+    def _write_definition(self):
+        self.stream.write(
+            b"""\
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "https://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
+"""
+        )
+
+    def _start_blastoutput(self):
+        self.stream.write(b"<BlastOutput>\n")
+
+    def _end_blastoutput(self):
+        self.stream.write(b"</BlastOutput>\n")
+
+    def _write_program(self, program):
+        self.stream.write(b"<BlastOutput_program>%b</BlastOutput_program>\n" % program)
+
+    def _write_version(self, version):
+        self.stream.write(b"<BlastOutput_version>%b</BlastOutput_version>\n" % version)
+
+    def _write_reference(self, reference):
+        self.stream.write(
+            b"<BlastOutput_reference>%b</BlastOutput_reference>\n" % reference
+        )
+
+    def _write_db(self, db):
+        self.stream.write(b"<BlastOutput_db>%b</BlastOutput_db>\n" % db)
+
+    def _write_query_id(self, query_id):
+        self.stream.write(
+            b"<BlastOutput_query-ID>%b</BlastOutput_query-ID>\n" % query_id
+        )
+
+    def _write_query_def(self, query_def):
+        self.stream.write(
+            b"<BlastOutput_query-def>%b</BlastOutput_query-def>\n" % query_def
+        )
+
+    def _write_query_len(self, query_len):
+        self.stream.write(
+            b"<BlastOutput_query-len>%d</BlastOutput_query-len>\n" % query_len
+        )
+
+    def _write_query_seq(self, query_seq):
+        self.stream.write(
+            b"<BlastOutput_query-seq>%b</BlastOutput_query-seq>\n" % query_seq
+        )
+
+    def _start_param(self):
+        self.stream.write(
+            b"""\
+  <BlastOutput_param>
+    <Parameters>
+"""
+        )
+
+    def _end_param(self):
+        self.stream.write(
+            b"""\
+    </Parameters>
+  </BlastOutput_param>
+"""
+        )
+
+    def _start_iterations(self):
+        self.stream.write(b"<BlastOutput_iterations>\n")
+
+    def _end_iterations(self):
+        self.stream.write(b"</BlastOutput_iterations>\n")
+
+    def _start_mbstat(self):
+        self.stream.write(b"  <BlastOutput_mbstat>\n")
+
+    def _end_mbstat(self):
+        self.stream.write(b"  </BlastOutput_mbstat>\n")
+
+    def _start_iteration(self, record):
+        self.stream.write(b"<Iteration>\n")
+        self._write_iteration_num(record.num)
+
+    def _end_iteration(self):
+        self.stream.write(b"</Iteration>\n")
+
+    def _write_iteration_num(self, num):
+        self.stream.write(b"  <Iteration_iter-num>%d</Iteration_iter-num>\n" % num)
+
+    def _write_iteration_query_id(self, query_id):
+        self.stream.write(b"<Iteration_query-ID>%b</Iteration_query-ID>\n" % query_id)
+
+    def _write_iteration_query_def(self, query_def):
+        self.stream.write(
+            b"<Iteration_query-def>%b</Iteration_query-def>\n" % query_def
+        )
+
+    def _write_iteration_query_len(self, query_len):
+        self.stream.write(
+            b"<Iteration_query-len>%d</Iteration_query-len>\n" % query_len
+        )
+
+    def _start_iteration_hits(self):
+        self.stream.write(b"<Iteration_hits>\n")
+
+    def _end_iteration_hits(self):
+        self.stream.write(b"</Iteration_hits>\n")
+
+    def _start_iteration_stat(self):
+        self.stream.write(b"  <Iteration_stat>\n")
+
+    def _end_iteration_stat(self):
+        self.stream.write(b"  </Iteration_stat>\n")
+
+    def _write_parameters_matrix(self, value):
+        self.stream.write(b"      <Parameters_matrix>%b</Parameters_matrix>\n" % value)
+
+    def _write_parameters_expect(self, value):
+        self.stream.write(b"      <Parameters_expect>%g</Parameters_expect>\n" % value)
+
+    def _write_parameters_include(self, value):
+        self.stream.write(
+            b"      <Parameters_include>%g</Parameters_include>\n" % value
+        )
+
+    def _write_parameters_sc_match(self, value):
+        self.stream.write(
+            b"      <Parameters_sc-match>%d</Parameters_sc-match>\n" % value
+        )
+
+    def _write_parameters_sc_mismatch(self, value):
+        self.stream.write(
+            b"      <Parameters_sc-mismatch>%d</Parameters_sc-mismatch>\n" % value
+        )
+
+    def _write_parameters_gap_open(self, value):
+        self.stream.write(
+            b"      <Parameters_gap-open>%d</Parameters_gap-open>\n" % value
+        )
+
+    def _write_parameters_gap_extend(self, value):
+        self.stream.write(
+            b"      <Parameters_gap-extend>%d</Parameters_gap-extend>\n" % value
+        )
+
+    def _write_parameters_filter(self, value):
+        self.stream.write(b"      <Parameters_filter>%b</Parameters_filter>\n" % value)
+
+    def _write_parameters_pattern(self, value):
+        self.stream.write(
+            b"      <Parameters_pattern>%b</Parameters_pattern>\n" % value
+        )
+
+    def _write_parameters_entrez_query(self, value):
+        self.stream.write(
+            b"      <Parameters_entrez-query>%b</Parameters_entrez-query>\n" % value
+        )
+
+    def _write_statistics_db_num(self, db_num):
+        self.stream.write(b"      <Statistics_db-num>%d</Statistics_db-num>\n" % db_num)
+
+    def _write_statistics_db_len(self, db_len):
+        self.stream.write(b"      <Statistics_db-len>%d</Statistics_db-len>\n" % db_len)
+
+    def _write_statistics_hsp_len(self, hsp_len):
+        self.stream.write(
+            b"      <Statistics_hsp-len>%d</Statistics_hsp-len>\n" % hsp_len
+        )
+
+    def _write_statistics_eff_space(self, value):
+        self.stream.write(
+            b"      <Statistics_eff-space>%s</Statistics_eff-space>\n" % value
+        )
+
+    def _write_statistics_kappa(self, value):
+        self.stream.write(b"      <Statistics_kappa>%r</Statistics_kappa>\n" % value)
+
+    def _write_statistics_lambda(self, value):
+        self.stream.write(b"      <Statistics_lambda>%r</Statistics_lambda>\n" % value)
+
+    def _write_statistics_entropy(self, value):
+        self.stream.write(
+            b"      <Statistics_entropy>%r</Statistics_entropy>\n" % value
+        )
+
+    def _start_iteration_hit(self):
+        self.stream.write(b"<Hit>\n")
+
+    def _end_iteration_hit(self):
+        self.stream.write(b"</Hit>\n")
+
+    def _write_hit_num(self, num):
+        self.stream.write(b"  <Hit_num>%d</Hit_num>\n" % num)
+
+    def _write_hit_id(self, hit_id):
+        self.stream.write(b"  <Hit_id>%b</Hit_id>\n" % hit_id)
+
+    def _write_hit_def(self, hit_def):
+        self.stream.write(b"  <Hit_def>%b</Hit_def>\n" % hit_def)
+
+    def _write_hit_accession(self, hit_accession):
+        self.stream.write(b"  <Hit_accession>%b</Hit_accession>\n" % hit_accession)
+
+    def _write_hit_len(self, hit_length):
+        self.stream.write(b"  <Hit_len>%d</Hit_len>\n" % hit_length)
+
+    def _start_hit_hsps(self):
+        self.stream.write(b"  <Hit_hsps>\n")
+
+    def _end_hit_hsps(self):
+        self.stream.write(b"  </Hit_hsps>\n")
+
+    def _start_hsp(self):
+        self.stream.write(b"    <Hsp>\n")
+
+    def _end_hsp(self):
+        self.stream.write(b"    </Hsp>\n")
+
+    def _write_hsp_num(self, num):
+        self.stream.write(b"    <Hsp_num>%d</Hsp_num>\n" % num)
+
+    def _write_hsp_bit_score(self, bit_score):
+        self.stream.write(b"    <Hsp_bit-score>%b</Hsp_bit-score>\n" % bit_score)
+
+    def _write_hsp_score(self, score):
+        self.stream.write(b"    <Hsp_score>%d</Hsp_score>\n" % score)
+
+    def _write_hsp_evalue(self, evalue):
+        self.stream.write(b"    <Hsp_evalue>%b</Hsp_evalue>\n" % evalue)
+
+    def _write_hsp_query_from(self, query_from):
+        self.stream.write(b"     <Hsp_query-from>%d</Hsp_query-from>\n" % query_from)
+
+    def _write_hsp_query_to(self, query_to):
+        self.stream.write(b"     <Hsp_query-to>%d</Hsp_query-to>\n" % query_to)
+
+    def _write_hsp_hit_from(self, hit_from):
+        self.stream.write(b"     <Hsp_hit-from>%d</Hsp_hit-from>\n" % hit_from)
+
+    def _write_hsp_hit_to(self, hit_to):
+        self.stream.write(b"     <Hsp_hit-to>%d</Hsp_hit-to>\n" % hit_to)
+
+    def _write_hsp_pattern_from(self, pattern_from):
+        self.stream.write(
+            b"     <Hsp_pattern-from>%d</Hsp_pattern-from>\n" % pattern_from
+        )
+
+    def _write_hsp_pattern_to(self, pattern_to):
+        self.stream.write(b"     <Hsp_pattern-to>%d</Hsp_pattern-to>\n" % pattern_to)
+
+    def _write_hsp_query_frame(self, query_frame):
+        self.stream.write(b"     <Hsp_query-frame>%d</Hsp_query-frame>\n" % query_frame)
+
+    def _write_hsp_hit_frame(self, hit_frame):
+        self.stream.write(b"     <Hsp_hit-frame>%d</Hsp_hit-frame>\n" % hit_frame)
+
+    def _write_hsp_identity(self, identity):
+        self.stream.write(b"     <Hsp_identity>%d</Hsp_identity>\n" % identity)
+
+    def _write_hsp_positive(self, positive):
+        self.stream.write(b"     <Hsp_positive>%d</Hsp_positive>\n" % positive)
+
+    def _write_hsp_gaps(self, gaps):
+        self.stream.write(b"     <Hsp_gaps>%d</Hsp_gaps>\n" % gaps)
+
+    def _write_hsp_align_len(self, align_len):
+        self.stream.write(b"     <Hsp_align-len>%d</Hsp_align-len>\n" % align_len)
+
+    def _write_hsp_density(self, density):
+        self.stream.write(b"     <Hsp_density>%d</Hsp_density>\n" % density)
+
+    def _write_hsp_qseq(self, qseq):
+        self.stream.write(b"      <Hsp_qseq>%b</Hsp_qseq>\n" % qseq)
+
+    def _write_hsp_hseq(self, hseq):
+        self.stream.write(b"      <Hsp_hseq>%b</Hsp_hseq>\n" % hseq)
+
+    def _write_hsp_midline(self, midline):
+        self.stream.write(b"      <Hsp_midline>%b</Hsp_midline>\n" % midline)
+
+
+class XML2Writer(BaseXMLWriter):
+    """XML2 Writer."""
+
+    def _start_blastoutput(self):
+        self.stream.write(
+            b"""\
+<BlastXML2
+    xmlns="http://www.ncbi.nlm.nih.gov"
+    xmlns:xs="http://www.w3.org/2001/XMLSchema-instance"
+    xs:schemaLocation="http://www.ncbi.nlm.nih.gov http://www.ncbi.nlm.nih.gov/data_specs/schema_alt/NCBI_BlastOutput2.xsd"
+>
+<BlastOutput2>
+  <report>
+    <Report>
+"""
+        )
+
+    def _end_blastoutput(self):
+        self.stream.write(
+            b"""\
+    </Report>
+  </report>
+</BlastOutput2>
+</BlastXML2>
+"""
+        )
+
+    def _write_program(self, program):
+        self.stream.write(b"      <program>%b</program>\n" % program)
+
+    def _write_version(self, version):
+        self.stream.write(b"      <version>%b</version>\n" % version)
+
+    def _write_reference(self, reference):
+        self.stream.write(b"      <reference>%b</reference>\n" % reference)
+
+    def _write_db(self, db):
+        self.stream.write(
+            b"""\
+      <search-target>
+        <Target>
+          <db>%b</db>
+        </Target>
+      </search-target>
+"""
+            % db
+        )
+
+    def _start_param(self):
+        self.stream.write(
+            b"""\
+      <params>
+        <Parameters>
+"""
+        )
+
+    def _end_param(self):
+        self.stream.write(
+            b"""\
+        </Parameters>
+      </params>
+"""
+        )
+
+    def _start_iterations(self):
+        self.stream.write(
+            b"""\
+      <results>
+        <Results>
+"""
+        )
+
+    def _end_iterations(self):
+        self.stream.write(
+            b"""\
+        </Results>
+      </results>
+"""
+        )
+
+    def _start_iteration(self, record):
+        try:
+            num = record.num
+        except AttributeError:
+            pass
+        else:  # PSIBLAST
+            self.stream.write(
+                b"""\
+            <Iteration>
+"""
+            )
+            self._write_iteration_num(num)
+        self.stream.write(
+            b"""\
+      <search>
+        <Search>
+"""
+        )
+
+    def _end_iteration(self):
+        self.stream.write(
+            b"""\
+        </Search>
+      </search>
+"""
+        )
+        if self._program == "psiblast":
+            self.stream.write(
+                b"""\
+            </Iteration>
+"""
+            )
+
+    def _write_iteration_num(self, num):
+        self.stream.write(b"              <iter-num>%d</iter-num>\n" % num)
+
+    def _write_iteration_query_id(self, query_id):
+        self.stream.write(
+            b"""\
+              <query-id>%b</query-id>
+"""
+            % query_id
+        )
+
+    def _write_iteration_query_def(self, query_def):
+        self.stream.write(
+            b"""\
+              <query-title>%b</query-title>
+"""
+            % query_def
+        )
+
+    def _write_iteration_query_len(self, query_len):
+        self.stream.write(
+            b"""\
+              <query-len>%d</query-len>
+"""
+            % query_len
+        )
+
+    def _write_iteration_query_masking(self, location):
+        self.stream.write(
+            b"""\
+              <query-masking>
+                <Range>
+                  <from>%d</from>
+                  <to>%d</to>
+                </Range>
+              </query-masking>
+"""
+            % (location.start + 1, location.end)
+        )
+
+    def _start_iteration_hits(self):
+        self.stream.write(
+            b"""\
+              <hits>
+"""
+        )
+
+    def _end_iteration_hits(self):
+        self.stream.write(
+            b"""\
+              </hits>
+"""
+        )
+
+    def _start_iteration_stat(self):
+        self.stream.write(
+            b"""\
+              <stat>
+"""
+        )
+
+    def _end_iteration_stat(self):
+        self.stream.write(
+            b"""\
+              </stat>
+"""
+        )
+
+    def _write_parameters_matrix(self, value):
+        self.stream.write(
+            b"""\
+          <matrix>%b</matrix>
+"""
+            % value
+        )
+
+    def _write_parameters_expect(self, value):
+        self.stream.write(
+            b"""\
+          <expect>%g</expect>
+"""
+            % value
+        )
+
+    def _write_parameters_include(self, value):
+        self.stream.write(
+            b"""\
+          <include>%g</include>
+"""
+            % value
+        )
+
+    def _write_parameters_sc_match(self, value):
+        self.stream.write(
+            b"""\
+          <sc-match>%d</sc-match>
+"""
+            % value
+        )
+
+    def _write_parameters_sc_mismatch(self, value):
+        self.stream.write(
+            b"""\
+          <sc-mismatch>%d</sc-mismatch>
+"""
+            % value
+        )
+
+    def _write_parameters_gap_open(self, value):
+        self.stream.write(
+            b"""\
+          <gap-open>%d</gap-open>
+"""
+            % value
+        )
+
+    def _write_parameters_gap_extend(self, value):
+        self.stream.write(
+            b"""\
+          <gap-extend>%d</gap-extend>
+"""
+            % value
+        )
+
+    def _write_parameters_filter(self, value):
+        self.stream.write(
+            b"""\
+          <filter>%b</filter>
+"""
+            % value
+        )
+
+    def _write_parameters_pattern(self, value):
+        self.stream.write(
+            b"""\
+          <pattern>%b</pattern>
+"""
+            % value
+        )
+
+    def _write_parameters_entrez_query(self, value):
+        self.stream.write(
+            b"""\
+          <entrez-query>%b</entrez-query>
+"""
+            % value
+        )
+
+    def _write_parameters_cbs(self, value):
+        self.stream.write(
+            b"""\
+          <cbs>%d</cbs>
+"""
+            % value
+        )
+
+    def _write_parameters_query_gencode(self, value):
+        self.stream.write(
+            b"""\
+          <query-gencode>%d</query-gencode>
+"""
+            % value
+        )
+
+    def _write_parameters_db_gencode(self, value):
+        self.stream.write(
+            b"""\
+          <db-gencode>%d</db-gencode>
+"""
+            % value
+        )
+
+    def _write_parameters_bl2seq_mode(self, value):
+        self.stream.write(
+            b"""\
+          <bl2seq-mode>%b</bl2seq-mode>
+"""
+            % value
+        )
+
+    def _write_statistics_db_num(self, db_num):
+        self.stream.write(
+            b"""\
+                  <db-num>%d</db-num>
+"""
+            % db_num
+        )
+
+    def _write_statistics_db_len(self, db_len):
+        self.stream.write(
+            b"""\
+                  <db-len>%d</db-len>
+"""
+            % db_len
+        )
+
+    def _write_statistics_hsp_len(self, hsp_len):
+        self.stream.write(
+            b"""\
+                  <hsp-len>%d</hsp-len>
+"""
+            % hsp_len
+        )
+
+    def _write_statistics_eff_space(self, value):
+        self.stream.write(
+            b"""\
+                  <eff-space>%s</eff-space>
+"""
+            % value
+        )
+
+    def _write_statistics_kappa(self, value):
+        self.stream.write(
+            b"""\
+                  <kappa>%r</kappa>
+"""
+            % value
+        )
+
+    def _write_statistics_lambda(self, value):
+        self.stream.write(
+            b"""\
+                  <lambda>%r</lambda>
+"""
+            % value
+        )
+
+    def _write_statistics_entropy(self, value):
+        self.stream.write(
+            b"""\
+                  <entropy>%r</entropy>
+"""
+            % value
+        )
+
+    def _start_iteration_hit(self):
+        self.stream.write(
+            b"""\
+                <Hit>
+"""
+        )
+
+    def _end_iteration_hit(self):
+        self.stream.write(
+            b"""\
+                </Hit>
+"""
+        )
+
+    def _write_hit_num(self, num):
+        self.stream.write(
+            b"""\
+                  <num>%d</num>
+"""
+            % num
+        )
+
+    def _start_hit_targets(self):
+        self.stream.write(
+            b"""\
+                  <description>
+"""
+        )
+
+    def _end_hit_targets(self):
+        self.stream.write(
+            b"""\
+                  </description>
+"""
+        )
+
+    def _start_hitdescr(self):
+        self.stream.write(
+            b"""\
+                    <HitDescr>
+"""
+        )
+
+    def _end_hitdescr(self):
+        self.stream.write(
+            b"""\
+                    </HitDescr>
+"""
+        )
+
+    def _write_hit_id(self, hit_id):
+        self.stream.write(
+            b"""\
+                      <id>%b</id>
+"""
+            % hit_id
+        )
+
+    def _write_hit_def(self, hit_def):
+        self.stream.write(
+            b"""\
+                      <title>%b</title>
+"""
+            % hit_def
+        )
+
+    def _write_hit_accession(self, hit_accession):
+        self.stream.write(
+            b"""\
+                      <accession>%b</accession>
+"""
+            % hit_accession
+        )
+
+    def _write_hit_len(self, hit_length):
+        self.stream.write(
+            b"""\
+                  <len>%d</len>
+"""
+            % hit_length
+        )
+
+    def _write_hit_taxid(self, taxid):
+        self.stream.write(
+            b"""\
+                      <taxid>%d</taxid>
+"""
+            % taxid
+        )
+
+    def _write_hit_sciname(self, sciname):
+        self.stream.write(
+            b"""\
+                      <sciname>%b</sciname>
+"""
+            % sciname
+        )
+
+    def _start_hit_hsps(self):
+        self.stream.write(
+            b"""\
+                  <hsps>
+"""
+        )
+
+    def _end_hit_hsps(self):
+        self.stream.write(
+            b"""\
+                  </hsps>
+"""
+        )
+
+    def _start_hsp(self):
+        self.stream.write(
+            b"""\
+                    <Hsp>
+"""
+        )
+
+    def _end_hsp(self):
+        self.stream.write(
+            b"""\
+                    </Hsp>
+"""
+        )
+
+    def _write_hsp_num(self, num):
+        self.stream.write(
+            b"""\
+                      <num>%d</num>
+"""
+            % num
+        )
+
+    def _write_hsp_bit_score(self, bit_score):
+        self.stream.write(
+            b"""\
+                      <bit-score>%b</bit-score>
+"""
+            % bit_score
+        )
+
+    def _write_hsp_score(self, score):
+        self.stream.write(
+            b"""\
+                      <score>%d</score>
+"""
+            % score
+        )
+
+    def _write_hsp_evalue(self, evalue):
+        self.stream.write(
+            b"""\
+                      <evalue>%b</evalue>
+"""
+            % evalue
+        )
+
+    def _write_hsp_query_from(self, query_from):
+        self.stream.write(
+            b"""\
+                      <query-from>%d</query-from>
+"""
+            % query_from
+        )
+
+    def _write_hsp_query_to(self, query_to):
+        self.stream.write(
+            b"""\
+                      <query-to>%d</query-to>
+"""
+            % query_to
+        )
+
+    def _write_hsp_hit_from(self, hit_from):
+        self.stream.write(
+            b"""\
+                      <hit-from>%d</hit-from>
+"""
+            % hit_from
+        )
+
+    def _write_hsp_hit_to(self, hit_to):
+        self.stream.write(
+            b"""\
+                      <hit-to>%d</hit-to>
+"""
+            % hit_to
+        )
+
+    def _write_hsp_pattern_from(self, pattern_from):
+        self.stream.write(
+            b"""\
+                      <pattern-from>%d</pattern-from>
+"""
+            % pattern_from
+        )
+
+    def _write_hsp_pattern_to(self, pattern_to):
+        self.stream.write(
+            b"""\
+                      <pattern-to>%d</pattern-to>
+"""
+            % pattern_to
+        )
+
+    def _write_hsp_query_frame(self, query_frame):
+        self.stream.write(
+            b"""\
+                      <query-frame>%d</query-frame>
+"""
+            % query_frame
+        )
+
+    def _write_hsp_hit_frame(self, hit_frame):
+        self.stream.write(
+            b"""\
+                      <hit-frame>%d</hit-frame>
+"""
+            % hit_frame
+        )
+
+    def _write_hsp_identity(self, identity):
+        self.stream.write(
+            b"""\
+                      <identity>%d</identity>
+"""
+            % identity
+        )
+
+    def _write_hsp_positive(self, positive):
+        self.stream.write(
+            b"""\
+                      <positive>%d</positive>
+"""
+            % positive
+        )
+
+    def _write_hsp_gaps(self, gaps):
+        self.stream.write(
+            b"""\
+                      <gaps>%d</gaps>
+"""
+            % gaps
+        )
+
+    def _write_hsp_align_len(self, align_len):
+        self.stream.write(
+            b"""\
+                      <align-len>%d</align-len>
+"""
+            % align_len
+        )
+
+    def _write_hsp_density(self, density):
+        self.stream.write(
+            b"""\
+                      <density>%d</density>
+"""
+            % density
+        )
+
+    def _write_hsp_qseq(self, qseq):
+        self.stream.write(
+            b"""\
+                      <qseq>%b</qseq>
+"""
+            % qseq
+        )
+
+    def _write_hsp_hseq(self, hseq):
+        self.stream.write(
+            b"""\
+                      <hseq>%b</hseq>
+"""
+            % hseq
+        )
+
+    def _write_hsp_midline(self, midline):
+        self.stream.write(
+            b"""\
+                      <midline>%b</midline>
+"""
+            % midline
+        )

.venv_haddock/lib/python3.12/site-packages/Bio/CAPS/__init__.py

@@ -0,0 +1,130 @@
+# Copyright 2005 by Jonathan Taylor.
+# All rights reserved.
+# This code is part of the Biopython distribution and governed by its
+# license.  Please see the LICENSE file that should have been included
+# as part of this package.
+"""Cleaved amplified polymorphic sequence (CAPS) markers.
+
+A CAPS marker is a location a DifferentialCutsite as described below and a
+set of primers that can be used to visualize this.  More information can
+be found in the paper `Konieczny and Ausubel (1993)`_ (PMID 8106085).
+
+.. _`Konieczny and Ausubel (1993)`: https://doi.org/10.1046/j.1365-313X.1993.04020403.x
+
+"""
+
+from Bio.Align import MultipleSeqAlignment
+from Bio.Seq import Seq
+
+
+class DifferentialCutsite:
+    """Differential enzyme cutsite in an alignment.
+
+    A differential cutsite is a location in an alignment where an enzyme cuts
+    at least one sequence and also cannot cut at least one other sequence.
+
+    Members:
+     - start - Where it lives in the alignment.
+     - enzyme - The enzyme that causes this.
+     - cuts_in - A list of sequences (as indexes into the alignment) the
+       enzyme cuts in.
+     - blocked_in - A list of sequences (as indexes into the alignment) the
+       enzyme is blocked in.
+
+    """
+
+    def __init__(self, **kwds):
+        """Initialize a DifferentialCutsite.
+
+        Each member (as listed in the class description) should be included as a
+        keyword.
+        """
+        self.start = int(kwds["start"])
+        self.enzyme = kwds["enzyme"]
+        self.cuts_in = kwds["cuts_in"]
+        self.blocked_in = kwds["blocked_in"]
+
+
+class AlignmentHasDifferentLengthsError(Exception):
+    """Exception where sequences in alignment have different lengths."""
+
+
+class CAPSMap:
+    """A map of an alignment showing all possible dcuts.
+
+    Members:
+     - alignment - The alignment that is mapped.
+     - dcuts - A list of possible CAPS markers in the form of
+       DifferentialCutsites.
+
+    """
+
+    def __init__(self, alignment, enzymes=None):
+        """Initialize the CAPSMap.
+
+        Required:
+         - alignment - The alignment to be mapped.
+
+        Optional:
+         - enzymes - List of enzymes to be used to create the map.
+           Defaults to an empty list.
+
+        """
+        if enzymes is None:
+            enzymes = []
+        if isinstance(alignment, MultipleSeqAlignment):
+            self.sequences = [rec.seq for rec in alignment]
+            self.size = len(self.sequences)
+            self.length = len(self.sequences[0])
+            for seq in self.sequences:
+                if len(seq) != self.length:
+                    raise AlignmentHasDifferentLengthsError
+        else:  # Alignment object
+            self.sequences = [Seq(s) for s in alignment]
+            self.size, self.length = alignment.shape
+
+        self.alignment = alignment
+        self.enzymes = enzymes
+
+        # look for dcuts
+        self._digest()
+
+    def _digest_with(self, enzyme):
+        cuts = []  # list of lists, one per sequence
+        all_seq_cuts = []
+
+        # go through each sequence
+        for seq in self.sequences:
+            # grab all the cuts in the sequence
+            seq_cuts = [cut - enzyme.fst5 for cut in enzyme.search(seq)]
+            # maintain a list of all cuts in all sequences
+            all_seq_cuts.extend(seq_cuts)
+            cuts.append(seq_cuts)
+
+        # we sort the all list and remove duplicates
+        all_seq_cuts = sorted(set(all_seq_cuts))
+
+        for cut in all_seq_cuts:
+            # test for dcuts
+
+            cuts_in = []
+            blocked_in = []
+
+            for i, seq in enumerate(self.sequences):
+                if cut in cuts[i]:
+                    cuts_in.append(i)
+                else:
+                    blocked_in.append(i)
+
+            if cuts_in and blocked_in:
+                self.dcuts.append(
+                    DifferentialCutsite(
+                        start=cut, enzyme=enzyme, cuts_in=cuts_in, blocked_in=blocked_in
+                    )
+                )
+
+    def _digest(self):
+        self.dcuts = []
+
+        for enzyme in self.enzymes:
+            self._digest_with(enzyme)