repo stringclasses 454
values | file_path stringlengths 5 201 | extension stringclasses 1
value | content stringlengths 8 509k | num_lines int64 3 16.9k | size_bytes int64 8 511k |
|---|---|---|---|---|---|
biopython | Tests/test_GenBank.py | .py | # Copyright 2001-2004 by Brad Chapman. All rights reserved.
# Revisions copyright 2007-2016 by Peter Cock. All rights reserved.
# Revisions copyright 2013 by Kai Blin. All rights reserved.
# Revisions copyright 2015-2016 by Peter Cock.
# Revisions copyright 2019 by Sergio Valqui.
# This code is part of the Biopython d... | 8,680 | 384,161 |
biopython | Tests/test_KEGG.py | .py | # Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
# Revisions copyright 2007 by Michiel de Hoon. All rights reserved.
# Revisions copyright 2017 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have be... | 208 | 8,233 |
biopython | Tests/test_prodoc.py | .py | # Copyright 1999 by Cayte Lindner. All rights reserved.
# Copyright 2009 by Michiel de Hoon. 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.
"""Tests for Bio.ExPASy.Prodoc modul... | 1,362 | 57,975 |
biopython | Tests/test_EMBL_unittest.py | .py | # Copyright 2015 by Kai Blin.
# 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.
"""Tests for EMBL module (using unittest framework)."""
import unittest
import warnings
from os import path
from Bio im... | 81 | 3,074 |
biopython | Tests/test_SwissProt.py | .py | # Copyright 2009 by Michiel de Hoon. All rights reserved.
# Revisions copyright 2010 by Peter Cock. 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.
"""Test for the SwissProt pars... | 6,789 | 341,375 |
biopython | Tests/test_prosite.py | .py | # Copyright 1999 by Cayte Lindner. 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.
"""Tests for Bio.ExPASy.Prosite module."""
import os
import unittest
from Bio.ExPASy import ... | 3,498 | 251,003 |
biopython | Tests/test_Align_emboss.py | .py | # Copyright 2008-2014 by Peter Cock. 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.
"""Tests for Bio.Align.emboss module."""
import unittest
from io import StringIO
from tempf... | 3,428 | 193,789 |
biopython | Tests/test_KEGG_online.py | .py | # Copyright 2014 by Kevin Wu.
# Copyright 2014 by Peter Cock.
# 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.
"""Tests for online functionality of the KEGG module."""
# Builti... | 278 | 10,641 |
biopython | Tests/test_PDB_StructureAlignment.py | .py | # Copyright 2017 by Francesco Gastaldello. All rights reserved.
#
# Converted by Francesco Gastaldello from an older unit test copyright 2004
# by Thomas Hamelryck.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Ple... | 228 | 8,861 |
biopython | Tests/test_PDB_binary_cif.py | .py | """
Tests for BinaryCIF code in the PDB package.
"""
import unittest
from Bio.PDB import MMCIFParser
from Bio.PDB.binary_cif import BinaryCIFParser
class TestBinaryCIFParser(unittest.TestCase):
def test_get_structure(self):
mmcif_parser = MMCIFParser(auth_chains=False)
bcif_parser = BinaryCIFPar... | 26 | 753 |
biopython | Tests/test_PDB_ResidueDepth.py | .py | # Copyright 2018 by Francesco Gastaldello. All rights reserved.
#
# Converted by Francesco Gastaldello from an older unit test copyright 2002
# by Thomas Hamelryck.
#
# Merged related test files into one, by Joao Rodrigues (2020)
#
# This file is part of the Biopython distribution and governed by your
# choice of the "... | 121 | 4,504 |
biopython | Tests/test_SearchIO_hhsuite2_text.py | .py | # Copyright 2019 by Jens Thomas. 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.
"""Tests for SearchIO HhsuiteIO parsers."""
import os
import unittest
from Bio.SearchIO import... | 548 | 21,779 |
biopython | Tests/test_MafIO_index.py | .py | # Copyright 2012 by Andrew Sczesnak. All rights reserved.
# Revisions Copyright 2017 by Blaise Li. 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.
"""Unit tests for Bio.AlignIO.... | 745 | 32,437 |
biopython | Tests/test_Align_format_matrix.py | .py | # Tests/test_format_matrix_unittest.py
"""Unit tests for Alignment.format() with substitution matrices.
These tests cover the behavior of pretty-printed alignments when a
substitution matrix (e.g., from Bio.Align.substitution_matrices) is
supplied directly or via a PairwiseAligner object.
Conventions being tested:
* ... | 154 | 5,173 |
biopython | Tests/test_SearchIO_fasta_m10.py | .py | # Copyright 2012 by Wibowo Arindrarto. 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.
"""Tests for SearchIO FastaIO parsers."""
import os
import unittest
from Bio.SearchIO im... | 3,138 | 139,531 |
biopython | Tests/test_SearchIO_blast_xml.py | .py | # Copyright 2012 by Wibowo Arindrarto. 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.
"""Tests for SearchIO BlastIO parsers."""
import os
import unittest
import warnings
from... | 4,068 | 172,918 |
biopython | Tests/test_Align_msf.py | .py | # Copyright 2021 by Michiel de Hoon. 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.
"""Tests for Bio.Align.msf module."""
import unittest
import warnings
from io import Strin... | 458 | 25,061 |
biopython | Tests/test_mmtf_online.py | .py | # Copyright 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.
"""Tests for mmtf online modu... | 36 | 1,078 |
biopython | Tests/test_PDB_MMCIFParser.py | .py | # Copyright 2012 Lenna X. Peterson (arklenna@gmail.com).
# 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.
#
... | 413 | 17,263 |
biopython | Tests/test_PDB_PDBList.py | .py | # Copyright 2016 by Jacek Smietanski. 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.
"""Testing access to th... | 260 | 9,882 |
biopython | Tests/test_PDB_Selection.py | .py | """
Run Bio.PDB.Selection tests.
Currently only tests unfold_entities.
"""
import unittest
from Bio.PDB import PDBParser
from Bio.PDB.PDBExceptions import PDBException
from Bio.PDB.Residue import Residue
from Bio.PDB.Selection import unfold_entities
def res_full_id(res: Residue):
"""Return full residue identif... | 155 | 5,947 |
biopython | Tests/test_bgzf.py | .py | # Copyright 2010-2016, 2024 by Peter Cock.
# 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.
"""Test code for working with BGZF files (used in BAM files).
See also the doctests i... | 523 | 20,642 |
biopython | Tests/common_BioSQL_online.py | .py | # 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.
"""Test storing biopython objects in a BioSQL relational db."""
import os
import platform
import tempfile
import time
import unittest
# Hide annoying ... | 129 | 4,388 |
biopython | Tests/test_SeqIO_index.py | .py | # Copyright 2009-2017 by Peter Cock. 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.
"""Unit tests for Bio.SeqIO.index(...) and index_db() functions."""
try:
import sqlite3
... | 805 | 31,453 |
biopython | Tests/test_geo.py | .py | # 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.
#
"""Tests the basic functionality of the GEO parsers."""
import unittest
from Bio import Geo
class TestGeo(unittest.TestCase):
def test_soft_e... | 4,988 | 289,276 |
biopython | Tests/test_SearchIO_blast_xml_index.py | .py | # Copyright 2012 by Wibowo Arindrarto. 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.
"""Tests for SearchIO blast-xml indexing."""
import unittest
from search_tests_common im... | 767 | 38,120 |
biopython | Tests/test_SearchIO_hmmer2_text.py | .py | # Copyright 2012 by Kai Blin.
# Revisions copyright 2012 by Wibowo Arindrarto
# 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.
"""Tests for SearchIO hmmer2 text module."""
import unittest
from os imp... | 540 | 23,046 |
biopython | Tests/test_SeqIO_SeqXML.py | .py | # Copyright 2010 by Thomas Schmitt. 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.
"""Tests for SeqIO SeqXML module."""
import unittest
from io import BytesIO
from Bio import ... | 257 | 10,375 |
biopython | Tests/test_PDB_PDBParser.py | .py | # Copyright 2009-2011 by Eric Talevich. All rights reserved.
# Revisions copyright 2009-2013 by Peter Cock. All rights reserved.
# Revisions copyright 2013 Lenna X. Peterson. All rights reserved.
# Revisions copyright 2020 Joao Rodrigues. All rights reserved.
#
# Converted by Eric Talevich from an older unit test cop... | 651 | 29,499 |
biopython | Tests/test_SCOP_Des.py | .py | # Copyright 2001 by Gavin E. Crooks. 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.
"""Unit test for Des."""
import unittest
from Bio.SCOP import Des
class DesTests(unittes... | 55 | 1,874 |
biopython | Tests/test_Consensus.py | .py | # Copyright (C) 2013 by Yanbo Ye (yeyanbo289@gmail.com)
# 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.
"""Unit tests for the Bio.Phylo.Consensus module."""
import os
import tempfile
import unittest
... | 182 | 7,916 |
biopython | Tests/test_Seq_objs.py | .py | # Copyright 2009 by Peter Cock. 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.
"""Unittests for the Seq objects."""
import array
import unittest
import warnings
from Bio impor... | 1,841 | 86,387 |
biopython | Tests/test_SearchIO_blat_psl.py | .py | # Copyright 2012 by Wibowo Arindrarto. 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.
"""Tests for SearchIO BlatIO parsers."""
import os
import unittest
from Bio.SearchIO imp... | 1,331 | 60,568 |
biopython | Tests/test_Medline.py | .py | # Copyright 2008 Michiel de Hoon
#
# 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.
"""Tests for Medline module."""
import unittest... | 369 | 20,479 |
biopython | Tests/test_SVDSuperimposer.py | .py | # Copyright 2017 by Maximilian Greil. 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.
"""Tests for SVDSuperimposer module."""
import unittest
try:
from numpy import around... | 131 | 4,294 |
biopython | Tests/test_align_substitution_matrices.py | .py | # 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.
"""Tests for Array in the Bio.Align.substitution_matrices module."""
try:
import numpy as np
except ImportError:
from Bio import MissingExtern... | 2,440 | 142,224 |
biopython | Tests/test_SearchIO_infernal_text_index.py | .py | # Copyright 2024 by Samuel Prince. 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.
"""Tests for SearchIO In... | 529 | 37,778 |
biopython | Tests/test_Enzyme.py | .py | # Copyright 1999 by Katharine Lindner. 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.
"""Tests for Enzyme module."""
import os
import unittest
from io import StringIO
from B... | 143 | 6,332 |
biopython | Tests/test_BioSQL_psycopg2_online.py | .py | # 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.
"""Run BioSQL tests using PostgreSQL."""
import unittest
import requires_internet
# Really do want "import *" to get all the test classes:
from comm... | 34 | 1,025 |
biopython | Tests/test_SearchIO_hmmer3_text.py | .py | # Copyright 2012 by Wibowo Arindrarto. 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.
"""Tests for SearchIO HmmerIO parsers."""
import os
import unittest
from Bio.SearchIO im... | 2,810 | 128,263 |
biopython | Tests/test_Entrez_online.py | .py | # Copyright 2012 by Wibowo Arindrarto. 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.
"""Tests for online Entrez access.
This file include tests for accessing the online Entre... | 270 | 9,875 |
biopython | Tests/test_Align_fasta.py | .py | # Copyright 2006-2014 by Peter Cock. All rights reserved.
# Copyright 2022 by Michiel de Hoon. 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.
"""Tests for Bio.Align.fasta modul... | 883 | 52,496 |
biopython | Tests/test_SCOP_Cla.py | .py | # Copyright 2001 by Gavin E. Crooks. All rights reserved.
# Modifications Copyright 2010 Jeffrey Finkelstein. 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.
"""Unit test for ... | 91 | 3,408 |
biopython | Tests/test_SearchIO_infernal_tab_index.py | .py | # Copyright 2024 by Samuel Prince. 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.
"""Tests for SearchIO In... | 86 | 4,467 |
biopython | Tests/test_GenomeDiagram.py | .py | # 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.
"""Tests for GenomeDiagram general functionality."""
import math
import os
import unittest
# Do we have ReportLab? Raise error if not present.
from B... | 1,278 | 47,046 |
biopython | Tests/test_NCBIXML.py | .py | # Copyright 2005 by Michiel de Hoon. 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.
"""Test the NCBI XML parser."""
import io
import os
import unittest
import warnings
from Bi... | 4,409 | 197,793 |
biopython | Tests/test_PDB_Superimposer.py | .py | # Copyright 2017 by Francesco Gastaldello. All rights reserved.
#
# Converted by Francesco Gastaldello from an older unit test copyright 2004
# by Thomas Hamelryck.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Ple... | 121 | 6,484 |
biopython | Tests/test_seq.py | .py | # 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.
"""Tests for seq module."""
import copy
import unittest
import warnings
try:
import numpy as np
except ImportError:
np = None
from Bio impor... | 1,359 | 51,821 |
biopython | Tests/test_PDB_KDTree.py | .py | # Copyright 2009-2010 by Eric Talevich. All rights reserved.
# Revisions copyright 2010 by Peter Cock. All rights reserved.
#
# Converted by Eric Talevich from an older unit test copyright 2002
# by Thomas Hamelryck.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython L... | 193 | 7,781 |
biopython | Tests/test_AlignIO_convert.py | .py | # Copyright 2009 by Peter Cock. 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.
"""Unit tests for Bio.SeqIO.convert(...) function."""
import unittest
from io import StringIO
fr... | 95 | 3,588 |
biopython | Tests/test_ExPASy.py | .py | # Copyright 2017 by Peter Cock. 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.
"""Testing Bio.ExPASy online code."""
import unittest
import requires_internet
# We want to te... | 90 | 2,960 |
biopython | Tests/test_SearchIO_hmmer3_tab.py | .py | # Copyright 2012 by Wibowo Arindrarto. 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.
"""Tests for SearchIO HmmerIO hmmer3-tab parser."""
import os
import unittest
from Bio.S... | 497 | 20,439 |
biopython | Tests/test_align.py | .py | # Copyright 2000-2001 by Brad Chapman. All rights reserved.
# Revisions copyright 2007-2003 by Peter Cock. 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.
"""Test alignment stu... | 1,113 | 75,232 |
biopython | Tests/test_PDB_PDBIO.py | .py | # Copyright 2009-2011 by Eric Talevich. All rights reserved.
# Revisions copyright 2009-2013 by Peter Cock. All rights reserved.
# Revisions copyright 2013 Lenna X. Peterson. All rights reserved.
# Revisions copyright 2020 Joao Rodrigues. All rights reserved.
#
# Converted by Eric Talevich from an older unit test cop... | 546 | 21,170 |
biopython | Tests/test_BioSQL_sqlite3.py | .py | # 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.
"""Run BioSQL tests using SQLite."""
import os
import unittest
# Really do want "import *" to get all the test classes:
from common_BioSQL import * ... | 77 | 2,602 |
biopython | Tests/test_SearchIO_exonerate_vulgar_index.py | .py | # Copyright 2012 by Wibowo Arindrarto. 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.
"""Tests for SearchIO exonerate-vulgar indexing."""
import os
import unittest
from searc... | 31 | 968 |
biopython | Tests/test_AlignIO_FastaIO.py | .py | # Copyright 2011 by Peter Cock. 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.
"""Unit tests for the Bio.AlignIO.FastaIO module."""
import unittest
from Bio.AlignIO import Fas... | 877 | 43,895 |
biopython | Tests/test_Phylo_networkx.py | .py | # Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
# 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.
"""Unit tests for Bio.Phylo functions with external dependencies."""
import unittest
#... | 39 | 1,154 |
biopython | Tests/test_PDB_MMCIFIO.py | .py | # Copyright 2009-2011 by Eric Talevich. All rights reserved.
# Revisions copyright 2009-2013 by Peter Cock. All rights reserved.
# Revisions copyright 2013 Lenna X. Peterson. All rights reserved.
# Revisions copyright 2020 Joao Rodrigues. All rights reserved.
#
# Converted by Eric Talevich from an older unit test cop... | 238 | 8,603 |
biopython | Tests/test_Align_Alignment.py | .py | # 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.
"""Tests for the Alignment class in Bio.Align."""
import os
import unittest
from io import StringIO
try:
import numpy as np
except ImportError:
... | 3,673 | 149,690 |
biopython | Tests/test_PAML_baseml.py | .py | # Copyright (C) 2011 by Brandon Invergo (b.invergo@gmail.com)
# 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.
"""Tests for PAML baseml module."""
import os
import os.path
import unittest
from Bio.Ph... | 305 | 12,295 |
biopython | Tests/test_File.py | .py | # Copyright 1999 by Jeffrey Chang. 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.
"""Tests for Bio.File module."""
import os.path
import shutil
import tempfile
import unittest
... | 127 | 4,043 |
biopython | Tests/requires_internet.py | .py | # Copyright 2002 by Jeffrey Chang. 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.
# This module attempts to detect whether the internet is available.
# To use it, import requir... | 35 | 1,212 |
biopython | Tests/test_BioSQL_psycopg2.py | .py | # 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.
"""Run BioSQL tests using PostgreSQL."""
import unittest
# Really do want "import *" to get all the test classes:
from common_BioSQL import * # noqa... | 27 | 805 |
biopython | Tests/test_SearchIO_hmmer2_text_index.py | .py | # Copyright 2012 by Wibowo Arindrarto. 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.
"""Tests for SearchIO hmmer2-text indexing."""
import os
import unittest
from search_tes... | 512 | 23,810 |
biopython | Tests/test_SearchIO_fasta_m10_index.py | .py | # Copyright 2012 by Wibowo Arindrarto. 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.
"""Tests for SearchIO fasta-m10 indexing."""
import os
import unittest
from search_tests... | 61 | 2,173 |
biopython | Tests/test_RCSBFormats.py | .py | # Copyright 2016 Joao P. Rodrigues (j.p.g.l.m.rodrigues@gmail.com).
# 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.
"""Unit tests to compare objects parsed by different struct... | 73 | 2,572 |
biopython | Tests/test_GraphicsChromosome.py | .py | # Copyright 2001 by Brad Chapman. 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.
"""Test the creation of Chromosome Graphics.
Provide tests for creating and manipulating pdf pi... | 487 | 38,715 |
biopython | Tests/test_AlignIO.py | .py | # Copyright 2008 by Peter Cock. 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.
"""Tests for AlignIO module."""
import unittest
import warnings
from io import StringIO
from Bio... | 1,417 | 60,280 |
biopython | Tests/PAML/gen_results.py | .py | # Copyright (C) 2012, 2013, 2016, 2019 by Brandon Invergo (b.invergo@gmail.com)
# 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.
"""Generate output for PAML tests."""
import os.path
import sys
VERSIO... | 181 | 6,629 |
biopython | Bio/_utils.py | .py | # Copyright 2010 by Eric Talevich. All rights reserved.
# Copyright 2012 by Wibowo Arindrarto. 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 in... | 93 | 2,918 |
biopython | Bio/Seq.py | .py | # Copyright 2000 Andrew Dalke.
# Copyright 2000-2002 Brad Chapman.
# Copyright 2004-2005, 2010 by M de Hoon.
# Copyright 2007-2023 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".
#... | 3,279 | 114,965 |
biopython | Bio/__init__.py | .py | # Copyright 1999-2003 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.
"""Collection of mod... | 148 | 5,416 |
biopython | Bio/pairwise2.py | .py | # Copyright 2002 by Jeffrey Chang.
# Copyright 2016, 2019, 2020 by Markus Piotrowski.
# 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 ... | 1,442 | 53,157 |
biopython | Bio/bgzf.py | .py | #!/usr/bin/env python
# Copyright 2010-2018 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.
... | 961 | 39,777 |
biopython | Bio/SeqFeature.py | .py | # Copyright 2000-2003 Jeff Chang.
# Copyright 2001-2008 Brad Chapman.
# Copyright 2005-2024 by Peter Cock.
# Copyright 2006-2009 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".
#... | 2,333 | 80,760 |
biopython | Bio/File.py | .py | # Copyright 1999 by Jeffrey Chang. All rights reserved.
# Copyright 2009-2018 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 inc... | 627 | 24,702 |
biopython | Bio/SeqRecord.py | .py | # Copyright 2000-2002 Andrew Dalke. All rights reserved.
# Copyright 2002-2004 Brad Chapman. All rights reserved.
# Copyright 2006-2023 by Peter Cock. All rights reserved.
# Copyright 2020 by Michael R. Crusoe
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License... | 1,545 | 61,659 |
biopython | Bio/Cluster/__init__.py | .py | # 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.
#
"""Cluster Analysis.
The Bio.Cluster provides commonly used clustering algorithms and was
designed with the application to gene expression data in mi... | 1,290 | 50,617 |
biopython | Bio/SCOP/Des.py | .py | # Copyright 2001 by Gavin E. Crooks. 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.
"""Handle the SCOP DEScri... | 90 | 3,004 |
biopython | Bio/SCOP/Cla.py | .py | # Copyright 2001 by Gavin E. Crooks. All rights reserved.
# Revisions copyright 2010 Jeffrey Finkelstein. 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 ... | 129 | 3,922 |
biopython | Bio/SCOP/__init__.py | .py | # Copyright 2001 by Gavin E. Crooks. All rights reserved.
# Modifications Copyright 2004/2005 James Casbon. All rights Reserved.
# Modifications Copyright 2010 Jeffrey Finkelstein. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement... | 912 | 31,276 |
biopython | Bio/SCOP/Residues.py | .py | # Copyright 2000 by Jeffrey Chang. All rights reserved.
# Revisions copyright 2001 by Gavin E. Crooks. 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 ... | 91 | 3,083 |
biopython | Bio/SCOP/Raf.py | .py | # Copyright 2001 by Gavin E. Crooks. 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.
"""ASTRAL RAF (Rapid Acce... | 320 | 10,317 |
biopython | Bio/SCOP/Hie.py | .py | # Copyright 2001 by Gavin E. Crooks. 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.
"""Handle the SCOP HIErar... | 107 | 2,963 |
biopython | Bio/SCOP/Dom.py | .py | # Copyright 2000 by Jeffrey Chang. All rights reserved.
# Revisions copyright 2001 by Gavin E. Crooks. 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 ... | 77 | 2,466 |
biopython | Bio/CAPS/__init__.py | .py | # 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 Dif... | 131 | 4,111 |
biopython | Bio/codonalign/codonalignment.py | .py | # Copyright 2013 by Zheng Ruan (zruan1991@gmail.com). 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... | 518 | 18,231 |
biopython | Bio/codonalign/__init__.py | .py | # Copyright 2013 by Zheng Ruan (zruan1991@gmail.com). 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... | 809 | 30,114 |
biopython | Bio/codonalign/codonseq.py | .py | # Copyright 2013 by Zheng Ruan (zruan1991@gmail.com). 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... | 1,320 | 47,934 |
biopython | Bio/UniGene/__init__.py | .py | # Copyright 2006 by Sean Davis, National Cancer Institute, NIH.
# 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
# pack... | 336 | 12,738 |
biopython | Bio/Affy/CelFile.py | .py | # Copyright 2004 by Harry Zuzan. All rights reserved.
# Copyright 2016 by Adam Kurkiewicz. 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... | 573 | 23,562 |
biopython | Bio/Pathway/__init__.py | .py | # Copyright 2001 by Tarjei Mikkelsen. 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.
"""BioPython Pathway ... | 316 | 10,800 |
biopython | Bio/Pathway/Rep/MultiGraph.py | .py | # Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
# Revisions copyright 2018 by Maximilian Greil. 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... | 197 | 6,779 |
biopython | Bio/Pathway/Rep/__init__.py | .py | # Copyright 2001 by Tarjei Mikkelsen. 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.
"""BioPython Pathway s... | 15 | 575 |
biopython | Bio/Pathway/Rep/Graph.py | .py | # Copyright 2002 by Tarjei Mikkelsen. All rights reserved.
# Revisions copyright 2018 by Maximilian Greil. 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... | 150 | 5,865 |
biopython | Bio/motifs/alignace.py | .py | # Copyright 2003 by Bartek Wilczynski. 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.
"""Parsing AlignACE ... | 69 | 2,118 |
biopython | Bio/motifs/xms.py | .py | # Copyright 2015 by Gert Hulselmans. 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.
"""Parse XMS motif files... | 107 | 3,942 |
biopython | Bio/motifs/mast.py | .py | # Copyright 2008 by Bartek Wilczynski.
# Adapted from Bio.MEME.Parser by Jason A. Hackney. 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.
"""Module for the support of Motif Alig... | 140 | 4,915 |
biopython | Bio/motifs/__init__.py | .py | # Copyright 2003-2009 by Bartek Wilczynski. All rights reserved.
# Copyright 2012-2013 by Michiel JL de Hoon. All rights reserved.
# Revisions copyright 2019 by Victor Lin. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or t... | 646 | 22,158 |
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