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_Affy.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 Affy module."""
import os
import struct
import unittest
try:
import numpy.testing
from numpy import array
except ImportError:
... | 342 | 13,848 |
biopython | Tests/test_Align_nexus.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.nexus module."""
import unittest
from io import StringIO
from tempfi... | 417 | 18,820 |
biopython | Tests/test_Cluster.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 Cluster module."""
import unittest
try:
import numpy as np
except ImportError:
from Bio import MissingPythonDependencyError
... | 3,116 | 111,233 |
biopython | Tests/test_Align_exonerate.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 Bio.Align Exonerate parsers."""
import io
import os
import unittest
from tem... | 8,689 | 384,690 |
biopython | Tests/test_PDB_vectors.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 the vector code ... | 308 | 12,294 |
biopython | Tests/test_Phylo_matplotlib.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
fr... | 101 | 3,656 |
biopython | Tests/test_Blast_Record.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 for Blast records."""
import unittest
from Bio.Blast.NCBIXML import HSP
class TestHsp(unittest.TestCase):
def test_str(self):
#... | 39 | 1,063 |
biopython | Tests/test_PDB_Disordered.py | .py | # Revisions copyright 2020 Joao Rodrigues. 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.
"""Unit tests for... | 219 | 7,550 |
biopython | Tests/test_SCOP_Scop.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 ... | 155 | 5,423 |
biopython | Tests/pairwise2_testCases.py | .py | #!/usr/bin/env python
# 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 pairwise2 module.
Put new test case here, the classes here will be imported and run
as TestCases in ``test_pairwis... | 918 | 27,399 |
biopython | Tests/test_PDB_NACCESS.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 2013 Gokcen Eraslan. All rights reserved.
# Revisions copyright 2020 Joao Rodrigues. All rights rese... | 73 | 2,417 |
biopython | Tests/test_NMR.py | .py | # Copyright 2019 by Sergio Valqui. All rights reserved.
# Adapted from Doc/examples/nmr/simplepredict.py by Robert Bussell, Jr
# 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 hav... | 130 | 5,068 |
biopython | Tests/test_PDB_internal_coords.py | .py | # Copyright 2020-2022 by Robert T. Miller. 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.
"""Unit tests for ... | 665 | 27,426 |
biopython | Tests/test_Chi2.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 Chi2 module."""
import unittest
from Bio.Phylo.PAML import chi2
class Mod... | 32 | 1,160 |
biopython | Tests/test_Phylo_CDAO.py | .py | # Copyright (C) 2013 by Ben Morris (ben@bendmorris.com)
# based on code 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 the CDAO and CDAOIO... | 108 | 3,270 |
biopython | Tests/test_PopGen_GenePop_nodepend.py | .py | # Copyright 2007 by Tiago Antao <tiagoantao@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.
"""Tests for PopGen GenePop nodepend module."""
import os
import tempfi... | 215 | 7,420 |
biopython | Tests/test_PDB_SMCRA.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... | 605 | 21,602 |
biopython | Tests/test_SearchIO_blast_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 BlastIO parsers."""
import os
import unittest
from Bio.SearchIO im... | 985 | 40,380 |
biopython | Tests/test_NCBI_qblast.py | .py | # Copyright 2008-2016 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 online code for fetching NCBI qblast.
Uses Bio.Blast.NCBIWWW.qblast() to run some... | 388 | 16,589 |
biopython | Tests/test_UniProt.py | .py | """Tests for the UniProt module."""
import unittest
from itertools import islice
import requires_internet
from Bio import UniProt
requires_internet.check()
class SearchTests(unittest.TestCase):
def test_search_result_count(self):
query = "(organism_id:2697049) AND (reviewed:true)"
results = Un... | 89 | 3,384 |
biopython | Tests/test_Ace.py | .py | # Copyright 2004 by Frank Kauff. All rights reserved.
# Revisions copyright 2008-2013 by Peter Cock. All rights reserved.
# Revisions copyright 2009-2009 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 ha... | 2,180 | 121,943 |
biopython | Tests/test_CodonTable.py | .py | # Copyright 2008 by Peter Cock.
# Revision copyright 2017 by Markus Piotrowski.
# 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 CodonTable module."""
import unitt... | 822 | 35,447 |
biopython | Tests/test_SeqIO_QualityIO.py | .py | # Copyright 2009-2013 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.
"""Additional unit tests for Bio.SeqIO.QualityIO (covering FASTQ and QUAL)."""
import os
imp... | 1,121 | 43,542 |
biopython | Tests/test_ExPASy_offline.py | .py | # Copyright 2025 by Timothy Dennis. 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 offline code."""
import io
import unittest
from Bio.ExPASy import ScanP... | 23 | 704 |
biopython | Tests/common_BioSQL.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.
"""Dealing with storage of biopython objects in a BioSQL relational db."""
import configparser
import os
import platform
import tempfile
import time
im... | 1,680 | 66,220 |
biopython | Tests/test_PDB_MMCIF2Dict.py | .py | # Copyright 2017 by Francesco Gastaldello. All rights reserved.
# Revisions copyright 2017 by Peter Cock. All rights reserved.
#
# Converted by Francesco Gastaldello 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 "B... | 353 | 17,681 |
biopython | Tests/test_mmtf.py | .py | # Copyright 2016 by Anthony Bradley. All rights reserved.
# Revisions copyright 2017 by Peter Cock. All rights reserved.
# Revisions copyright 2019 by Joe Greener. 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-C... | 247 | 10,676 |
biopython | Tests/test_Align_phylip.py | .py | # Copyright 2006-2014 by Peter Cock. All rights reserved.
# Revisions copyright 2011 Brandon Invergo. 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.phyli... | 1,099 | 56,435 |
biopython | Tests/test_SearchIO_hmmer3_tab_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 hmmer3-tab indexing."""
import os
import unittest
from search_test... | 80 | 4,534 |
biopython | Tests/test_motifs.py | .py | # Copyright 2008 by Bartek Wilczynski. All rights reserved.
# Revisions copyright 2019 by Victor Lin.
# Adapted from test_Mymodule.py by Jeff Chang.
# 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 LICEN... | 5,163 | 260,094 |
biopython | Tests/test_PDB_Exposure.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.
#
# Converted by Eric Talevich from an older unit test copyright 2002
# by Thomas Hamelryck.
#
# Merged related test files... | 128 | 5,228 |
biopython | Tests/test_phenotype.py | .py | # Copyright 2014-2016 Marco Galardini. All rights reserved.
# Adapted from test_Mymodule.py by Jeff Chang
#
# 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... | 334 | 13,153 |
biopython | Tests/test_SearchIO_hmmer3_domtab.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-domtab parsers."""
import os
import unittest
from B... | 648 | 27,800 |
biopython | Tests/test_SeqIO_Gck.py | .py | # Copyright 2019 Damien Goutte-Gattat. 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 the SeqI... | 96 | 3,547 |
biopython | Tests/test_Entrez.py | .py | # Copyright 2015 by Carlos Pena. 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.
"""Offline tests for two Entrez features.
(1) the URL construction of NCBI's Entrez services.
(... | 459 | 16,226 |
biopython | Tests/test_Restriction.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.
#
"""Testing code for Restriction enzyme classes of Biopython."""
import unittest
from Bio import BiopythonWarning
from Bio.Restriction import AanI
f... | 631 | 25,561 |
biopython | Tests/test_SeqIO_features.py | .py | # Copyright 2009-2016 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.
"""SeqFeature related tests for SeqRecord objects from Bio.SeqIO.
Initially this takes match... | 1,376 | 60,237 |
biopython | Tests/test_EmbossPrimer.py | .py | # Copyright 2001 by Brad Chapman. All rights reserved.
# Revisions copyright 2008-2009 by Michiel de Hoon. All rights reserved.
# Revisions copyright 2010-2011 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 h... | 198 | 9,309 |
biopython | Tests/test_GraphicsBitmaps.py | .py | # Copyright 2001 by Brad Chapman. All rights reserved.
# 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.
"""Test for bitmap output via ReportLab (... | 138 | 4,440 |
biopython | Tests/test_SCOP_Astral.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 Astral."""
import unittest
from Bio.SCOP import Astral
from Bio.SCOP impo... | 61 | 2,265 |
biopython | Tests/test_SearchIO_exonerate.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 ExonerateIO parsers."""
import os
import unittest
from Bio.SearchI... | 2,676 | 111,022 |
biopython | Tests/test_PDB_parse_pdb_header.py | .py | # Copyright 2017 by Bernhard Thiel. All rights reserved.
# Revisions copyright 2024 James Krieger.
# 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... | 198 | 8,512 |
biopython | Tests/test_SeqIO_TwoBitIO.py | .py | """Tests for SeqIO TwoBitIO module."""
import unittest
from Bio import SeqIO
from Bio.Seq import MutableSeq
from Bio.Seq import Seq
from Bio.Seq import UndefinedSequenceError
from Bio.SeqRecord import SeqRecord
class Parsing(unittest.TestCase):
"""Test parsing 2bit files."""
def setUp(self):
path =... | 527 | 22,096 |
biopython | Tests/test_UniProt_GOA.py | .py | # Copyright 2019-2020 by Sergio Valqui. 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.
"""Unit tests for the... | 183 | 7,614 |
biopython | Tests/test_BioSQL_mysql_connector.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 MySQL."""
import unittest
# Really do want "import *" to get all the test classes:
from common_BioSQL import * # noqa: F40... | 28 | 827 |
biopython | Tests/test_SearchIO_infernal_tab.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... | 507 | 20,153 |
biopython | Tests/test_SearchIO_write.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 writing."""
import os
import unittest
from search_tests_common imp... | 223 | 9,439 |
biopython | Tests/test_TreeConstruction.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.TreeConstruction module."""
import os
import tempfile
import un... | 509 | 20,128 |
biopython | Tests/test_AlignIO_PhylipIO.py | .py | # Copyright 2006-2014 by Peter Cock. All rights reserved.
# Revisions copyright 2011 Brandon Invergo. 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.AlignIO.Phy... | 130 | 4,584 |
biopython | Tests/test_pairwise2_no_C.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 pairwise2 module using the pure Python fallback functions.
This test file imports the TestCases from ``pairwise2_testCases.py``.
If you w... | 33 | 1,150 |
biopython | Tests/test_PhyloXML.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 the PhyloXML and PhyloXMLIO modules."""
import os
import platform # ... | 826 | 31,387 |
biopython | Tests/test_TogoWS.py | .py | # Copyright 2010-2013 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.
"""Testing Bio.TogoWS o... | 621 | 21,929 |
biopython | Tests/test_SeqIO.py | .py | # Copyright 2007-2016,2020 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 SeqIO module."""
import copy
import gzip
import unittest
import warnings
f... | 5,912 | 235,592 |
biopython | Tests/test_KGML_nographics.py | .py | # Copyright 2013 by Leighton Pritchard. 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 general functionality of the KGML parser and pathway model."""
# Builtins
i... | 132 | 4,783 |
biopython | Tests/test_BioSQL_mysql_connector_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 MySQL."""
import unittest
import requires_internet
# Really do want "import *" to get all the test classes:
from common_Bi... | 35 | 1,031 |
biopython | Tests/test_AlignIO_MauveIO.py | .py | # Copyright 2006-2014 by Peter Cock. All rights reserved.
# Revisions copyright 2011 Brandon Invergo. 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.AlignIO.Mau... | 122 | 5,255 |
biopython | Tests/test_Tutorial.py | .py | # Copyright 2011-2023 by Peter Cock. All rights reserved.
# Revisions copyright 2019 by Anil Tuncel. 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 script looks for e... | 309 | 10,038 |
biopython | Tests/test_Align_bigbed.py | .py | # 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 Align.bigbed module."""
import os
import sys
import tempfile
import unittest
fro... | 8,016 | 322,340 |
biopython | Tests/test_PAML_tools.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 tools module."""
import os
import sys
import unittest
from Bio import ... | 141 | 4,898 |
biopython | Tests/test_SeqIO_NibIO.py | .py | """Tests for SeqIO NibIO module."""
import unittest
from io import BytesIO
from Bio import SeqIO
class TestNibReaderWriter(unittest.TestCase):
def test_read_even(self):
with open("Nib/test_even.fa") as handle:
record = SeqIO.read(handle, "fasta")
sequence = record.seq
with op... | 62 | 2,068 |
biopython | Tests/test_SearchIO_model.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 objects.
Tests the methods and behaviors of QueryResult, Hit, and H... | 1,598 | 67,810 |
biopython | Tests/test_SeqFeature.py | .py | # Copyright 2001 by Brad Chapman. All rights reserved.
# Revisions copyright 2011-2013 by Peter Cock. All rights reserved.
# Copyright 2015-2017 by Kai Blin. 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 include... | 383 | 15,441 |
biopython | Tests/test_PDB_alphafold_db.py | .py | """Tests for the alphafold_db module."""
import os
import unittest
import requires_internet
from Bio.PDB import alphafold_db
requires_internet.check()
class AlphafoldDBTests(unittest.TestCase):
def test_get_predictions(self):
predictions = alphafold_db.get_predictions("P00520")
for prediction... | 27 | 768 |
biopython | Tests/test_PAML_codeml.py | .py | # Copyright (C) 2011, 2015, 2016 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 codeml module."""
import itertools
import os
import os.path... | 578 | 26,828 |
biopython | Tests/test_pairwise2.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 pairwise2 module using the default C functions.
This test file imports the TestCases from ``pairwise2_testCases.py``.
If you want to add ... | 29 | 844 |
biopython | Tests/test_SCOP_Raf.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.
#
"""Unit test for Raf."""
import unittest
from io import StringIO
from Bio.SCOP import Raf
class RafTests(unittest.TestCase):
rafLine = "101m_... | 101 | 4,199 |
biopython | Tests/test_AlignIO_EmbossIO.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.AlignIO.EmbossIO module."""
import unittest
from io import StringIO
from... | 74 | 2,726 |
biopython | Tests/test_SeqIO_Gfa.py | .py | """Tests for SeqIO GFA module."""
import unittest
from Bio import BiopythonWarning
from Bio import SeqIO
class TestRead(unittest.TestCase):
def test_read_GFA1(self):
"""Test parsing valid GFA 1.x files."""
records = list(SeqIO.parse("GFA/seq.gfa", "gfa1"))
self.assertEqual(len(records), ... | 79 | 3,339 |
biopython | Tests/test_Align_chain.py | .py | # Copyright 2023 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 Align.chain module."""
import unittest
from io import StringIO
from tempfile imp... | 7,282 | 290,594 |
biopython | Tests/test_Compass.py | .py | # Copyright 2009 by James Casbon. All rights reserved.
# Revisions copyright 2009-2010 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 parsing C... | 104 | 4,002 |
biopython | Tests/test_SCOP_Dom.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 Dom.
This test requires the mini DOM file 'testDom.txt'
"""
import unitte... | 55 | 1,763 |
biopython | Tests/test_Nexus.py | .py | # Copyright 2005 by Iddo Friedberg. All rights reserved.
# Revisions copyright 2006-2013,2017 by Peter Cock. All rights reserved.
# Revisions copyright 2008 by Frank Kauff. All rights reserved.
# Revisions copyright 2009 by Michiel de Hoon. All rights reserved.
# Revisions copyright 2015 by Joe Cora. All rights reserv... | 1,608 | 62,903 |
biopython | Tests/test_SeqIO_SffIO.py | .py | # Copyright 2012 by Jeff Hussmann. All rights reserved.
# Revisions copyright 2013-2016 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 SffIO module... | 579 | 21,773 |
biopython | Tests/test_SearchIO_infernal_text.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 Inf... | 1,056 | 45,668 |
biopython | Tests/test_BioSQL_MySQLdb.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 MySQL."""
import unittest
# Really do want "import *" to get all the test classes:
from common_BioSQL import * # noqa: F40... | 28 | 810 |
biopython | Tests/test_SeqIO_Insdc.py | .py | # Copyright 2013 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 SeqIO Insdc module."""
import unittest
import warnings
from io import StringIO
from... | 156 | 5,767 |
biopython | Tests/test_ColorSpiral.py | .py | # Copyright 2013 by Leighton Pritchard. 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 general functionality of the ColorSpiral utility."""
# Builtins
import colo... | 130 | 4,287 |
biopython | Tests/test_SeqIO_FastaIO.py | .py | # Copyright 2009-2013 by Peter Cock. All rights reserved.
# Parts 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.SeqIO.FastaIO... | 234 | 8,999 |
biopython | Tests/test_SearchIO_interproscan_xml.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 SearchIO InterproscanIO parsers."""
import os
import unittest
from Bio.SearchIO import parse
# test case files are in the Blast directo... | 84 | 2,678 |
biopython | Tests/test_phenotype_fit.py | .py | # Copyright 2014-2016 Marco Galardini. All rights reserved.
# Adapted from test_Mymodule.py by Jeff Chang
#
# 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... | 78 | 2,482 |
biopython | Tests/test_SearchIO_blast_tab_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-tab indexing."""
import unittest
from search_tests_common im... | 175 | 9,732 |
biopython | Tests/test_ProtParam.py | .py | # Copyright 2003-2004 by Iddo Friedberg. All rights reserved.
# Revisions copyright 2008-2010 by Peter Cock. All rights reserved.
# Revisions copyright 2012 by Matt Fenwick. All rights reserved.
# Revisions copyright 2012 by Kai Blin. All rights reserved.
# This code is part of the Biopython distribution and governed ... | 260 | 12,918 |
biopython | Tests/test_SearchIO_blat_psl_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 blat-psl indexing."""
import os
import unittest
from search_tests_... | 71 | 2,609 |
biopython | Tests/test_BioSQL_sqlite3_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 SQLite."""
import unittest
import requires_internet
# Really do want "import *" to get all the test classes:
from common_B... | 39 | 1,076 |
biopython | Tests/test_PDB_Dice.py | .py | # Copyright 2019 by Sergio Valqui. 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.
"""Unit tests for the Bio.PD... | 61 | 2,184 |
biopython | Tests/test_PDB_Polypeptide.py | .py | # Copyright 2017 by Francesco Gastaldello. All rights reserved.
# Revisions copyright 2020 Joao Rodrigues. 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 "B... | 190 | 6,814 |
biopython | Tests/test_PDB_DSSP.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... | 276 | 10,937 |
biopython | Tests/test_SearchIO_exonerate_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 exonerate-text indexing."""
import os
import unittest
from search_... | 31 | 955 |
biopython | Tests/test_SearchIO_hmmer3_domtab_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 hmmer3-domtab indexing."""
import os
import unittest
from search_t... | 84 | 5,490 |
biopython | Tests/test_KGML_graphics.py | .py | # Copyright 2013, 2014 by Leighton Pritchard. 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 general functionality of the KGML modules."""
# Builtins
import os
im... | 194 | 7,785 |
biopython | Tests/test_PDB_QCPSuperimposer.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 QCPSuperimposer module."""
import unittest
try:
import numpy as np
excep... | 186 | 6,040 |
biopython | Tests/test_Pathway.py | .py | # Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
# Revisions copyright 2018 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.
# python unittest fram... | 209 | 8,512 |
biopython | Tests/test_cellosaurus.py | .py | # Copyright 2016 by Stephen Marshall. 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 cellosaurus module."""
import unittest
from Bio.ExPASy import cellosaurus
... | 208 | 10,765 |
biopython | Tests/test_UniGene.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 UniGene module."""
import unittest
from Bio import UniGene
class TestUniGene(unittest.TestCase):
def test_parse(self):
# S... | 1,214 | 74,974 |
biopython | Tests/test_SeqUtils.py | .py | # Copyright 2003 by Iddo Friedberg. All rights reserved.
# Copyright 2007-2009 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.
"""Tests for SeqUtils module."""
i... | 433 | 19,362 |
biopython | Tests/test_Entrez_parser.py | .py | # Copyright 2008-2010 by Michiel de Hoon. All rights reserved.
# Revisions copyright 2009-2016 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 code for ... | 8,917 | 422,732 |
biopython | Tests/test_motifs_online.py | .py | # Copyright 2015 by Peter Cock. All rights reserved.
# Copyright 2015 by Antony Lee. 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 p... | 58 | 1,709 |
biopython | Tests/test_Align_stockholm.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 Align.stockholm module."""
import unittest
from io import StringIO
from Bio import A... | 7,693 | 506,847 |
biopython | Tests/test_Align_sam.py | .py | # 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 Align.sam module."""
import unittest
from io import StringIO
from Bio import Al... | 9,632 | 392,416 |
biopython | Tests/run_tests.py | .py | #!/usr/bin/env python
# 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 a set of PyUnit-based regression tests.
This will find all modules whose name is "test_*.py" in the test
directory, and ru... | 347 | 12,057 |
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