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$ ruff check --fix --select=I \ --config=lint.isort.force-single-line=true \ --config=lint.isort.order-by-type=false \ BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py Using ruff version 0.4.10
94 lines
3.5 KiB
Python
94 lines
3.5 KiB
Python
# Copyright 2009 by Peter Cock. All rights reserved.
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# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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"""Unit tests for Bio.SeqIO.convert(...) function."""
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import unittest
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from io import StringIO
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from Bio import AlignIO
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class ConvertTests(unittest.TestCase):
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def check_convert(self, in_filename, in_format, out_format, molecule_type):
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# Write it out using parse/write
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msg = f"Failed converting {in_filename} from {in_format} to {out_format}"
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handle = StringIO()
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aligns = list(AlignIO.parse(in_filename, in_format, None))
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if molecule_type:
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# Applying the molecule type explicitly:
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for align in aligns:
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for record in align:
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record.annotations["molecule_type"] = molecule_type
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try:
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count = AlignIO.write(aligns, handle, out_format)
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except ValueError:
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count = 0
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# Write it out using convert passing filename and handle
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handle2 = StringIO()
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try:
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count2 = AlignIO.convert(
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in_filename, in_format, handle2, out_format, molecule_type
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)
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except ValueError:
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count2 = 0
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self.assertEqual(count, count2, msg=msg)
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self.assertEqual(handle.getvalue(), handle2.getvalue(), msg=msg)
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# Write it out using convert passing handle and handle
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handle2 = StringIO()
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try:
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with open(in_filename) as handle1:
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count2 = AlignIO.convert(
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handle1, in_format, handle2, out_format, molecule_type
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)
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except ValueError:
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count2 = 0
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self.assertEqual(count, count2, msg=msg)
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self.assertEqual(handle.getvalue(), handle2.getvalue(), msg=msg)
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# TODO - convert passing an output filename?
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def test_convert(self):
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tests = [
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("Clustalw/hedgehog.aln", "clustal", None),
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("Nexus/test_Nexus_input.nex", "nexus", None),
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("Stockholm/simple.sth", "stockholm", None),
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("GFF/multi.fna", "fasta", "DNA"),
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("Quality/example.fastq", "fastq", None),
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("Quality/example.fastq", "fastq-sanger", "DNA"),
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("Fasta/output001.m10", "fasta-m10", None),
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("IntelliGenetics/VIF_mase-pro.txt", "ig", "protein"),
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("NBRF/clustalw.pir", "pir", None),
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]
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output_formats = ["fasta"] + sorted(AlignIO._FormatToWriter)
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for filename, in_format, mol_type in tests:
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for out_format in output_formats:
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self.check_convert(filename, in_format, out_format, mol_type)
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def test_clustal_to_nexus_without_mol_type(self):
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"""Converting Clustal to NEXUS without a molecule type."""
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handle = StringIO()
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self.assertRaises(
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ValueError,
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AlignIO.convert,
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"Clustalw/protein.aln",
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"clustal",
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handle,
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"nexus",
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)
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def test_clustal_to_nexus_with_mol_type(self):
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"""Converting Clustal to NEXUS with a molecule type."""
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handle = StringIO()
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self.assertEqual(
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1,
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AlignIO.convert(
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"Clustalw/protein.aln", "clustal", handle, "nexus", "protein"
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),
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)
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self.assertIn(" datatype=protein ", handle.getvalue())
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if __name__ == "__main__":
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runner = unittest.TextTestRunner(verbosity=2)
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unittest.main(testRunner=runner)
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