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# 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
from Bio import AlignIO
class ConvertTests(unittest.TestCase):
def check_convert(self, in_filename, in_format, out_format, molecule_type):
# Write it out using parse/write
msg = "Failed converting %s from %s to %s" % (
in_filename,
in_format,
out_format,
)
handle = StringIO()
aligns = list(AlignIO.parse(in_filename, in_format, None))
if molecule_type:
# Applying the molecule type explicitly:
for align in aligns:
for record in align:
record.annotations["molecule_type"] = molecule_type
try:
count = AlignIO.write(aligns, handle, out_format)
except ValueError:
count = 0
# Write it out using convert passing filename and handle
handle2 = StringIO()
try:
count2 = AlignIO.convert(
in_filename, in_format, handle2, out_format, molecule_type
)
except ValueError:
count2 = 0
self.assertEqual(count, count2, msg=msg)
self.assertEqual(handle.getvalue(), handle2.getvalue(), msg=msg)
# Write it out using convert passing handle and handle
handle2 = StringIO()
try:
with open(in_filename) as handle1:
count2 = AlignIO.convert(
handle1, in_format, handle2, out_format, molecule_type
)
except ValueError:
count2 = 0
self.assertEqual(count, count2, msg=msg)
self.assertEqual(handle.getvalue(), handle2.getvalue(), msg=msg)
# TODO - convert passing an output filename?
def test_convert(self):
tests = [
("Clustalw/hedgehog.aln", "clustal", None),
("Nexus/test_Nexus_input.nex", "nexus", None),
("Stockholm/simple.sth", "stockholm", None),
("GFF/multi.fna", "fasta", "DNA"),
("Quality/example.fastq", "fastq", None),
("Quality/example.fastq", "fastq-sanger", "DNA"),
("Fasta/output001.m10", "fasta-m10", None),
("IntelliGenetics/VIF_mase-pro.txt", "ig", "protein"),
("NBRF/clustalw.pir", "pir", None),
]
output_formats = ["fasta"] + sorted(AlignIO._FormatToWriter)
for filename, in_format, mol_type in tests:
for out_format in output_formats:
self.check_convert(filename, in_format, out_format, mol_type)
def test_clustal_to_nexus_without_mol_type(self):
"""Converting Clustal to NEXUS without a molecule type."""
handle = StringIO()
self.assertRaises(
ValueError,
AlignIO.convert,
"Clustalw/protein.aln",
"clustal",
handle,
"nexus",
)
def test_clustal_to_nexus_with_mol_type(self):
"""Converting Clustal to NEXUS with a molecule type."""
handle = StringIO()
self.assertEqual(
1,
AlignIO.convert(
"Clustalw/protein.aln", "clustal", handle, "nexus", "protein"
),
)
self.assertIn(" datatype=protein ", handle.getvalue())
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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