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# 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 Bio.AlignIO.EmbossIO import EmbossIterator
# http://emboss.sourceforge.net/docs/themes/alnformats/align.simple
with open("Emboss/alignret.txt") as handle:
simple_example = handle.read()
# http://emboss.sourceforge.net/docs/themes/alnformats/align.pair
with open("Emboss/water.txt") as handle:
pair_example = handle.read()
with open("Emboss/needle.txt") as handle:
pair_example2 = handle.read()
with open("Emboss/needle_overhang.txt") as handle:
pair_example3 = handle.read()
class TestEmbossIO(unittest.TestCase):
def test_pair_example(self):
alignments = list(EmbossIterator(StringIO(pair_example)))
self.assertEqual(len(alignments), 1)
self.assertEqual(len(alignments[0]), 2)
self.assertEqual([r.id for r in alignments[0]], ["IXI_234", "IXI_235"])
def test_simple_example(self):
alignments = list(EmbossIterator(StringIO(simple_example)))
self.assertEqual(len(alignments), 1)
self.assertEqual(len(alignments[0]), 4)
self.assertEqual(
[r.id for r in alignments[0]], ["IXI_234", "IXI_235", "IXI_236", "IXI_237"]
)
def test_pair_plus_simple(self):
alignments = list(EmbossIterator(StringIO(pair_example + simple_example)))
self.assertEqual(len(alignments), 2)
self.assertEqual(len(alignments[0]), 2)
self.assertEqual(len(alignments[1]), 4)
self.assertEqual([r.id for r in alignments[0]], ["IXI_234", "IXI_235"])
self.assertEqual(
[r.id for r in alignments[1]], ["IXI_234", "IXI_235", "IXI_236", "IXI_237"]
)
def test_pair_example2(self):
alignments = list(EmbossIterator(StringIO(pair_example2)))
self.assertEqual(len(alignments), 5)
self.assertEqual(len(alignments[0]), 2)
self.assertEqual(
[r.id for r in alignments[0]], ["ref_rec", "gi|94968718|receiver"]
)
self.assertEqual(
[r.id for r in alignments[4]], ["ref_rec", "gi|94970041|receiver"]
)
def test_pair_example3(self):
alignments = list(EmbossIterator(StringIO(pair_example3)))
self.assertEqual(len(alignments), 1)
self.assertEqual(len(alignments[0]), 2)
self.assertEqual([r.id for r in alignments[0]], ["asis", "asis"])
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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