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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
73 lines
2.7 KiB
Python
73 lines
2.7 KiB
Python
# Copyright 2008-2014 by Peter Cock. All rights reserved.
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#
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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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"""Tests for Bio.AlignIO.EmbossIO module."""
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import unittest
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from io import StringIO
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from Bio.AlignIO.EmbossIO import EmbossIterator
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# http://emboss.sourceforge.net/docs/themes/alnformats/align.simple
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with open("Emboss/alignret.txt") as handle:
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simple_example = handle.read()
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# http://emboss.sourceforge.net/docs/themes/alnformats/align.pair
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with open("Emboss/water.txt") as handle:
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pair_example = handle.read()
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with open("Emboss/needle.txt") as handle:
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pair_example2 = handle.read()
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with open("Emboss/needle_overhang.txt") as handle:
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pair_example3 = handle.read()
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class TestEmbossIO(unittest.TestCase):
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def test_pair_example(self):
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alignments = list(EmbossIterator(StringIO(pair_example)))
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self.assertEqual(len(alignments), 1)
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self.assertEqual(len(alignments[0]), 2)
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self.assertEqual([r.id for r in alignments[0]], ["IXI_234", "IXI_235"])
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def test_simple_example(self):
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alignments = list(EmbossIterator(StringIO(simple_example)))
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self.assertEqual(len(alignments), 1)
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self.assertEqual(len(alignments[0]), 4)
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self.assertEqual(
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[r.id for r in alignments[0]], ["IXI_234", "IXI_235", "IXI_236", "IXI_237"]
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)
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def test_pair_plus_simple(self):
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alignments = list(EmbossIterator(StringIO(pair_example + simple_example)))
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self.assertEqual(len(alignments), 2)
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self.assertEqual(len(alignments[0]), 2)
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self.assertEqual(len(alignments[1]), 4)
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self.assertEqual([r.id for r in alignments[0]], ["IXI_234", "IXI_235"])
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self.assertEqual(
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[r.id for r in alignments[1]], ["IXI_234", "IXI_235", "IXI_236", "IXI_237"]
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)
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def test_pair_example2(self):
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alignments = list(EmbossIterator(StringIO(pair_example2)))
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self.assertEqual(len(alignments), 5)
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self.assertEqual(len(alignments[0]), 2)
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self.assertEqual(
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[r.id for r in alignments[0]], ["ref_rec", "gi|94968718|receiver"]
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)
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self.assertEqual(
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[r.id for r in alignments[4]], ["ref_rec", "gi|94970041|receiver"]
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)
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def test_pair_example3(self):
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alignments = list(EmbossIterator(StringIO(pair_example3)))
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self.assertEqual(len(alignments), 1)
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self.assertEqual(len(alignments[0]), 2)
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self.assertEqual([r.id for r in alignments[0]], ["asis", "asis"])
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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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