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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
129 lines
4.5 KiB
Python
129 lines
4.5 KiB
Python
# Copyright 2006-2014 by Peter Cock. All rights reserved.
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# Revisions copyright 2011 Brandon Invergo. 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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"""Tests for Bio.AlignIO.PhylipIO module."""
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import unittest
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from io import StringIO
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from Bio.AlignIO.PhylipIO import PhylipIterator
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from Bio.AlignIO.PhylipIO import PhylipWriter
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class TestPhylipIO(unittest.TestCase):
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def test_one(self):
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input_file = "Phylip/one.dat"
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with open(input_file) as handle:
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ids = []
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for alignment in PhylipIterator(handle):
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for record in alignment:
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ids.append(record.id)
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self.assertEqual(
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ids,
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[
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"V_Harveyi_",
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"B_subtilis",
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"B_subtilis",
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"YA80_HAEIN",
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"FLIY_ECOLI",
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"E_coli_Gln",
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"Deinococcu",
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"HISJ_E_COL",
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],
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)
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expected = (
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"""mkklvlslsl vlafssataa faaipqniri gtdptyapfe sknsqgelvg
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fdidlakelc krintqctfv enpldalips lkakkidaim sslsitekrq qeiaftdkly
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aadsrlvvak nsdiqptves lkgkrvgvlq gttqetfgne hwapkgieiv syqgqdniys
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dltagridaafqdevaaseg flkqpvgkdy kfggpsvkde klfgvgtgmg lrkednelre
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alnkafaemradgtyeklak kyfdfdvygg""".replace(
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" ", ""
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)
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.replace("\n", "")
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.upper()
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)
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self.assertEqual(str(record.seq).replace("-", ""), expected)
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def test_two_and_three(self):
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path = "Phylip/two.dat"
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# derived from http://atgc.lirmm.fr/phyml/usersguide.html
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with open(path) as handle:
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list2 = list(PhylipIterator(handle))
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self.assertEqual(len(list2), 1)
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self.assertEqual(len(list2[0]), 5)
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path = "Phylip/three.dat"
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with open(path) as handle:
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list3 = list(PhylipIterator(handle))
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self.assertEqual(len(list3), 1)
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self.assertEqual(len(list3[0]), 5)
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for i in range(5):
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self.assertEqual(list2[0][i].id, list3[0][i].id)
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self.assertEqual(list2[0][i].seq, list3[0][i].seq)
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def test_four(self):
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path = "Phylip/four.dat"
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# File derived from here:
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# http://evolution.genetics.washington.edu/phylip/doc/sequence.html
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# Note the lack of any white space between names 2 and 3 and their seqs.
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with open(path) as handle:
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list4 = list(PhylipIterator(handle))
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self.assertEqual(len(list4), 1)
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self.assertEqual(len(list4[0]), 5)
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def test_five(self):
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# File derived rom here:
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# http://evolution.genetics.washington.edu/phylip/doc/sequence.html
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path = "Phylip/five.dat"
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with open(path) as handle:
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self.assertRaises(ValueError, list, PhylipIterator(handle))
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def test_six(self):
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# File derived rom here:
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# http://evolution.genetics.washington.edu/phylip/doc/sequence.html
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path = "Phylip/six.dat"
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with open(path) as handle:
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list5 = list(PhylipIterator(handle))
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self.assertEqual(len(list5), 1)
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def test_concatenation(self):
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path = "Phylip/one.dat"
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with open(path) as handle:
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phylip_text = handle.read()
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path = "Phylip/three.dat"
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with open(path) as handle:
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phylip_text3 = handle.read()
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path = "Phylip/four.dat"
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with open(path) as handle:
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phylip_text4 = handle.read()
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handle = StringIO(phylip_text4 + "\n" + phylip_text4)
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self.assertEqual(len(list(PhylipIterator(handle))), 2)
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handle = StringIO(phylip_text3 + "\n" + phylip_text4 + "\n\n\n" + phylip_text)
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self.assertEqual(len(list(PhylipIterator(handle))), 3)
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def test_write_read(self):
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path = "Phylip/six.dat"
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with open(path) as handle:
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list5 = list(PhylipIterator(handle))
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handle = StringIO()
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PhylipWriter(handle).write_file(list5)
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handle.seek(0)
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list6 = list(PhylipIterator(handle))
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self.assertEqual(len(list5), len(list6))
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for a1, a2 in zip(list5, list6):
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self.assertEqual(len(a1), len(a2))
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for r1, r2 in zip(a1, a2):
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self.assertEqual(r1.id, r2.id)
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self.assertEqual(r1.seq, r2.seq)
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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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