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84 lines
2.7 KiB
Python
84 lines
2.7 KiB
Python
# 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 Wise module."""
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import doctest
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import sys
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import unittest
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from io import StringIO
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from Bio import Wise
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if "requires_wise" in sys.modules:
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del sys.modules["requires_wise"]
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import requires_wise # noqa: E402
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class TestWiseDryRun(unittest.TestCase):
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def setUp(self):
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self.old_stdout = sys.stdout
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sys.stdout = StringIO()
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def test_dnal(self):
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"""Call dnal, and do a trivial check on its output."""
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Wise.align(["dnal"], ("seq1.fna", "seq2.fna"), kbyte=100000, dry_run=True)
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# If test output is redirected to a file, the wrapper adds -quiet
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output = sys.stdout.getvalue().replace(" -quiet ", " ")
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self.assertTrue(
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output.startswith("dnal -kbyte 100000 seq1.fna seq2.fna"), output[:200]
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)
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def test_psw(self):
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"""Call psw, and do a trivial check on its output."""
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Wise.align(["psw"], ("seq1.faa", "seq2.faa"), dry_run=True, kbyte=4)
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# If test output is redirected to a file, the wrapper adds -quiet
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output = sys.stdout.getvalue().replace(" -quiet ", " ")
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self.assertTrue(
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output.startswith("psw -kbyte 4 seq1.faa seq2.faa"), output[:200]
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)
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def tearDown(self):
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sys.stdout = self.old_stdout
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class TestWise(unittest.TestCase):
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def test_align(self):
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"""Call dnal with optional arguments, and do a trivial check on the output."""
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temp_file = Wise.align(
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["dnal"],
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("Wise/human_114_g01_exons.fna_01", "Wise/human_114_g02_exons.fna_01"),
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kbyte=100000,
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force_type="DNA",
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quiet=True,
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)
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line = temp_file.readline().rstrip()
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if line == "Score 114":
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# Wise 2.4.1 includes a score line, even in quiet mode, ignore this
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line = temp_file.readline().rstrip()
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if (
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line
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== "ENSG00000172135 AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCC"
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):
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# This is what we expect from wise 2.2.0 (and earlier)
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pass
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elif (
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line
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== "ENSG00000172135 AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAG-TGGGGTCC"
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):
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# This is what we expect from wise 2.4.1
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pass
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else:
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# Bad!
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self.fail(line)
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if __name__ == "__main__":
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unittest_suite = unittest.TestLoader().loadTestsFromName("test_Wise")
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doctest_suite = doctest.DocTestSuite(Wise)
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suite = unittest.TestSuite((unittest_suite, doctest_suite))
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runner = unittest.TextTestRunner(sys.stdout, verbosity=2)
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runner.run(suite)
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