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