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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 random
import sys
import unittest
import warnings
from subprocess import getoutput
from io import StringIO
from Bio import BiopythonDeprecationWarning, MissingExternalDependencyError
# check if command line tool wise is installed:
if sys.platform == "win32":
# Someone needs to find out if dnal works nicely on windows,
# and if so where it is typically installed.
raise MissingExternalDependencyError(
"Don't know how to find the Wise2 tool dnal on Windows."
)
not_found_types = ["command not found", "dnal: not found", "not recognized"]
dnal_output = getoutput("dnal")
for not_found in not_found_types:
if not_found in dnal_output:
raise MissingExternalDependencyError(
"Install Wise2 (dnal) if you want to use Bio.Wise."
)
with warnings.catch_warnings():
warnings.simplefilter("ignore", category=BiopythonDeprecationWarning)
from Bio import Wise
from Bio.Wise import psw
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)
class TestPSW(unittest.TestCase):
def test_Alignment_normal(self):
a = psw.Alignment()
a.append(psw.ColumnUnit(0, 98, "SEQUENCE"))
a.append(psw.ColumnUnit(1, 200, "SEQUENCE"))
a.append(psw.ColumnUnit(0, 98, "INSERT"))
a.append(psw.ColumnUnit(1, 201, "SEQUENCE"))
a.append(psw.ColumnUnit(0, 98, "END"))
a.append(psw.ColumnUnit(1, 201, "END"))
self.assertEqual(str(a), "[SEQUENCE(98, 200), INSERT(98, 201), END(98, 201)]")
def test_Alignment_assertions(self):
a = psw.Alignment()
self.assertRaises(AssertionError, a.append, psw.ColumnUnit(1, 200, "SEQUENCE"))
a.append(psw.ColumnUnit(0, 98, "SEQUENCE"))
self.assertRaises(AssertionError, a.append, psw.ColumnUnit(0, 200, "SEQUENCE"))
a.append(psw.ColumnUnit(1, 200, "SEQUENCE"))
self.assertRaises(AssertionError, a.append, psw.ColumnUnit(1, 200, "SEQUENCE"))
def test_AlignmentColumn_kinds(self):
ac = psw.AlignmentColumn(psw.ColumnUnit(0, random.randint(0, 9999), "SEQUENCE"))
ac.append(psw.ColumnUnit(1, random.randint(0, 9999), "INSERT"))
self.assertEqual(ac.kind, "INSERT")
ac = psw.AlignmentColumn(psw.ColumnUnit(0, random.randint(0, 9999), "INSERT"))
ac.append(psw.ColumnUnit(1, random.randint(0, 9999), "SEQUENCE"))
self.assertEqual(ac.kind, "INSERT")
ac = psw.AlignmentColumn(psw.ColumnUnit(0, random.randint(0, 9999), "SEQUENCE"))
ac.append(psw.ColumnUnit(1, random.randint(0, 9999), "SEQUENCE"))
self.assertEqual(ac.kind, "SEQUENCE")
ac = psw.AlignmentColumn(psw.ColumnUnit(0, random.randint(0, 9999), "SEQUENCE"))
ac.append(psw.ColumnUnit(1, random.randint(0, 9999), "END"))
self.assertEqual(ac.kind, "END")
def test_AlignmentColumn_repr(self):
ac = psw.AlignmentColumn(psw.ColumnUnit(0, 34, "SEQUENCE"))
ac.append(psw.ColumnUnit(1, 55, "END"))
self.assertEqual(repr(ac), "END(34, 55)")
def test_AlignmentColumn_full(self):
ac = psw.AlignmentColumn(psw.ColumnUnit(0, random.randint(0, 9999), "SEQUENCE"))
ac.append(psw.ColumnUnit(1, random.randint(0, 9999), "END"))
self.assertRaises(
psw.AlignmentColumnFullException,
ac.append,
psw.ColumnUnit(1, random.randint(0, 9999), "END"),
)
def test_AlignmentColumn_assertions(self):
self.assertRaises(
AssertionError,
psw.AlignmentColumn,
psw.ColumnUnit(1, random.randint(0, 9999), "SEQUENCE"),
)
ac = psw.AlignmentColumn(psw.ColumnUnit(0, random.randint(0, 9999), "SEQUENCE"))
self.assertRaises(
AssertionError,
ac.append,
psw.ColumnUnit(0, random.randint(0, 9999), "SEQUENCE"),
)
def test_ColumnUnit(self):
self.assertEqual(
repr(psw.ColumnUnit(0, 33, "SEQUENCE")),
"ColumnUnit(unit=0, column=33, kind='SEQUENCE')",
)
self.assertEqual(
repr(psw.ColumnUnit(1, 33, "INSERT")),
"ColumnUnit(unit=1, column=33, kind='INSERT')",
)
self.assertEqual(
repr(psw.ColumnUnit(1, 33, "END")),
"ColumnUnit(unit=1, column=33, kind='END')",
)
PARSED = (
"[SEQUENCE(39, 22), SEQUENCE(40, 23), SEQUENCE(41, 24), "
"SEQUENCE(42, 25), SEQUENCE(43, 26), SEQUENCE(44, 27), END(0, 27)]"
)
def run_tests(argv):
test_suite = testing_suite()
runner = unittest.TextTestRunner(sys.stdout, verbosity=2)
runner.run(test_suite)
def testing_suite():
"""Generate the suite of tests."""
unittest_suite = unittest.TestSuite()
test_loader = unittest.TestLoader()
test_loader.testMethodPrefix = "test_"
tests = [TestPSW]
for test in tests:
cur_suite = test_loader.loadTestsFromTestCase(test)
unittest_suite.addTest(cur_suite)
doctest_suite = doctest.DocTestSuite(psw)
big_suite = unittest.TestSuite((unittest_suite, doctest_suite))
return big_suite
if __name__ == "__main__":
unittest_suite = unittest.TestLoader().loadTestsFromName("test_Wise")
wise_doctest_suite = doctest.DocTestSuite(Wise)
psw_doctest_suite = doctest.DocTestSuite(psw)
suite = unittest.TestSuite(
(unittest_suite, wise_doctest_suite, psw_doctest_suite),
)
runner = unittest.TextTestRunner(sys.stdout, verbosity=2)
runner.run(suite)
|
