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#!/usr/bin/env python
# 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.
__version__ = "$Revision: 1.5 $"
import cStringIO
import doctest, unittest
import sys
if sys.modules.has_key('requires_wise'):
del sys.modules['requires_wise']
import requires_wise
from Bio import Wise
class TestWiseDryRun(unittest.TestCase):
def setUp(self):
self.old_stdout = sys.stdout
sys.stdout = cStringIO.StringIO()
def test_dnal(self):
Wise.align(["dnal"], ("seq1.fna", "seq2.fna"), kbyte=100000, dry_run=True)
self.assert_(sys.stdout.getvalue().startswith("dnal -kbyte 100000 seq1.fna seq2.fna"))
def test_psw(self):
Wise.align(["psw"], ("seq1.faa", "seq2.faa"), dry_run=True, kbyte=4)
self.assert_(sys.stdout.getvalue().startswith("psw -kbyte 4 seq1.faa seq2.faa"))
def tearDown(self):
sys.stdout = self.old_stdout
class TestWise(unittest.TestCase):
def test_align(self):
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)
self.assertEqual(temp_file.readline().rstrip(), "ENSG00000172135 AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCC")
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 = [TestWiseDryRun, TestWise]
for test in tests:
cur_suite = test_loader.loadTestsFromTestCase(test)
unittest_suite.addTest(cur_suite)
doctest_suite = doctest.DocTestSuite(Wise)
big_suite = unittest.TestSuite((unittest_suite, doctest_suite))
return big_suite
if __name__ == "__main__":
sys.exit(run_tests(sys.argv))
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