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119 lines
4.1 KiB
Python
119 lines
4.1 KiB
Python
"""Tests for parsing Compass output.
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"""
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import os
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import sys
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import unittest
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from Bio import Compass
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def run_tests(argv):
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test_suite = testing_suite()
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runner = unittest.TextTestRunner(sys.stdout, verbosity = 2)
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runner.run(test_suite)
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def testing_suite():
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"""Generate the suite of tests.
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"""
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test_suite = unittest.TestSuite()
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test_loader = unittest.TestLoader()
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test_loader.testMethodPrefix = 'test'
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tests = [CompassTest]
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for test in tests:
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cur_suite = test_loader.loadTestsFromTestCase(test)
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test_suite.addTest(cur_suite)
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return test_suite
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class CompassTest(unittest.TestCase):
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def setUp(self):
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file_dir = os.path.join("Compass")
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self.test_files = [
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os.path.join(file_dir, "comtest1"),
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os.path.join(file_dir, "comtest2")]
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def testCompassScanAndConsume(self):
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cons = Compass._Consumer()
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scan = Compass._Scanner()
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scan.feed(open(self.test_files[0]), cons)
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com_record = cons.data
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self.assertEquals("60456.blo.gz.aln", com_record.query)
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self.assertEquals("60456.blo.gz.aln", com_record.hit)
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self.assertEquals(0.5, com_record.gap_threshold)
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self.assertEquals(388, com_record.query_length)
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self.assertEquals(386, com_record.query_filtered_length)
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self.assertEquals(388, com_record.hit_length)
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self.assertEquals(386, com_record.hit_filtered_length)
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self.assertEquals(399, com_record.query_nseqs)
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self.assertEquals(12.972, com_record.query_neffseqs)
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self.assertEquals(399, com_record.hit_nseqs)
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self.assertEquals(12.972, com_record.hit_neffseqs)
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self.assertEquals(2759, com_record.sw_score)
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self.assertEquals(float("0.00e+00"), com_record.evalue)
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def testCompassParser(self):
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parser = Compass.RecordParser()
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com_record = parser.parse(open(self.test_files[0]))
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self.assertEquals("60456.blo.gz.aln", com_record.query)
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def testCompassIteratorEasy(self):
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it = Compass.Iterator(open(self.test_files[0]))
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com_record = it.next()
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self.assertEquals("60456.blo.gz.aln", com_record.query)
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com_record = it.next()
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self.assertEquals(None, com_record)
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pass
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def testCompassIteratorHard(self):
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it = Compass.Iterator(open(self.test_files[1]))
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com_record = it.next()
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self.assertEquals("allscop//14982.blo.gz.aln", com_record.hit)
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self.assertEquals(float('1.01e+03'), com_record.evalue)
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com_record = it.next()
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self.assertEquals("allscop//14983.blo.gz.aln", com_record.hit)
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self.assertEquals(float('1.01e+03'), com_record.evalue)
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com_record = it.next()
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self.assertEquals("allscop//14984.blo.gz.aln", com_record.hit)
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self.assertEquals(float('5.75e+02'), com_record.evalue)
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def testAlignmentParsingOne(self):
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it = Compass.Iterator(open(self.test_files[1]))
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com_record = it.next()
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self.assertEquals(178, com_record.query_start)
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self.assertEquals("KKDLEEIAD", com_record.query_aln)
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self.assertEquals(9, com_record.hit_start)
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self.assertEquals("QAAVQAVTA", com_record.hit_aln)
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self.assertEquals("++ ++++++", com_record.positives)
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com_record = it.next()
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com_record = it.next()
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self.assertEquals(371, com_record.query_start)
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self.assertEquals("LEEAMDRMER~~~V", com_record.query_aln)
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self.assertEquals(76, com_record.hit_start)
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self.assertEquals("LQNFIDQLDNpddL", com_record.hit_aln)
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self.assertEquals("+ ++++ + + +", com_record.positives)
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def testAlignmentParsingTwo(self):
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it = Compass.Iterator(open(self.test_files[0]))
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com_record = it.next()
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self.assertEquals(2, com_record.query_start)
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self.assertEquals(2, com_record.hit_start)
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self.assertEquals("LKERKL", com_record.hit_aln[-6:])
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if __name__ == "__main__":
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sys.exit(run_tests(sys.argv))
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