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104 lines
3.9 KiB
Python
104 lines
3.9 KiB
Python
# Copyright 2009 by James Casbon. All rights reserved.
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# Revisions copyright 2009-2010 by Michiel de Hoon. All rights reserved.
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# 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 parsing Compass output."""
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import os
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import unittest
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from Bio import Compass
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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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]
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def testCompassScanAndConsume(self):
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with open(self.test_files[0]) as handle:
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com_record = Compass.read(handle)
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self.assertEqual("60456.blo.gz.aln", com_record.query)
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self.assertEqual("60456.blo.gz.aln", com_record.hit)
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self.assertAlmostEqual(0.5, com_record.gap_threshold)
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self.assertEqual(388, com_record.query_length)
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self.assertEqual(386, com_record.query_filtered_length)
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self.assertEqual(388, com_record.hit_length)
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self.assertEqual(386, com_record.hit_filtered_length)
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self.assertEqual(399, com_record.query_nseqs)
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self.assertAlmostEqual(12.972, com_record.query_neffseqs)
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self.assertEqual(399, com_record.hit_nseqs)
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self.assertAlmostEqual(12.972, com_record.hit_neffseqs)
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self.assertEqual(2759, com_record.sw_score)
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self.assertAlmostEqual(0.0, com_record.evalue)
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def testCompassParser(self):
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with open(self.test_files[0]) as handle:
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com_record = Compass.read(handle)
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self.assertEqual("60456.blo.gz.aln", com_record.query)
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def testCompassIteratorEasy(self):
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with open(self.test_files[0]) as handle:
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records = Compass.parse(handle)
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com_record = next(records)
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self.assertEqual("60456.blo.gz.aln", com_record.query)
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self.assertRaises(StopIteration, next, records)
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def testCompassIteratorHard(self):
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with open(self.test_files[1]) as handle:
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records = Compass.parse(handle)
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com_record = next(records)
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self.assertEqual("allscop//14982.blo.gz.aln", com_record.hit)
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self.assertAlmostEqual(1.01e03, com_record.evalue)
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com_record = next(records)
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self.assertEqual("allscop//14983.blo.gz.aln", com_record.hit)
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self.assertAlmostEqual(1.01e03, com_record.evalue)
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com_record = next(records)
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self.assertEqual("allscop//14984.blo.gz.aln", com_record.hit)
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self.assertAlmostEqual(5.75e02, com_record.evalue)
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def testAlignmentParsingOne(self):
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with open(self.test_files[1]) as handle:
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records = Compass.parse(handle)
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com_record = next(records)
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self.assertEqual(178, com_record.query_start)
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self.assertEqual("KKDLEEIAD", com_record.query_aln)
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self.assertEqual(9, com_record.hit_start)
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self.assertEqual("QAAVQAVTA", com_record.hit_aln)
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self.assertEqual("++ ++++++", com_record.positives)
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com_record = next(records)
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com_record = next(records)
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self.assertEqual(371, com_record.query_start)
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self.assertEqual("LEEAMDRMER~~~V", com_record.query_aln)
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self.assertEqual(76, com_record.hit_start)
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self.assertEqual("LQNFIDQLDNpddL", com_record.hit_aln)
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self.assertEqual("+ ++++ + + +", com_record.positives)
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def testAlignmentParsingTwo(self):
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with open(self.test_files[0]) as handle:
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records = Compass.parse(handle)
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com_record = next(records)
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self.assertEqual(2, com_record.query_start)
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self.assertEqual(2, com_record.hit_start)
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self.assertEqual("LKERKL", com_record.hit_aln[-6:])
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if __name__ == "__main__":
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runner = unittest.TextTestRunner(verbosity=2)
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unittest.main(testRunner=runner)
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