def testCompassIteratorEasy(self):
handle = open(self.test_files[0])
records = Compass.parse(handle)
com_record = next(records)
self.assertEqual("60456.blo.gz.aln", com_record.query)
self.assertRaises(StopIteration, next, records)
handle.close()
def testAlignmentParsingTwo(self):
with open(self.test_files[0]) as handle:
records = Compass.parse(handle)
com_record = next(records)
self.assertEqual(2, com_record.query_start)
self.assertEqual(2, com_record.hit_start)
self.assertEqual("LKERKL", com_record.hit_aln[-6:])
def testCompassIteratorEasy(self):
records = Compass.parse(open(self.test_files[0]))
com_record = records.next()
self.assertEqual("60456.blo.gz.aln", com_record.query)
self.assertRaises(StopIteration, records.next)
def testCompassIteratorEasy(self):
handle = open(self.test_files[0])
records = Compass.parse(handle)
com_record = next(records)
self.assertEqual("60456.blo.gz.aln", com_record.query)
self.assertRaises(StopIteration, next, records)
handle.close()
def testAlignmentParsingTwo(self):
it = Compass.Iterator(open(self.test_files[0]))
com_record = it.next()
self.assertEquals(2, com_record.query_start)
self.assertEquals(2, com_record.hit_start)
self.assertEquals("LKERKL", com_record.hit_aln[-6:])
def testAlignmentParsingTwo(self):
records = Compass.parse(open(self.test_files[0]))
com_record = records.next()
self.assertEqual(2, com_record.query_start)
self.assertEqual(2, com_record.hit_start)
self.assertEqual("LKERKL", com_record.hit_aln[-6:])
def testAlignmentParsingTwo(self):
handle = open(self.test_files[0])
records = Compass.parse(handle)
com_record = records.next()
self.assertEqual(2, com_record.query_start)
self.assertEqual(2, com_record.hit_start)
self.assertEqual("LKERKL", com_record.hit_aln[-6:])
handle.close()
def testAlignmentParsingTwo(self):
handle = open(self.test_files[0])
records = Compass.parse(handle)
com_record = next(records)
self.assertEqual(2, com_record.query_start)
self.assertEqual(2, com_record.hit_start)
self.assertEqual("LKERKL", com_record.hit_aln[-6:])
handle.close()
def testCompassIteratorEasy(self):
it = Compass.Iterator(open(self.test_files[0]))
com_record = it.next()
self.assertEquals("60456.blo.gz.aln", com_record.query)
com_record = it.next()
self.assertEquals(None, com_record)
pass
def testCompassScanAndConsume(self):
cons = Compass._Consumer()
scan = Compass._Scanner()
scan.feed(open(self.test_files[0]), cons)
com_record = cons.data
self.assertEquals("60456.blo.gz.aln", com_record.query)
self.assertEquals("60456.blo.gz.aln", com_record.hit)
self.assertEquals(0.5, com_record.gap_threshold)
self.assertEquals(388, com_record.query_length)
self.assertEquals(386, com_record.query_filtered_length)
self.assertEquals(388, com_record.hit_length)
self.assertEquals(386, com_record.hit_filtered_length)
self.assertEquals(399, com_record.query_nseqs)
self.assertEquals(12.972, com_record.query_neffseqs)
self.assertEquals(399, com_record.hit_nseqs)
self.assertEquals(12.972, com_record.hit_neffseqs)
self.assertEquals(2759, com_record.sw_score)
self.assertEquals(float("0.00e+00"), com_record.evalue)
def testCompassIteratorHard(self):
records = Compass.parse(open(self.test_files[1]))
com_record = records.next()
self.assertEqual("allscop//14982.blo.gz.aln", com_record.hit)
self.assertEqual(float('1.01e+03'), com_record.evalue)
com_record = records.next()
self.assertEqual("allscop//14983.blo.gz.aln", com_record.hit)
self.assertEqual(float('1.01e+03'), com_record.evalue)
com_record = records.next()
self.assertEqual("allscop//14984.blo.gz.aln", com_record.hit)
self.assertEqual(float('5.75e+02'), com_record.evalue)
def testCompassScanAndConsume(self):
cons = Compass._Consumer()
scan = Compass._Scanner()
scan.feed(open(self.test_files[0]), cons)
com_record = cons.data
self.assertEquals("60456.blo.gz.aln", com_record.query)
self.assertEquals("60456.blo.gz.aln", com_record.hit)
self.assertEquals(0.5, com_record.gap_threshold)
self.assertEquals(388, com_record.query_length)
self.assertEquals(386, com_record.query_filtered_length)
self.assertEquals(388, com_record.hit_length)
self.assertEquals(386, com_record.hit_filtered_length)
self.assertEquals(399, com_record.query_nseqs)
self.assertEquals(12.972, com_record.query_neffseqs)
self.assertEquals(399, com_record.hit_nseqs)
self.assertEquals(12.972, com_record.hit_neffseqs)
self.assertEquals(2759, com_record.sw_score)
self.assertEquals(float("0.00e+00"), com_record.evalue)
def testCompassIteratorHard(self):
it = Compass.Iterator(open(self.test_files[1]))
com_record = it.next()
self.assertEquals("allscop//14982.blo.gz.aln", com_record.hit)
self.assertEquals(float('1.01e+03'), com_record.evalue)
com_record = it.next()
self.assertEquals("allscop//14983.blo.gz.aln", com_record.hit)
self.assertEquals(float('1.01e+03'), com_record.evalue)
com_record = it.next()
self.assertEquals("allscop//14984.blo.gz.aln", com_record.hit)
self.assertEquals(float('5.75e+02'), com_record.evalue)
def testCompassIteratorHard(self):
with open(self.test_files[1]) as handle:
records = Compass.parse(handle)
com_record = next(records)
self.assertEqual("allscop//14982.blo.gz.aln", com_record.hit)
self.assertEqual(float("1.01e+03"), com_record.evalue)
com_record = next(records)
self.assertEqual("allscop//14983.blo.gz.aln", com_record.hit)
self.assertEqual(float("1.01e+03"), com_record.evalue)
com_record = next(records)
self.assertEqual("allscop//14984.blo.gz.aln", com_record.hit)
self.assertEqual(float("5.75e+02"), com_record.evalue)
def testCompassIteratorHard(self):
handle = open(self.test_files[1])
records = Compass.parse(handle)
com_record = next(records)
self.assertEqual("allscop//14982.blo.gz.aln", com_record.hit)
self.assertEqual(float('1.01e+03'), com_record.evalue)
com_record = next(records)
self.assertEqual("allscop//14983.blo.gz.aln", com_record.hit)
self.assertEqual(float('1.01e+03'), com_record.evalue)
com_record = next(records)
self.assertEqual("allscop//14984.blo.gz.aln", com_record.hit)
self.assertEqual(float('5.75e+02'), com_record.evalue)
handle.close()
def testAlignmentParsingOne(self):
records = Compass.parse(open(self.test_files[1]))
com_record = records.next()
self.assertEqual(178, com_record.query_start)
self.assertEqual("KKDLEEIAD", com_record.query_aln)
self.assertEqual(9, com_record.hit_start)
self.assertEqual("QAAVQAVTA", com_record.hit_aln)
self.assertEqual("++ ++++++", com_record.positives)
com_record = records.next()
com_record = records.next()
self.assertEqual(371, com_record.query_start)
self.assertEqual("LEEAMDRMER~~~V", com_record.query_aln)
self.assertEqual(76, com_record.hit_start)
self.assertEqual("LQNFIDQLDNpddL", com_record.hit_aln)
self.assertEqual("+ ++++ + + +", com_record.positives)
def testCompassIteratorHard(self):
handle = open(self.test_files[1])
records = Compass.parse(handle)
com_record = next(records)
self.assertEqual("allscop//14982.blo.gz.aln", com_record.hit)
self.assertEqual(float('1.01e+03'), com_record.evalue)
com_record = next(records)
self.assertEqual("allscop//14983.blo.gz.aln", com_record.hit)
self.assertEqual(float('1.01e+03'), com_record.evalue)
com_record = next(records)
self.assertEqual("allscop//14984.blo.gz.aln", com_record.hit)
self.assertEqual(float('5.75e+02'), com_record.evalue)
handle.close()
def testAlignmentParsingOne(self):
it = Compass.Iterator(open(self.test_files[1]))
com_record = it.next()
self.assertEquals(178, com_record.query_start)
self.assertEquals("KKDLEEIAD", com_record.query_aln)
self.assertEquals(9, com_record.hit_start)
self.assertEquals("QAAVQAVTA", com_record.hit_aln)
self.assertEquals("++ ++++++", com_record.positives)
com_record = it.next()
com_record = it.next()
self.assertEquals(371, com_record.query_start)
self.assertEquals("LEEAMDRMER~~~V", com_record.query_aln)
self.assertEquals(76, com_record.hit_start)
self.assertEquals("LQNFIDQLDNpddL", com_record.hit_aln)
self.assertEquals("+ ++++ + + +", com_record.positives)
def testAlignmentParsingOne(self):
with open(self.test_files[1]) as handle:
records = Compass.parse(handle)
com_record = next(records)
self.assertEqual(178, com_record.query_start)
self.assertEqual("KKDLEEIAD", com_record.query_aln)
self.assertEqual(9, com_record.hit_start)
self.assertEqual("QAAVQAVTA", com_record.hit_aln)
self.assertEqual("++ ++++++", com_record.positives)
com_record = next(records)
com_record = next(records)
self.assertEqual(371, com_record.query_start)
self.assertEqual("LEEAMDRMER~~~V", com_record.query_aln)
self.assertEqual(76, com_record.hit_start)
self.assertEqual("LQNFIDQLDNpddL", com_record.hit_aln)
self.assertEqual("+ ++++ + + +", com_record.positives)
def testCompassScanAndConsume(self):
com_record = Compass.read(open(self.test_files[0]))
self.assertEqual("60456.blo.gz.aln", com_record.query)
self.assertEqual("60456.blo.gz.aln", com_record.hit)
self.assertEqual(0.5, com_record.gap_threshold)
self.assertEqual(388, com_record.query_length)
self.assertEqual(386, com_record.query_filtered_length)
self.assertEqual(388, com_record.hit_length)
self.assertEqual(386, com_record.hit_filtered_length)
self.assertEqual(399, com_record.query_nseqs)
self.assertEqual(12.972, com_record.query_neffseqs)
self.assertEqual(399, com_record.hit_nseqs)
self.assertEqual(12.972, com_record.hit_neffseqs)
self.assertEqual(2759, com_record.sw_score)
self.assertEqual(float("0.00e+00"), com_record.evalue)
def testCompassScanAndConsume(self):
with open(self.test_files[0]) as handle:
com_record = Compass.read(handle)
self.assertEqual("60456.blo.gz.aln", com_record.query)
self.assertEqual("60456.blo.gz.aln", com_record.hit)
self.assertEqual(0.5, com_record.gap_threshold)
self.assertEqual(388, com_record.query_length)
self.assertEqual(386, com_record.query_filtered_length)
self.assertEqual(388, com_record.hit_length)
self.assertEqual(386, com_record.hit_filtered_length)
self.assertEqual(399, com_record.query_nseqs)
self.assertEqual(12.972, com_record.query_neffseqs)
self.assertEqual(399, com_record.hit_nseqs)
self.assertEqual(12.972, com_record.hit_neffseqs)
self.assertEqual(2759, com_record.sw_score)
self.assertEqual(float("0.00e+00"), com_record.evalue)
def testCompassParser(self):
with open(self.test_files[0]) as handle:
com_record = Compass.read(handle)
self.assertEqual("60456.blo.gz.aln", com_record.query)
def testCompassParser(self):
handle = open(self.test_files[0])
com_record = Compass.read(handle)
handle.close()
self.assertEqual("60456.blo.gz.aln", com_record.query)
def testCompassParser(self):
com_record = Compass.read(open(self.test_files[0]))
self.assertEqual("60456.blo.gz.aln", com_record.query)
def testCompassParser(self):
parser = Compass.RecordParser()
com_record = parser.parse(open(self.test_files[0]))
self.assertEquals("60456.blo.gz.aln", com_record.query)
def testCompassParser(self):
handle = open(self.test_files[0])
com_record = Compass.read(handle)
handle.close()
self.assertEqual("60456.blo.gz.aln", com_record.query)
