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 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 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):
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):
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 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 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 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 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 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):
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)