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 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 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)