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 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 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 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)