def test_phred33(self): """parse_qseq should return one record as tuple.""" f = list(parse_qseq(self.one_seq, phred_offset=33)) self.assertEqual(len(f), 1) a = f[0] # First record. self.assertEqual(a[0], 'CRESSIA_242:1:2204:1491:1930#0/1') self.assertEqual(a[1], '.TTGATAAGAATGTCTGTTGTGGCTTAAAA') npt.assert_equal(a[2], [33, 58, 58, 58, 54, 60, 58, 56, 58, 57, 66, 67, 66, 66, 66, 66, 66, 66, 66, 59, 66, 66, 66, 64, 66, 62, 62, 62, 62, 62]) record = a[3] self.assertEqual(record.machine_name, 'CRESSIA') self.assertEqual(record.run, 242) self.assertEqual(record.lane, 1) self.assertEqual(record.tile, 2204) self.assertEqual(record.x, 1491) self.assertEqual(record.y, 1930) self.assertEqual(record.index, 0) self.assertEqual(record.read, 1) self.assertTrue(record.filtered)
def test_two_seq(self): """parse_qseq should return two records as tuple.""" f = list(parse_qseq(self.two_seq, phred_offset=64)) self.assertEqual(len(f), 2) a, b = f # First record. self.assertEqual(a[0], 'CRESSIA_242:1:2204:1453:1918#0/1') self.assertEqual(a[1], '.TTAATAAGAATGTCTGTTGTGGCTTAAAA') npt.assert_equal(a[2], [ 2, 27, 27, 27, 23, 29, 27, 25, 27, 26, 35, 35, 35, 35, 35, 35, 35, 35, 35, 28, 35, 35, 35, 33, 35, 31, 31, 31, 31, 31 ]) record = a[3] self.assertEqual(record.machine_name, 'CRESSIA') self.assertEqual(record.run, 242) self.assertEqual(record.lane, 1) self.assertEqual(record.tile, 2204) self.assertEqual(record.x, 1453) self.assertEqual(record.y, 1918) self.assertEqual(record.index, 0) self.assertEqual(record.read, 1) self.assertTrue(record.filtered) # Second record. self.assertEqual(b[0], 'CRESSIA_242:1:2204:1490:1921#0/2') self.assertEqual(b[1], '..GTAAAACCCATATATTGAAAACTACAAA') npt.assert_equal(b[2], [ 2, 23, 21, 20, 23, 35, 24, 22, 24, 24, 35, 35, 35, 35, 31, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 31, 35, 35, 35, 35 ]) record = b[3] self.assertEqual(record.machine_name, 'CRESSIA') self.assertEqual(record.run, 242) self.assertEqual(record.lane, 1) self.assertEqual(record.tile, 2204) self.assertEqual(record.x, 1490) self.assertEqual(record.y, 1921) self.assertEqual(record.index, 0) self.assertEqual(record.read, 2) self.assertFalse(record.filtered)
def test_phred33(self): """parse_qseq should return one record as tuple.""" f = list(parse_qseq(self.one_seq, phred_offset=33)) self.assertEqual(len(f), 1) a = f[0] # First record. self.assertEqual(a[0], 'CRESSIA_242:1:2204:1491:1930#0/1') self.assertEqual(a[1], '.TTGATAAGAATGTCTGTTGTGGCTTAAAA') npt.assert_equal(a[2], [ 33, 58, 58, 58, 54, 60, 58, 56, 58, 57, 66, 67, 66, 66, 66, 66, 66, 66, 66, 59, 66, 66, 66, 64, 66, 62, 62, 62, 62, 62 ]) record = a[3] self.assertEqual(record.machine_name, 'CRESSIA') self.assertEqual(record.run, 242) self.assertEqual(record.lane, 1) self.assertEqual(record.tile, 2204) self.assertEqual(record.x, 1491) self.assertEqual(record.y, 1930) self.assertEqual(record.index, 0) self.assertEqual(record.read, 1) self.assertTrue(record.filtered)
def test_one_seq(self): """parse_qseq should return one record as tuple. """ f = list(parse_qseq(self.one_seq, phred_offset=64)) self.assertEqual(len(f), 1) a = f[0] # First record. self.assertEqual(a[0], 'CRESSIA_242:1:2204:1491:1930#0/1') self.assertEqual(a[1], '.TTGATAAGAATGTCTGTTGTGGCTTAAAA') npt.assert_equal(a[2], [2, 27, 27, 27, 23, 29, 27, 25, 27, 26, 35, 36, 35, 35, 35, 35, 35, 35, 35, 28, 35, 35, 35, 33, 35, 31, 31, 31, 31, 31]) record = a[3] self.assertEqual(record.machine_name, 'CRESSIA') self.assertEqual(record.run, 242) self.assertEqual(record.lane, 1) self.assertEqual(record.tile, 2204) self.assertEqual(record.x, 1491) self.assertEqual(record.y, 1930) self.assertEqual(record.index, 0) self.assertEqual(record.read, 1) self.assertTrue(record.filtered)
def test_one_seq(self): """parse_qseq should return one record as tuple. """ f = list(parse_qseq(self.one_seq, phred_offset=64)) self.assertEqual(len(f), 1) a = f[0] # First record. self.assertEqual(a[0], 'CRESSIA_242:1:2204:1491:1930#0/1') self.assertEqual(a[1], '.TTGATAAGAATGTCTGTTGTGGCTTAAAA') npt.assert_equal(a[2], [ 2, 27, 27, 27, 23, 29, 27, 25, 27, 26, 35, 36, 35, 35, 35, 35, 35, 35, 35, 28, 35, 35, 35, 33, 35, 31, 31, 31, 31, 31 ]) record = a[3] self.assertEqual(record.machine_name, 'CRESSIA') self.assertEqual(record.run, 242) self.assertEqual(record.lane, 1) self.assertEqual(record.tile, 2204) self.assertEqual(record.x, 1491) self.assertEqual(record.y, 1930) self.assertEqual(record.index, 0) self.assertEqual(record.read, 1) self.assertTrue(record.filtered)
def test_two_seq(self): """parse_qseq should return two records as tuple.""" f = list(parse_qseq(self.two_seq, phred_offset=64)) self.assertEqual(len(f), 2) a, b = f # First record. self.assertEqual(a[0], 'CRESSIA_242:1:2204:1453:1918#0/1') self.assertEqual(a[1], '.TTAATAAGAATGTCTGTTGTGGCTTAAAA') npt.assert_equal(a[2], [2, 27, 27, 27, 23, 29, 27, 25, 27, 26, 35, 35, 35, 35, 35, 35, 35, 35, 35, 28, 35, 35, 35, 33, 35, 31, 31, 31, 31, 31]) record = a[3] self.assertEqual(record.machine_name, 'CRESSIA') self.assertEqual(record.run, 242) self.assertEqual(record.lane, 1) self.assertEqual(record.tile, 2204) self.assertEqual(record.x, 1453) self.assertEqual(record.y, 1918) self.assertEqual(record.index, 0) self.assertEqual(record.read, 1) self.assertTrue(record.filtered) # Second record. self.assertEqual(b[0], 'CRESSIA_242:1:2204:1490:1921#0/2') self.assertEqual(b[1], '..GTAAAACCCATATATTGAAAACTACAAA') npt.assert_equal(b[2], [2, 23, 21, 20, 23, 35, 24, 22, 24, 24, 35, 35, 35, 35, 31, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 31, 35, 35, 35, 35]) record = b[3] self.assertEqual(record.machine_name, 'CRESSIA') self.assertEqual(record.run, 242) self.assertEqual(record.lane, 1) self.assertEqual(record.tile, 2204) self.assertEqual(record.x, 1490) self.assertEqual(record.y, 1921) self.assertEqual(record.index, 0) self.assertEqual(record.read, 2) self.assertFalse(record.filtered)
def test_invalid_record(self): """parse_qseq should raise QseqParseError with invalid record.""" with self.assertRaises(QseqParseError): list(parse_qseq(self.missing, phred_offset=64))
def test_phred_offset_error(self): """parse_qseq should raise ValueError with invalid phred offset.""" with self.assertRaises(ValueError): list(parse_qseq(self.one_seq, phred_offset=99))