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))
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))
