def test_left_softclipping(self):
ref = 'TAAGCTTCTTCCTTTTTCTATGCCACCTACATAGGCATTTTGCATGGTCAGATTGGAATTTACATAATGCATACATGCAAAGAAATATATAGAAGCCAGATATATAAGGTAGTACATTGGCAGGCTTCATATATATAGACTCCCCCATATTGTCTATATGCTAAAAAAGTATTTTAAATCCTTAAATTTTATTTTTGTTCTCTGCATTTGAAATCTTTATCAACTAGGTCATGAAAATAGCCAGTCGGTTCTCCTTTTGGTCTATTAGAATAAAATCTGGACTGCAACTGAGAAGCAGAAGGTAATGTCAGAATGTAT'
seq = 'GCTAAAAAAGTATTTTAAATCCTTAAATGTTATTTTTGTTCTC'
alignments = _read.nsb_align(ref, seq, min_consecutive_match=6)
self.assertEqual(1, len(alignments))
print(alignments)
seq = 'CTTATAAAGCTGGAGTATCTGCTGAGAGCATCAGGAATTGACATCTAGGATAATGAGAGAAGGCTGATCATGGACAACATATAGCCTTTCTAGTAGATGCAGCTGAGGCTAAAAAAGTATTTTAAATCCTTAAATGTTATTTTTGTTCTC'
alignments = _read.nsb_align(ref, seq, min_consecutive_match=6, min_overlap_percent=0.5)
self.assertEqual(1, len(alignments))
def test_length_seq_le_ref(self):
ref = 'GATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAG' \
'TTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTG'
seq = 'TGTAGGAAGCCATTATCTGAAGTGTAAGCAACTGCATAGTGCTATTTTAATTATGCATTGCAGGGAAACTGTGAGCAGAGCTATATATTTAGGTAGAC' \
'TGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCACGACCAGGAAC'
alignment = _read.nsb_align(ref, seq)
self.assertEqual(1, len(alignment))
alignment = _read.nsb_align(ref, seq, min_consecutive_match=20)
self.assertEqual(0, len(alignment))
def test_nsb_align(self):
ref = (
'GATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAG'
'TTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTG'
)
seq = (
'TGTAGGAAGCCATTATCTGAAGTGTAAGCAACTGCATAGTGCTATTTTAATTATGCATTGCAGGGAAACTGTGAGCAGAGCTATATATTTAGGTAGAC'
'TGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCACGACCAGGAAC'
)
_read.nsb_align(ref, seq)
def test_length_seq_le_ref(self):
ref = (
'GATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAG'
'TTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTG'
)
seq = (
'TGTAGGAAGCCATTATCTGAAGTGTAAGCAACTGCATAGTGCTATTTTAATTATGCATTGCAGGGAAACTGTGAGCAGAGCTATATATTTAGGTAGAC'
'TGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCACGACCAGGAAC'
)
alignment = _read.nsb_align(ref, seq)
assert len(alignment) == 1
alignment = _read.nsb_align(ref, seq, min_consecutive_match=20)
assert len(alignment) == 0
def test_long_ref_seq(self):
ref = str(REFERENCE_GENOME['test_bam_long_ref'].seq)
seq = (
'TGAGGTCAGGAGTTTGAGACCAGCCTGGACAACATGGTGAAACCCCATCTCTACTAAAAATACAAAAAAATTAGCCAGGCATGGTGGTGGATGCCTGTAAT'
'CGCAGCTACTCAGGAGATCGGAAG'
)
alignment = _read.nsb_align(ref, seq, min_consecutive_match=6)
self.assertEqual(1, len(alignment))
def test_min_overlap(self):
ref = 'ATTACATTAAAGATTCAAACTCCTAGAGTTTTTTTGATTTTTAGTATGATCTTTAGATAAAAAAAAAGGAAGAAAAAGAAAAAAAAACAGAGTCTATTAAGGCATCTTCTATGGTCAGATATATCTATTTTTTTCTTTCTTTTTTTTACTTTCATTAAGTGCCACTAAAAAATTAGGTTCAATTAAACTTTATTAATCTCTTCTGAGTTTTGAT'
seq = 'GATATATCTATTTTTTTCTTTCTTTTTTTTACTTTCATTAAGTGCCACTAAAAAATTAGGTTCAATTAAACTTTATTAATCTCTTCTGAGTTTTGATTGAGTGTATATATATATATATATATATATATATATATACCCAGTTTCAAGCAG'
alignments = _read.nsb_align(ref,
seq,
min_consecutive_match=15,
min_match=0.95,
min_overlap_percent=(len(seq) - 15) /
len(seq))
print(alignments)
self.assertEqual(0, len(alignments))