def test_pslx_row_to_pysam_duplication(self):
reference = {
'14':
MockObject(seq=MockLongString(
'TTCTTCCATGCCCCCTAATCATGGCCACATTGTATCAGCCTGAGCATGAGCAACAGCACCATGGCCACATACGGGAATGGGCCTCATTGGTGTAATATTTGGCAGATTCTCTCCACACCCCCCGTGGCGGTCTGGCTTACTGTTAAGAAGGGTAACCTTAAAAAATACATTTCCCACTCCAGAAAATACTCATATGTGGCCTGTTAGCAGCACAAGAAGGGTGAAAGCAATGCCCATTCCTGCCTCCCTCCCCCTGCTCACCTCCACGTCCCTGTTTGCCCCTTTGTAGGTGAAGTGAGTATATTCAGCGTCTTCATGGCAGGGGAGAGGGTGTATTAATCCGTCTATGTCCGCTGGAAAGGCAGTCTCTGAGCGGGCCACAAGGGTTCAGCCATGGCCCATCCAATAACCTTTTTGATGACTTGGATGAAGAGACAAACATTCCAACCACATTCAAAGATCCAGACCTCCAAAGTGTGGCTCATTTGGTAGATAATGGAATTATATTTGGAAAGCATTTCCCGCAGCTGGGATGATGGGTCAAAAACAGATAGCATTTTACCAGATCATATTTGTGTGTGTGTGTGTGCGCGCGTGTGTGTGTGTGTGTGTGTGTGTTTTAAATTCAGTTTCCCAACTACAGGATG',
offset=73014463,
))
}
pslx_row = {
'block_count': 2,
'tstarts': [73014606, 73014747],
'block_sizes': [141, 30],
'qname': '',
'tname': '14',
'qstarts': [0, 239],
'strand': '+',
'qseq_full':
'AAGAAGGGTAACCTTAAAAAATACATTTCCCACTCCAGAAAATACTCATATGTGGCCTGTTAGCAGCACAAGAAGGGTGAAAGCAATGCCCATTCCTGCCTCCCTCCCCCTGCTCACCTCCACGTCCCTGTTTGCCCCTTTACTCATATGTGGCCTGTTAGCAGCACAAGAAGGGTGAAAGCAATGCCCATTCCTGCCTCCCTCCCCCTGCTCACCTCCACGTCCCTGTTTGCCCCTTTGTAGGTGAAGTGAGTATATTCAGCGTCTTC',
'score': 1,
}
read2 = Blat.pslx_row_to_pysam(pslx_row, self.cache, reference)
self.assertEqual(13, read2.reference_id)
self.assertEqual(73014606, read2.reference_start)
self.assertEqual([(CIGAR.M, 141), (CIGAR.I, 98), (CIGAR.M, 30)],
_cigar.convert_for_igv(read2.cigar))
self.assertEqual(Interval(0,
len(pslx_row['qseq_full']) - 1),
query_coverage_interval(read2))
def test_convert_for_igv(self):
c = [(CIGAR.M, 10), (CIGAR.EQ, 10), (CIGAR.X, 10)]
self.assertEqual([(CIGAR.M, 30)], convert_for_igv(c))
def test_convert_for_igv(self):
c = [(CIGAR.M, 10), (CIGAR.EQ, 10), (CIGAR.X, 10)]
assert convert_for_igv(c) == [(CIGAR.M, 30)]