def test_write_soft_clipped_to_file(self):
'''test _write_soft_clipped_to_file'''
tmp_file = 'tmp.soft_clipped'
bam = os.path.join(data_dir, 'dummy.bam')
bp = bam_parse.Parser(bam,
{'x': pyfastaq.sequences.Fasta('x', 'ACGT')})
soft_clipped = {'ref1': {42: [142, 242], 43: [44, 45]}}
bp.soft_clipped = soft_clipped
bp._write_soft_clipped_to_file(tmp_file)
expected_lines = ['ref1\t43\t142\t242', 'ref1\t44\t44\t45']
got_lines = file_to_lines(tmp_file)
self.assertEqual(got_lines, expected_lines)
os.unlink(tmp_file)
def test_sam_to_soft_clipped(self):
'''test _sam_to_soft_clipped'''
bam = os.path.join(data_dir, 'bam_parse_test_sam_to_soft_clipped.bam')
bp = bam_parse.Parser(bam,
{'x': pyfastaq.sequences.Fasta('x', 'ACGT')})
sam_reader = pysam.Samfile(bam, "rb")
i = 0
expected = [
None, (False, False), (True, False), (False, True), (True, True)
]
for sam in sam_reader.fetch(until_eof=True):
if i == 0:
with self.assertRaises(bam_parse.Error):
bp._sam_to_soft_clipped(sam)
else:
self.assertEqual(expected[i], bp._sam_to_soft_clipped(sam))
i += 1
def test_parse(self):
'''test parse'''
ref_seqs = {}
ref_fasta = os.path.join(data_dir, 'bam_parse_test_parse.ref.fa')
bam = os.path.join(data_dir, 'bam_parse_test_parse.bam')
pyfastaq.tasks.file_to_dict(ref_fasta, ref_seqs)
bp = bam_parse.Parser(bam, ref_seqs)
bp.parse()
expected_soft_clipped = {'ref1': {2: [1, 0], 58: [0, 1]}}
expected_unmapped_mates = {'ref1': {2: 1}}
l = link.Link(
None,
None,
None,
s='\t'.join(['ref1', '500', 'R', '240', 'ref2', '500', 'L',
'299']))
expected_link_keys = [('ref1', 'ref2')]
self.assertEqual(expected_soft_clipped, bp.soft_clipped)
self.assertEqual(expected_unmapped_mates, bp.unmapped_mates)
self.assertEqual(list(bp.scaff_graph.links.keys()), expected_link_keys)
self.assertEqual(len(bp.scaff_graph.links[expected_link_keys[0]]), 1)
self.assertEqual(bp.scaff_graph.links[expected_link_keys[0]][0], l)