def test_tag_no_cycle_shift(self):
write_path = './data/write_test_rg.bam'
tm.run_multiome_tagging_cmd(
f'./data/mini_nla_test.bam -method nla -o {write_path}'.split(' '))
with pysam.AlignmentFile(write_path) as f:
self.assertTrue(1 == len([
x for x in f.header['PG']
if 'bamtagmultiome' in x.get('PN', '')
]))
i = 0
qc_failed_R1 = 0
# Test if the file has reads.
for read in f:
self.assertTrue(read.has_tag('RG'))
if read.is_read1:
i += 1
if read.is_qcfail:
qc_failed_R1 += 1
self.assertEqual(i, 293)
self.assertEqual(qc_failed_R1, 13)
self.assertTrue(os.path.exists(write_path))
os.remove(write_path)
os.remove(write_path + '.bai')
def test_write_to_read_grouped_multi(self):
write_path = './data/write_test_chic_rg.bam'
tm.run_multiome_tagging_cmd(
f'./data/chic_test_region.bam -method chic --multiprocess -o {write_path}'
.split(' '))
with pysam.AlignmentFile(write_path) as f:
# Test program header:
self.assertTrue(1 == len([
x for x in f.header['PG']
if 'bamtagmultiome' in x.get('PN', '')
]))
i = 0
# Test if the file has reads.
for read in f:
if read.is_read1:
i += 1
# Test if the reads have read groups:
self.assertTrue(read.has_tag('RG'))
self.assertEqual(i, 17)
self.assertTrue(os.path.exists(write_path))
os.remove(write_path)
os.remove(write_path + '.bai')
def test_write_to_read_grouped_multi():
write_path = './data/write_test_chic_rg.bam'
tm.run_multiome_tagging_cmd(
f'./data/chic_test_region.bam -method chic --multiprocess -contig 8 -o {write_path}'
.split(' '))
with pysam.AlignmentFile(write_path) as f:
# Test program header:
i = 0
# Test if the file has reads.
for read in f:
if read.is_read1:
i += 1
# Test if the reads have read groups:
os.remove(write_path)
os.remove(write_path + '.bai')
def test_skip_contig_invert(self):
write_path = './data/write_test_rg.bam'
tm.run_multiome_tagging_cmd(
f'./data/mini_nla_test.bam --no_rejects --allow_cycle_shift -method nla -skip_contig chr2,chr3 -o {write_path}'
.split(' '))
with pysam.AlignmentFile(write_path) as f:
self.assertTrue(1 == len([
x for x in f.header['PG']
if 'bamtagmultiome' in x.get('PN', '')
]))
i = 0
# Test if the file has reads.
for read in f:
if read.is_read1:
i += 1
self.assertEqual(i, 283)
self.assertTrue(os.path.exists(write_path))
os.remove(write_path)
os.remove(write_path + '.bai')