def test_quality_filter(self):
reads = Reads(self.sam1_file)
reads.filter_quality(30, queue=False)
for row in reads._reads._iter_visible_and_masked():
if row['mapq'] < 30:
assert row[reads._reads._mask_field] == 2
else:
assert row[reads._reads._mask_field] == 0
reads.close()
def test_queue_filters(self):
reads = Reads(self.sam1_file)
l = len(reads)
reads.filter_quality(30, queue=True)
reads.filter_non_unique(strict=True, queue=True)
assert len(reads) == l
reads.run_queued_filters()
assert len(reads) < l
reads.close()
def test_iterate_exclude_filters(self):
reads = Reads(self.sam1_file)
reads.filter_unmapped(queue=True)
reads.filter_quality(35, queue=True)
reads.filter_non_unique(strict=True, queue=True)
reads.run_queued_filters()
assert len(
list(
reads.reads(
excluded_filters=['unmapped', 'mapq', 'uniqueness'
]))) == 271
assert len(
list(reads.reads(
excluded_filters=['unmapped', 'uniqueness']))) == 246
assert len(list(
reads.reads(excluded_filters=['unmapped', 'mapq']))) == 153
assert len(list(
reads.reads(excluded_filters=['mapq', 'uniqueness']))) == 271
assert len(list(reads.reads(excluded_filters=['unmapped']))) == 153
assert len(list(reads.reads(excluded_filters=['mapq']))) == 153
assert len(list(reads.reads(excluded_filters=['uniqueness']))) == 246
reads.close()