def test_uniqueness_filter(self):
reads = Reads(self.sam1_file)
reads.filter_non_unique(strict=True)
for row in reads._reads._iter_visible_and_masked():
if row['pos'] > 0:
tags_str = reads._tags[row['ix']]
try:
tags = pickle.loads(tags_str)
except pickle.UnpackValueError:
tags = pickle.loads(tags_str + '\x00')
tags = [(key.decode() if isinstance(key, bytes) else key,
value.decode() if isinstance(value, bytes) else value)
for key, value in tags]
has_xs = False
for tag in tags:
if tag[0] == 'XS':
has_xs = True
break
if has_xs:
assert row[reads._reads._mask_field] == 2
else:
assert row[reads._reads._mask_field] == 0
reads.close()
def test_select(self):
reads = Reads(self.sam1_file)
assert reads[0].qname == 'SRR038105.1'
reads.filter_non_unique()
assert reads[0].qname == 'SRR038105.10'
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_iter(self):
pairs = Reads(self.sam1_file)
counter = 0
for _ in pairs:
counter += 1
assert counter == 271
pairs.filter_non_unique()
after_counter = 0
for _ in pairs:
after_counter += 1
assert after_counter < counter
pairs.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()
