def test_filter_passesAllThroughWhenNoFilters(self):
base_collection = [1, 2, 3, 4, 5]
filters = {}
generator = utils.FilteredGenerator(filters)
actual_collection = [x for x in generator.filter(base_collection)]
self.assertEqual([(1, None), (2, None), (3, None), (4, None),
(5, None)], actual_collection)
def test_filter_singleFilter(self):
filters = {'div by 2': lambda x: x % 2 == 0}
generator = utils.FilteredGenerator(filters)
base_collection = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
actual_collection = [x for x in generator.filter(base_collection)]
self.assertEqual([(1, None), (2, 'div by 2'), (3, None),
(4, 'div by 2'), (5, None), (6, 'div by 2'),
(7, None), (8, 'div by 2'), (9, None),
(10, 'div by 2')], actual_collection)
def test_filter_multipleFilterAreSortedByName(self):
filters = {
'div by 5': lambda x: x % 5 == 0,
'div by 2': lambda x: x % 2 == 0
}
generator = utils.FilteredGenerator(filters)
base_collection = [1, 10]
actual_collection = [x for x in generator.filter(base_collection)]
self.assertEqual([(1, None), (10, 'div by 2; div by 5')],
actual_collection)
def filter_alignments(pysam_alignments, excluded_writer=AlignWriter.NULL):
filters = {'cigar unavailable': \
lambda a: a.cigarstring is None,
'mapping quality < 1': \
lambda a: a.mapping_quality < 1,
'not in proper pair': \
lambda a: a.flag & BamFlag.PROPER_PAIR == 0,
'qc failed': \
lambda a: a.flag & BamFlag.QCFAIL != 0,
'secondary alignment': \
lambda a: a.flag & BamFlag.SECONDARY != 0,
'supplementary alignment': \
lambda a: a.flag & BamFlag.SUPPLEMENTARY != 0,
}
generator = utils.FilteredGenerator(filters)
for pysam_align, filter_value in generator.filter(pysam_alignments):
connor_align = ConnorAlign(pysam_align, filter_value)
if filter_value:
excluded_writer.write(family=None,
paired_align=None,
connor_align=connor_align)
else:
yield connor_align
def test_filter_returnsEmptyIfBaseEmpty(self):
generator = utils.FilteredGenerator({})
base_collection = []
actual_collection = [x for x in generator.filter(base_collection)]
self.assertEqual([], actual_collection)
