def in_features(reads, features):
"""Returns a boolean indicating whether any of the reads in the first
argument overlap with any of the features in the second.
"""
overlap = False
r0, r1 = sam.coverage(reads)
for f in features:
if f.start <= r0 <= f.end or f.start <= r1 <= f.end:
overlap = True
break
elif f.start > r1:
break
return overlap
def in_features(reads, features):
"""Returns a boolean indicating whether any of the reads in the first
argument overlap with any of the features in the second.
"""
overlap = False
r0, r1 = sam.coverage(reads)
for f in features:
if f.start <= r0 <= f.end or f.start <= r1 <= f.end:
overlap = True
break
elif f.start > r1:
break
return overlap
def test_coverage(self):
self.expressed_locus_alignment.rewind()
test_reads = list(self.expressed_locus_alignment)
assert sam.coverage(test_reads[:1]) == (1,5)
assert sam.coverage(test_reads[:2]) == (1,7)
assert sam.coverage(test_reads[:3]) == (1,17)
assert sam.coverage(test_reads[:4]) == (1,18)
assert sam.coverage(test_reads[2:]) == (13,18)
assert sam.coverage(test_reads[1:]) == (3,18)