def test_Interval_merge():
l1 = Interval.from_string('chr1:10000-10967:1')
l2 = Interval.from_string('chr1:10858-12964:-1')
l3 = Interval.from_string('chr1:10858-10964:-1')
merged = Interval.merge([l1,l2,l3])
assert len(merged) == 1
m = merged[0]
assert m.start == 10000
assert m.end == 12964
def intervals(self):
if self.bed_file is None:
return {}
if not self.bed_file.exists:
raise ValueError(f"can not find the bed file: {self.bed_file}")
intervals = defaultdict(list)
with open(self.bed_file) as fp:
for line in fp:
chrom, start, end, *_ = line.strip().split('\t')
intervals[chrom].append(
Interval(int(start), int(end), chrom=chrom))
return {chrom: Interval.merge(intervals[chrom]) for chrom in intervals}
