def make_hits_union(ids, d1, d2):
d = {}
for id in ids:
d[id] = []
if id in d1:
d[id].extend(d1[id])
if id in d2:
d[id].extend(d2[id])
genome_intervals.merge_overlapping_in_list(d[id])
return d
def test_merge_overlapping_in_list(self):
'''merge_overlapping_in_list() merges correctly'''
a = [
genome_intervals.Interval(1, 2),
genome_intervals.Interval(51, 60),
genome_intervals.Interval(10, 20),
genome_intervals.Interval(20, 30),
genome_intervals.Interval(20, 30),
genome_intervals.Interval(29, 50),
genome_intervals.Interval(65, 70)
]
b = [
genome_intervals.Interval(1, 2),
genome_intervals.Interval(10, 60),
genome_intervals.Interval(65, 70)
]
genome_intervals.merge_overlapping_in_list(a)
self.assertSequenceEqual(a, b)
def get_nucmer_hits(coords_file):
qry_hits = {}
ref_hits = {}
nucmer_reader = nucmer.file_reader(coords_file)
for hit in nucmer_reader:
# nucmer hits are 1-based. INside the script, use 0-based.
start, end = sorted([hit.ref_start - 1, hit.ref_end - 1])
if hit.ref_name not in ref_hits:
ref_hits[hit.ref_name] = []
ref_hits[hit.ref_name].append(genome_intervals.Interval(start, end))
start, end = sorted([hit.qry_start - 1, hit.qry_end - 1])
if hit.qry_name not in qry_hits:
qry_hits[hit.qry_name] = []
qry_hits[hit.qry_name].append(genome_intervals.Interval(start, end))
for l in ref_hits.values():
genome_intervals.merge_overlapping_in_list(l)
for l in qry_hits.values():
genome_intervals.merge_overlapping_in_list(l)
return ref_hits, qry_hits
def file2regions(fname):
regions = {}
f = utils.open_file_read(fname)
for line in f:
if line.startswith('#'):
continue
(chr, start, end) = line.rstrip().split()
if chr not in regions:
regions[chr] = []
regions[chr].append(genome_intervals.Interval(start, end))
utils.close(f)
return regions
regions = file2regions(options.infile)
f = utils.open_file_write(options.outfile)
for chr, l in sorted(regions.items()):
genome_intervals.merge_overlapping_in_list(l)
for region in l:
print(chr, region.start, region.end, sep='\t', file=f)
utils.close(f)