def overlap_repeats(self):
"""Overlaps event coordinates with repeatmasker, simple repeats"""
event_groups_by_chr = self.group_by_chr()
for chrom, events in event_groups_by_chr.iteritems():
proper_chrom = tools.proper_chrom(chrom, chrom_proper=self.chrom_proper)
for snv_type, snv_groups in events.iteritems():
print 'processing repeat', snv_type
for snvs in snv_groups:
overlaps = repeat.find_overlaps({'chrom':proper_chrom, 'start':int(snvs[0].ref_start),
'end':int(snvs[0].ref_end)}, self.repeat_overlaps)
if overlaps:
attrs = {}
for repeat_type, types in overlaps.iteritems():
if repeat_type == 'simple_repeats':
attr = 'within_simple_repeats'
elif repeat_type == 'segdup':
attr = 'within_segdup'
elif repeat_type == 'rmsk':
attr = 'repeatmasker'
if types:
# only report one with shortest name
types_sorted = types.keys()
types_sorted.sort(lambda x,y: len(x)-len(y))
attrs[attr] = types_sorted[0]
if attrs:
for snv in snvs:
tools.set_attrs(snv, attrs)
# clears cache
for repeat_olap in self.repeat_overlaps.values():
repeat_olap.finish()
def is_within_repeats(self, proper_chrom, span):
"""Determines if given coordinate span overlaps segdups or simple_repeats"""
overlaps = repeat.find_overlaps({'chrom':proper_chrom, 'start':span[0], 'end':span[1]}, self.repeat_overlaps)
if overlaps:
for repeat_type in overlaps.keys():
if overlaps[repeat_type]:
if repeat_type == 'segdup' or repeat_type == 'simple_repeats':
return True
return False
