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 parse(cls, record):
"""Parses tabulated output into object"""
cols = record.rstrip('\n').split('\t')
data = {}
headers = cls.headers[:]
headers.extend(cls.headers_support)
for i in range(len(headers)):
if cols[i+1] != 'na' and (headers[i] == 'spanning_reads' or headers[i] == 'coverage'):
if ',' in cols[i+1]:
data[headers[i]] = [int(n) for n in cols[i+1].split(',')]
else:
data[headers[i]] = int(cols[i+1])
else:
data[headers[i]] = cols[i+1]
e = Event(cols[1])
set_attrs(e, data)
return e
def parse_results(self, snv_file, select_types=None, chrom=None):
"""Parses results from single file into SNV objects"""
names = SNVCaller.output_headers
# conversion between header name and object attribute
field_name_conversion = {
'type': 'snv_type',
'chr': 'ref',
'chr_start': 'ref_start',
'chr_end': 'ref_end',
'ctg': 'var',
'ctg_len': 'var_len',
'ctg_start': 'var_start',
'ctg_end': 'var_end',
'len': 'snv_len',
'ref': 'ref_seq',
'alt': 'var_seq',
'event_reads': 'nreads_event',
'contig_reads': 'nreads_contig',
'genome_reads': 'nreads_genome',
'gene': 'gene',
'from_end': 'from_end',
'ctg_strand': 'query_strand',
}
for line in open(snv_file, 'r'):
cols = line.rstrip('\n').split('\t')
if cols[0] == 'id':
continue
attributes = {}
for i in range(1, len(cols)):
name = names[i]
value = cols[i]
if field_name_conversion.has_key(name):
name = field_name_conversion[name]
if name in ('expansion', 'from_end'):
value = int(value)
elif name == 'confirm_contig_region':
value = value.split('-')
value[0] = int(value[0])
value[1] = int(value[1])
elif name == 'at_least_1_read_opposite':
if value == 'true':
value = True
else:
value = False
attributes[name] = value
if select_types and not attributes['snv_type'] in select_types:
continue
if chrom and attributes['ref'] != chrom:
continue
snv = SNV(method='psl')
tools.set_attrs(snv, attributes)
self.snvs.append(snv)
