def get_events(self, sample_name=CURRENT_SAMPLE):
'''Returns VCF records for a single sample, grouped by event id'''
# TODO experimenting here
global json_records
if sample_name != CURRENT_SAMPLE:
self.load_sample(sample_name)
json_records = {}
for event_id in GROUPED_CURRENT_RECORDS:
event_type, sv_id = self.get_event_type(event_id)
description = self.get_event_type_description(event_type)
breakends = self.record_list_to_dict(GROUPED_CURRENT_RECORDS[event_id])
breakend_locations = ', '.join(['{0}:{1}'.format(
'chr' + b['CHROM'] if vcf_sv_specific_variables.formatChromID(b['CHROM']) == 'chr' + b['CHROM'] else b['CHROM'],
b['POS']) for b in breakends]) # TODO fix hack
breakend_locations_array = [{
'chrom': b['CHROM'],
'ucsc_chrom': vcf_sv_specific_variables.formatChromID(b['CHROM']),
'pos': b['POS'],
'sv_id': sv_id}
for b in breakends]
fused, genes_hit = self.any_fusion_in_event(event_id, sample_name);
record = {'id': sv_id,
'type': event_type,
'vcf_id': event_id,
'description': description,
'breakend locations': breakend_locations,
'breakend locations array': breakend_locations_array,
'breakends': breakends,
'fused': 'X' if fused else '',
'genes hit': ', '.join(genes_hit) if len(genes_hit) > 0 else ''}
json_records[event_id] = record; # TODO simplify structure
return list(json_records.values())
def get_chrom_size(self, chrom_id, species='human', vcf_type='meerkat'):
'''Returns size of given chromosome'''
chrom_id = vcf_sv_specific_variables.formatChromID(chrom_id, species, vcf_type)
chrom_size = vcf_sv_specific_variables.chromosome_sizes[species][chrom_id] if chrom_id else 0
return chrom_size
