def get_common_location(location_array):
"""Merges a compound location array into an overall location"""
contig = location_array[0][0]
strand = location_array[0][2]
min_pos = min([get_start(loc) for loc in location_array])
max_pos = max([get_end(loc) for loc in location_array])
common_length = max_pos - min_pos + 1
common_start = min_pos if strand == '+' else max_pos
return [contig, common_start, strand, common_length]
def feature_sort(feat):
order = ('gene', 'mRNA', 'CDS')
if feat.get('children'):
priority = 0
elif feat['type'] not in order:
priority = len(order)
else:
priority = order.index(feat['type'])
return get_start(self.get_common_location(
feat['location'])), priority
def make_feature(self, location, in_feature, is_gtf):
"""Make a single feature line for the file"""
try:
out_feature = {
'seqname': location[0],
'source': 'KBase',
'type': in_feature.get('type', 'exon'),
'start': str(get_start(location)),
'end': str(get_end(location)),
'score': '.',
'strand': location[2],
'frame': '0',
}
if is_gtf:
out_feature['attribute'] = self.gen_gtf_attr(in_feature)
else:
out_feature['attribute'] = self.gen_gff_attr(in_feature)
except Exception as e:
traceback.print_exc()
raise Exception(f'Unable to parse {in_feature}:{e}')
return out_feature