def get_start_stop_codons(self, annot='havana'):
"""gets start and stop codons position
start codon is always first"""
trans_start_stop = {}
for linea in open(self.gtf_path).readlines():
dic = self._parse_line(linea, feature='start_codon|stop_codon', annot=annot)
if not dic:
continue
trans_start_stop = fn.add2dict(trans_start_stop, dic['attr']['transcript_id'], [dic['start'], dic['stop']])
return trans_start_stop
def get_seqs(trans_exons, parser):
trans_seqs = {}
for trans in trans_exons.keys():
seqs = {}
for exon in trans_exons[trans]:
region = parser.get_region(exon[1], exon[2], exon[3])
for key, obj in region.items():
seqs = fn.add2dict(seqs, key, obj)
for key, obj in seqs.items():
seqs[key] = ''.join(obj)
trans_seqs[trans] = seqs
return trans_seqs
def get_seqs(trans_exons, parser):
trans_seqs = {}
for trans in trans_exons.keys():
seqs = {}
for exon in trans_exons[trans]:
region = parser.get_region(exon[1], exon[2], exon[3])
for key, obj in region.items():
seqs = fn.add2dict(seqs, key, obj)
for key, obj in seqs.items():
seqs[key] = ''.join(obj)
trans_seqs[trans] = seqs
return trans_seqs
def get_start_stop_codons(self, annot='havana'):
"""gets start and stop codons position
start codon is always first"""
trans_start_stop = {}
for linea in open(self.gtf_path).readlines():
dic = self._parse_line(linea,
feature='start_codon|stop_codon',
annot=annot)
if not dic:
continue
trans_start_stop = fn.add2dict(trans_start_stop,
dic['attr']['transcript_id'],
[dic['start'], dic['stop']])
return trans_start_stop