def analyze_intergenic(self):
last_transcript_end = None
last_transcript_neg = None
for key in self.transcript_keys:
transcript = self.transcripts[
key] #loop through certain chrom transcripts in order
if last_transcript_end is None:
last_transcript_end = transcript.end_pos
last_transcript_neg = transcript.negative_dir
else:
sign = "-" if last_transcript_neg and transcript.negative_dir else "+"
self.intergenic_lines.append(
Line.creat_line_by_name_and_corr(transcript.chr,
"Intergenic",
last_transcript_end,
transcript.start_pos,
sign=sign))
last_transcript_end = transcript.end_pos
last_transcript_neg = transcript.negative_dir
self.analyze_interonics(transcript)
def creat_intronics(self, transcript):
transcript.exons.sort()
last_exon_end = transcript.exons[0].end_pos
for exon in transcript.exons[1:]:
self.interonic_lines.append(
Line.creat_line_by_name_and_corr(
exon.chr,
"intron",
last_exon_end,
exon.start_pos,
sign="-" if exon.negative_dir else "+",
gene_name=transcript.gene_name))
last_exon_end = exon.end_pos
