def get_introns(self):
"""Returns a list of coordinates that represent the introns for
this transcript"""
introns = []
for i in range(len(self.exons)-1):
ex1 = self.exons[i]
ex2 = self.exons[i+1]
if self.strand == -1:
intron = Coord(self.chrom, ex2.end+1, ex1.start-1,
strand=self.strand)
else:
intron = Coord(self.chrom, ex1.end+1, ex2.start-1,
strand=self.strand)
intron.exon_5p = ex1
intron.exon_3p = ex2
introns.append(intron)
if self.intron_scores is not None:
intron.score = self.intron_scores[i]
if self.known_intron_flags is not None:
if self.known_intron_flags[i] == "1":
intron.is_known = True
else:
intron.is_known = False
return introns
def get_introns(self):
"""Returns a list of coordinates that represent the introns for
this transcript"""
introns = []
for i in range(len(self.exons) - 1):
ex1 = self.exons[i]
ex2 = self.exons[i + 1]
if self.strand == -1:
intron = Coord(self.chrom,
ex2.end + 1,
ex1.start - 1,
strand=self.strand)
else:
intron = Coord(self.chrom,
ex1.end + 1,
ex2.start - 1,
strand=self.strand)
intron.exon_5p = ex1
intron.exon_3p = ex2
introns.append(intron)
if self.intron_scores is not None:
intron.score = self.intron_scores[i]
if self.known_intron_flags is not None:
if self.known_intron_flags[i] == "1":
intron.is_known = True
else:
intron.is_known = False
return introns
