def del_is_intron(self, start, end, txt):
"""Determines if coordinate is intron"""
for i in range(len(txt.exons)-1):
intron = [int(txt.exons[i][1])+1, int(txt.exons[i+1][0])-1]
olap_size = overlap([start, end], intron)
if float(olap_size) / float(cardinality([start, end])) > 0.9 and\
float(olap_size) / float(cardinality(intron)) > 0.9:
return True
return False
def details(self, refseq=None):
"""Sets relevant attributes of events"""
if self.event_type == "retained_intron":
apart = int(self.exon_coords[1][0]) - 1 - int(self.exon_coords[0][1])
self.multi_3 = self.multiple_3(apart)
else:
self.multi_3 = None
# splice sites
self.splice = None
if self.event_type in ("AS5", "AS3"):
ss = self.get_splice_sites(self.align_blocks[0], left=self.left, right=self.right)
if ss and len(ss) > 0:
self.splice = ss[0]
elif self.event_type in ("novel_exon", "AS53", "novel_transcript", "novel_utr"):
splice_sites = []
for block in self.align_blocks:
ss = ",".join(self.get_splice_sites(block, left=True, right=True))
if ss:
splice_sites.append(ss)
if splice_sites:
self.splice = "-".join(splice_sites)
elif self.event_type == "novel_intron":
ss = self.get_splice_sites(self.align_blocks[0], left=False, right=True, whole=True)
if ss and len(ss) > 0:
self.splice = ss[0]
# size
self.size = None
if self.event_type in ("novel_exon", "AS53", "novel_transcript", "novel_utr", "novel_intron"):
sizes = []
for block in self.align_coords:
sizes.append(str(cardinality(block)))
self.size = ",".join(sizes)
# orf
if refseq:
self.find_pep_change(refseq)