def find_pep_change(self, refseq):
"""Finds effect on protein sequence given event"""
if self.event_type == 'novel_transcript':
return self.longest_orf()
coord = re.split('[:-]', self.coordinate())
variant = None
if self.event_type == 'novel_utr':
# include the block that's 'matching' (partially)
if min(self.align_blocks) == 1:
b1 = self.align_blocks[0]
b2 = self.align_blocks[-1] + 1
else:
b1 = self.align_blocks[0] - 1
b2 = self.align_blocks[-1]
qcoord1 = self.align.query_blocks[b1-1][0]
qcoord2 = self.align.query_blocks[b2-1][1]
else:
qcoord1 = self.align.query_blocks[self.align_blocks[0]-1][0]
qcoord2 = self.align.query_blocks[self.align_blocks[-1]-1][1]
if qcoord1 < qcoord2:
variant = self.align.contig.sequence[qcoord1-1:qcoord2]
else:
variant = self.align.contig.sequence[qcoord2-1:qcoord1]
variant = reverse_complement(variant)
# constructs cDNA sequence of both reference and sequence with event
cdna_original = self.construct_cdna(coord, self.txt, refseq)
cdna_changed = self.construct_cdna(coord, self.txt, refseq, variant=variant, change=self.event_type, exons=self.exons)
frame = 0
if self.event_type == 'novel_utr':
frame = None
if self.txt.strand == '+':
pep_original = translate(cdna_original, orient='+', frame=0)
pep_changed = translate(cdna_changed, orient='+', frame=frame)
else:
pep_original = translate(cdna_original, orient='-', frame=0)
pep_changed = translate(cdna_changed, orient='-', frame=frame)
if not pep_changed or not pep_original or self.event_type == 'read-through':
return 'na'
self.orf = pep_change(pep_original, pep_changed)
def find_pep_change(self, coord, txt, refseq, variant, change):
"""Finds peptide change due to variant"""
cdna_original = self.construct_cdna(coord, txt, refseq)
cdna_changed = self.construct_cdna(coord, txt, refseq, variant, change)
if txt.strand == '+':
pep_original = translate(cdna_original, orient='+', frame=0)
pep_changed = translate(cdna_changed, orient='+', frame=0)
else:
pep_original = translate(cdna_original, orient='-', frame=0)
pep_changed = translate(cdna_changed, orient='-', frame=0)
if not pep_changed or not pep_original:
return 'na'
mutation = pep_change(pep_original, pep_changed)
return mutation
