def GetPTDPrimerInfo(self, primer_info): #{
# [event_id, chimera.id, chimera.left, chimera.right, gene.id,
# gene.left, gene.right]
# event_id
event_id = primer_info.EventID()
# contig_id
contig = PrimerSeqCls(primer_info.ctg_id)
# contig_left
contig.left = min(primer_info.c2t_aligns[0].ctg_end,
primer_info.c2t_aligns[1].ctg_start)
# contig_right
contig.right = max(primer_info.c2t_aligns[0].ctg_end,
primer_info.c2t_aligns[1].ctg_start)
# gene_id
gene = PrimerSeqCls(primer_info.c2t_aligns[0].transcript)
# gene.left
gene.left = min(primer_info.c2t_aligns[0].transcript_end,
primer_info.c2t_aligns[1].transcript_start)
# gene.right
gene.right = max(primer_info.c2t_aligns[0].transcript_end,
primer_info.c2t_aligns[1].transcript_start)
# dup_length
dup_length = (gene.right - gene.left) + 1
# construct inferred chimera sequence
ctg_overlap = primer_info.C2TAlignOverlap()
extra = ""
if (0 > ctg_overlap): #{
extra = self.contigs[primer_info.ctg_id][contig_left+1:contig_right]
#} end if
if ("-" == primer_info.c2t_aligns[0].strand): #{
extra = ReverseComplement(extra)
#} end if
# chimera_id
chimera = PrimerSeqCls("G%i_%s_%s" % (primer_info.group_id,
primer_info.ctg_id, gene.id))
chimera.seq = (self.transcripts[gene.id][:gene.right] + extra +
self.transcripts[gene.id][gene.left-1:])
if (chimera.id in self.transcripts and
self.transcripts[chimera.id] != chimera.seq): #{
raise PrimerDesignerError("conflicting chimeric PTD sequences: %s" %
chimera.id)
#} end if
self.transcripts[chimera.id] = chimera.seq
# chimera_left
chimera.left = gene.left
# chimera_right
chimera.right = gene.right + len(extra) + dup_length
DebugMsg(self, "Overlap: %i, Extra: \"%s\", WT_Length: %i, Dup_Length: "
"%i, CT_Length: %i, Calc_Length: %i" % (ctg_overlap, extra,
len(self.transcripts[gene.id]), dup_length, len(chimera.seq),
len(self.transcripts[gene.id])+len(extra)+dup_length))
return map(str, [event_id, chimera.id, chimera.left, chimera.right,
gene.id, gene.left, gene.right])
def ConstructFusionSeq(self, primer_info, contig, ctg_overlap): #{
# chimera_id
chimera = PrimerSeqCls("G%i_%s_%s/%s" % (primer_info.group_id,
primer_info.ctg_id, primer_info.c2t_aligns[0].transcript,
primer_info.c2t_aligns[1].transcript))
left_seq = self.RefSeqFromAlign0(primer_info.c2t_aligns[0])
right_seq = self.RefSeqFromAlign1(primer_info.c2t_aligns[1])
extra = ""
if (0 > ctg_overlap): #{
extra = self.contigs[primer_info.ctg_id][contig.left:contig.right-1]
else:
right_seq = right_seq[ctg_overlap:]
#} end if
chimera.seq = (left_seq + extra + right_seq)
# chimera_left
chimera.left = min(len(left_seq), len(left_seq)+ctg_overlap)
# chimera_right
chimera.right = max(len(left_seq), len(left_seq)+ctg_overlap)
DebugMsg(self, "Left: %s\nExtra: %s\nRight: %s\nOverlap: %i, "
"WT_Length0: %i, WT_Length1: %i, Extra_len: %i, CT_Length: %i, "
"Calc_Length: %i" % (left_seq, extra, right_seq, ctg_overlap,
len(left_seq), len(right_seq)+max(0,ctg_overlap), len(extra),
len(chimera.seq), len(left_seq)+len(right_seq)+len(extra)))
return chimera
