def run(self): self.getAlignmentDict() self.getTranscriptDict() detailsDict = {} classifyDict = {} for aId, aln in self.alignmentDict.iteritems(): if aId not in self.transcriptDict: continue if aln.strand == "+" and aln.tEnd == aln.tSize and aln.qEnd != aln.qSize: detailsDict[aId] = seq_lib.transcript_to_bed(self.transcriptDict[aId], self.rgb, self.column) classifyDict[aId] = 1 elif aln.strand == "-" and aln.tStart == 0 and aln.qStart != 0: detailsDict[aId] = seq_lib.transcript_to_bed(self.transcriptDict[aId], self.rgb, self.column) classifyDict[aId] = 1 else: classifyDict[aId] = 0 self.dumpValueDicts(classifyDict, detailsDict)
def run(self, cdsCutoff=75): self.getTranscriptDict() self.getAnnotationDict() detailsDict = {} classifyDict = {} for aId, t in self.transcriptDict.iteritems(): # do not include noncoding transcripts a = self.annotationDict[psl_lib.remove_alignment_number(aId)] if a.getCdsLength() < 3: continue elif a.getCdsLength() <= cdsCutoff: detailsDict[aId] = seq_lib.transcript_to_bed(t, self.colors["input"], self.column) classifyDict[aId] = 1 elif t.getCdsLength() <= cdsCutoff: detailsDict[aId] = seq_lib.transcript_to_bed(t, self.rgb, self.column) classifyDict[aId] = 1 else: classifyDict[aId] = 0 self.dumpValueDicts(classifyDict, detailsDict)
def run(self): self.getTranscriptDict() counts = Counter(psl_lib.remove_alignment_number(aId) for aId in self.transcriptDict) detailsDict = {} classifyDict = {} for aId, t in self.transcriptDict.iteritems(): if counts[psl_lib.remove_alignment_number(aId)] > 1: detailsDict[aId] = seq_lib.transcript_to_bed(t, self.rgb, self.column + "_{}_Copies".format( counts[psl_lib.remove_alignment_number(aId)] - 1)) classifyDict[aId] = 1 else: classifyDict[aId] = 0 self.dumpValueDicts(classifyDict, detailsDict)
def run(self): self.getAugustusTranscriptDict() self.getTranscriptDict() classify_dict = {} details_dict = defaultdict(list) for aug_aId, aug_t in self.augustusTranscriptDict.iteritems(): if psl_lib.remove_augustus_alignment_number(aug_aId) not in self.transcriptDict: continue t = self.transcriptDict[psl_lib.remove_augustus_alignment_number(aug_aId)] if aug_t.strand != t.strand or aug_t.chromosome != t.chromosome: classify_dict[aug_aId] = 1 details_dict[aug_aId] = seq_lib.transcript_to_bed(aug_t, self.rgb, self.column) else: classify_dict[aug_aId] = 0 self.dumpValueDicts(classify_dict, details_dict)
def run(self): r = re.compile("-[0-9]+-") self.getAugustusTranscriptDict() counts = Counter("-".join(r.split(aug_aId)) for aug_aId in self.augustusTranscriptDict) details_dict = {} classify_dict = {} for aug_aId, aug_t in self.augustusTranscriptDict.iteritems(): if counts[psl_lib.remove_augustus_alignment_number(aug_aId)] > 1: details_dict[aug_aId] = seq_lib.transcript_to_bed( aug_t, self.rgb, self.column + "_{}_Copies".format(counts[psl_lib.remove_augustus_alignment_number(aug_aId)] - 1), ) classify_dict[aug_aId] = 1 else: classify_dict[aug_aId] = 0 self.dumpValueDicts(classify_dict, details_dict)
def run(self): r = re.compile("-[0-9]+-") self.getAugustusTranscriptDict() counts = Counter("-".join(r.split(aug_aId)) for aug_aId in self.augustusTranscriptDict) details_dict = {} classify_dict = {} for aug_aId, aug_t in self.augustusTranscriptDict.iteritems(): if counts[psl_lib.remove_augustus_alignment_number(aug_aId)] > 1: details_dict[aug_aId] = seq_lib.transcript_to_bed( aug_t, self.rgb, self.column + "_{}_Copies".format(counts[ psl_lib.remove_augustus_alignment_number(aug_aId)] - 1)) classify_dict[aug_aId] = 1 else: classify_dict[aug_aId] = 0 self.dumpValueDicts(classify_dict, details_dict)
def run(self): self.getAugustusTranscriptDict() self.getTranscriptDict() classify_dict = {} details_dict = defaultdict(list) for aug_aId, aug_t in self.augustusTranscriptDict.iteritems(): if psl_lib.remove_augustus_alignment_number( aug_aId) not in self.transcriptDict: continue t = self.transcriptDict[psl_lib.remove_augustus_alignment_number( aug_aId)] if aug_t.strand != t.strand or aug_t.chromosome != t.chromosome: classify_dict[aug_aId] = 1 details_dict[aug_aId] = seq_lib.transcript_to_bed( aug_t, self.rgb, self.column) else: classify_dict[aug_aId] = 0 self.dumpValueDicts(classify_dict, details_dict)