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)
