def run(self):
self.getTranscriptDict()
self.getAnnotationDict()
self.getSeqDict()
self.getRefDict()
self.getAlignmentDict()
detailsDict = defaultdict(list)
classifyDict = {}
for aId, t in self.transcriptDict.iteritems():
a = self.annotationDict[psl_lib.remove_alignment_number(aId)]
aln = self.alignmentDict[aId]
if a.getCdsLength() <= 75 or t.getCdsLength() <= 75:
continue
# TODO: this will miss an inframe stop if it is the last 3 bases that are not the annotated stop.
# use the logic from EndStop to flag this
codons = list(codonPairIterator(a, t, aln, self.seqDict, self.refDict))[:-1]
for i, target_codon, query_codon in codons:
if seq_lib.codon_to_amino_acid(target_codon) == "*":
if target_codon == query_codon:
detailsDict[aId].append(seq_lib.cds_coordinate_to_bed(t, i, i + 3, self.colors["input"],
self.column))
else:
detailsDict[aId].append(seq_lib.cds_coordinate_to_bed(t, i, i + 3, self.rgb, self.column))
classifyDict[aId] = 1
if aId not in classifyDict:
classifyDict[aId] = 0
self.dumpValueDicts(classifyDict, detailsDict)
def run(self):
self.getTranscriptDict()
self.getAnnotationDict()
self.getSeqDict()
self.getRefDict()
self.getAlignmentDict()
detailsDict = defaultdict(list)
classifyDict = {}
for aId, aln in self.alignmentDict.iteritems():
if aId not in self.transcriptDict:
continue
t = self.transcriptDict[aId]
a = self.annotationDict[psl_lib.remove_alignment_number(aId)]
if a.getCdsLength() <= 75 or t.getCdsLength() <= 75:
continue
for i, target_codon, query_codon in codonPairIterator(a, t, aln, self.seqDict, self.refDict):
if target_codon != query_codon and seq_lib.codon_to_amino_acid(target_codon) == \
seq_lib.codon_to_amino_acid(query_codon):
detailsDict[aId].append(seq_lib.cds_coordinate_to_bed(t, i, i + 3, self.rgb, self.column))
classifyDict[aId] = 1
if aId not in classifyDict:
classifyDict[aId] = 0
self.dumpValueDicts(classifyDict, detailsDict)