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):
stopCodons = ('TAA', 'TGA', 'TAG')
self.getAlignmentDict()
self.getTranscriptDict()
self.getAnnotationDict()
self.getSeqDict()
self.getRefDict()
detailsDict = {}
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
s = t.getCdsLength()
cds_positions = [t.chromosome_coordinate_to_cds(aln.query_coordinate_to_target(a.cds_coordinate_to_transcript(i)))
for i in xrange(s - 4, s - 1)]
if None in cds_positions or t.get_cds(self.seqDict)[-3:] not in stopCodons:
# does this problem exist in the reference?
if a.get_cds(self.refDict)[-3:] not in stopCodons:
detailsDict[aId] = seq_lib.cds_coordinate_to_bed(t, s - 3, s, self.colors["input"], self.column)
else:
detailsDict[aId] = seq_lib.cds_coordinate_to_bed(t, s - 3, s, self.rgb, self.column)
classifyDict[aId] = 1
else:
classifyDict[aId] = 0
self.dumpValueDicts(classifyDict, detailsDict)
def run(self):
self.getTranscriptDict()
self.getAlignmentDict()
self.getAnnotationDict()
self.getSeqDict()
self.getRefDict()
detailsDict = {}
classifyDict = {}
for aId, t in self.transcriptDict.iteritems():
a = self.annotationDict[psl_lib.remove_alignment_number(aId)]
aln = self.alignmentDict[aId]
# do not include noncoding transcripts or lift-overs that contain less than 25 codons
if a.getCdsLength() <= 75 or t.getCdsLength() <= 75:
continue
cds_positions = [t.chromosome_coordinate_to_cds(aln.query_coordinate_to_target(a.cds_coordinate_to_transcript(i)))
for i in xrange(3)]
if None in cds_positions:
detailsDict[aId] = seq_lib.cds_coordinate_to_bed(t, 0, 3, self.rgb, self.column)
classifyDict[aId] = 1
elif t.get_cds(self.seqDict)[:3] != "ATG":
if a.get_cds(self.refDict)[:3] != "ATG":
detailsDict[aId] = seq_lib.cds_coordinate_to_bed(t, 0, 3, self.colors["input"], self.column)
else:
detailsDict[aId] = seq_lib.cds_coordinate_to_bed(t, 0, 3, self.rgb, self.column)
classifyDict[aId] = 1
else:
classifyDict[aId] = 0
self.dumpValueDicts(classifyDict, detailsDict)
def run(self):
self.getTranscriptDict()
self.getAnnotationDict()
detailsDict = {}
classifyDict = {}
for aId, t in self.transcriptDict.iteritems():
a = self.annotationDict[psl_lib.remove_alignment_number(aId)]
# do not include noncoding transcripts or lift-overs that contain less than 25 codon
if a.getCdsLength() <= 75 or t.getCdsLength() <= 75:
continue
# is this is a problem in the reference?
# remove all -1 frames because those are UTR exons
a_frames = [x for x in a.exonFrames if x != -1]
if a.strand is True and a_frames[0] != 0 or a.strand is False and a_frames[-1] != 0:
classifyDict[aId] = 1
detailsDict[aId] = seq_lib.cds_coordinate_to_bed(t, 0, 3, self.colors["input"], self.column)
continue
# remove all -1 frames because those are UTR exons
t_frames = [x for x in t.exonFrames if x != -1]
if t.strand is True and t_frames[0] != 0 or t.strand is False and t_frames[-1] != 0:
classifyDict[aId] = 1
detailsDict[aId] = seq_lib.cds_coordinate_to_bed(t, 0, 3, self.rgb, self.column)
continue
classifyDict[aId] = 0
self.dumpValueDicts(classifyDict, detailsDict)
def run(self):
self.getAugustusTranscriptDict()
self.getTranscriptDict()
classify_dict = {}
details_dict = {}
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 or t.thickStart == t.thickStop:
continue
if t.thickStart != aug_t.thickStart or t.thickStop != aug_t.thickStop:
classify_dict[aug_aId] = 1
s = aug_t.getCdsLength()
if s > 9:
details_dict[aug_aId] = [
seq_lib.cds_coordinate_to_bed(aug_t, 0, 3, self.rgb,
self.column),
seq_lib.cds_coordinate_to_bed(aug_t, s - 3, s,
self.rgb, self.column)
]
else:
details_dict[aug_aId] = seq_lib.cds_coordinate_to_bed(
aug_t, 0, s, self.rgb, self.column)
else:
classify_dict[aug_aId] = 0
self.dumpValueDicts(classify_dict, details_dict)
def run(self):
self.getAugustusTranscriptDict()
self.getTranscriptDict()
classify_dict = {}
details_dict = {}
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 or t.thickStart == t.thickStop:
continue
if t.thickStart != aug_t.thickStart or t.thickStop != aug_t.thickStop:
classify_dict[aug_aId] = 1
s = aug_t.getCdsLength()
if s > 9:
details_dict[aug_aId] = [
seq_lib.cds_coordinate_to_bed(aug_t, 0, 3, self.rgb, self.column),
seq_lib.cds_coordinate_to_bed(aug_t, s - 3, s, self.rgb, self.column),
]
else:
details_dict[aug_aId] = seq_lib.cds_coordinate_to_bed(aug_t, 0, s, self.rgb, self.column)
else:
classify_dict[aug_aId] = 0
self.dumpValueDicts(classify_dict, details_dict)
def run(self, cds=False):
self.getTranscriptDict()
self.getSeqDict()
detailsDict = {}
classifyDict = {}
r = re.compile("[atgcATGC][N]+[atgcATGC]")
for aId, t in self.transcriptDict.iteritems():
if cds is True:
s = t.get_cds(self.seqDict)
tmp = [seq_lib.cds_coordinate_to_bed(t, m.start() + 1, m.end() - 1, self.rgb, self.column) for m in
re.finditer(r, s)]
else:
s = t.get_mrna(self.seqDict)
tmp = [seq_lib.transcript_coordinate_to_bed(t, m.start() + 1, m.end() - 1, self.rgb, self.column) for m in
re.finditer(r, s)]
if len(tmp) > 0:
detailsDict[aId] = tmp
classifyDict[aId] = 1
else:
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)
