def updateContext(oFN, wigDir, chrom, strand, rn = None, tn = None):
oNX = cgNexusFlat.Nexus(oFN, degPeak.degPeak)
oNX.load(['context', 'tcc'], [rn, tn])
print 'loading wig'
coord_contexts = cgWig.loadSingleWigContext(wigDir, chrom, strand, 'context')
print 'done loading'
ds = bioLibCG.dominantSpotter(['C_EXON', 'C_3UTR', 'C_5UTR', 'NC_EXON', 'NC_3UTR', 'NC_5UTR', 'C_INTRON', 'NC_INTRON', 'INTER'])
for oID in oNX.tcc:
oChrom, oStrand, start, end = bioLibCG.tccSplit(oNX.tcc[oID])
#deg wigs is AS to actual clipping site
if oStrand == '1':
oStrand = '-1'
else:
oStrand = '1'
if oChrom == chrom and oStrand == strand:
contexts = coord_contexts.get(start, 'INTER').split(',')
oNX.context[oID] = ds.spotItem(contexts)
oNX.save()
def updateContext(oFN, wigDir, chrom, strand, switchStrand = False):
oNX = cgNexusFlat.Nexus(oFN, cgDegPeak.Peak)
oNX.load(['tcc', 'context'])
if switchStrand:
strand = str(-int(strand))
else:
strand = str(strand)
print 'loading wig'
coord_contexts = cgWig.loadSingleWigContext(wigDir, chrom, strand, 'context')
print 'done loading'
ds = bioLibCG.dominantSpotter(['C_EXON', 'C_3UTR', 'C_5UTR', 'NC_EXON', 'NC_3UTR', 'NC_5UTR', 'C_INTRON', 'NC_INTRON', 'INTER'])
for oID in oNX.tcc:
oChrom, oStrand, start, end = bioLibCG.tccSplit(oNX.tcc[oID])
#deg wigs is AS to actual clipping site
if switchStrand:
oStrand = str(-int(strand))
else:
oStrand = str(oStrand)
if oChrom == chrom and oStrand == strand:
contexts = coord_contexts.get(start, 'INTER').split(',')
oNX.context[oID] = ds.spotItem(contexts)
oNX.save()
def updateContext(fN, fF, wigDir, chrom, strand, switchStrand = False):
NX = Nexus(fN, fF)
NX.load(['tcc', 'context'])
if switchStrand:
strand = str(-int(strand))
else:
strand = str(strand)
print 'loading wig'
coord_contexts = cgWig.loadSingleWigContext(wigDir, chrom, strand, 'context')
print 'done loading'
ds = bioLibCG.dominantSpotter(['C_EXON', 'C_3UTR', 'C_5UTR', 'NC_EXON', 'NC_3UTR', 'NC_5UTR', 'C_INTRON', 'NC_INTRON', 'INTER'])
while NX.nextID():
oChrom, oStrand, start, end = bioLibCG.tccSplit(NX.tcc)
#deg wigs is AS to actual clipping site
if switchStrand:
oStrand = str(-int(strand))
else:
oStrand = str(oStrand)
if oChrom == chrom and oStrand == strand:
contexts = coord_contexts.get(start, 'INTER').split(',')
NX.context = ds.spotItem(contexts)
NX.save()
def updateContext(oFN, wigDir, chrom, strand, rn=None, tn=None):
oNX = cgNexusFlat.Nexus(oFN, degPeak.degPeak)
oNX.load(['context', 'tcc'], [rn, tn])
print 'loading wig'
coord_contexts = cgWig.loadSingleWigContext(wigDir, chrom, strand,
'context')
print 'done loading'
ds = bioLibCG.dominantSpotter([
'C_EXON', 'C_3UTR', 'C_5UTR', 'NC_EXON', 'NC_3UTR', 'NC_5UTR',
'C_INTRON', 'NC_INTRON', 'INTER'
])
for oID in oNX.tcc:
oChrom, oStrand, start, end = bioLibCG.tccSplit(oNX.tcc[oID])
#deg wigs is AS to actual clipping site
if oStrand == '1':
oStrand = '-1'
else:
oStrand = '1'
if oChrom == chrom and oStrand == strand:
contexts = coord_contexts.get(start, 'INTER').split(',')
oNX.context[oID] = ds.spotItem(contexts)
oNX.save()
def updateTypeAlignment(oFN, wigDir, chrom, strand, rn = None, tn = None):
'''This is for ALIGNMENTS...NOT DEG PEAKS!'''
oNX = cgNexusFlat.Nexus(oFN, cgAlignmentFlat.cgAlignment)
oNX.load(['tTcc', 'type'], [rn, tn])
if strand == '1':
strand = '-1'
else:
strand = '1'
print 'loading wig'
coord_types = cgWig.loadSingleWigContext(wigDir, chrom, strand, 'tType')
print 'done loading'
domOrder = ['microRNA_noncoding',
'lincRNA_noncoding',
'longNC_noncoding',
'miRNA_pseudogene_noncoding',
'Mt_rRNA_noncoding',
'Mt_tRNA_noncoding',
'Mt_tRNA_pseudogene_noncoding',
'rRNA_noncoding',
'rRNA_pseudogene_noncoding',
'scRNA_pseudogene_noncoding',
'snoRNA_noncoding',
'snoRNA_pseudogene_noncoding',
'snRNA_noncoding',
'snRNA_pseudogene_noncoding',
'tRNA_pseudogene_noncoding',
'pseudogene_noncoding',
'protein_coding',
'None']
ds = bioLibCG.dominantSpotter(domOrder)
for oID in oNX.tTcc:
oChrom, oStrand, start, end = bioLibCG.tccSplit(oNX.tTcc[oID])
#deg wigs is AS to actual clipping site
if oStrand == '1':
oStrand = '-1'
else:
oStrand = '1'
if oChrom == chrom and oStrand == strand:
tranTypes = coord_types.get(start, 'None').split(',')
types = [x.split(':')[1] if x != 'None' else 'None' for x in tranTypes]
types = list(set(types))
oNX.type[oID] = ds.spotItem(types)
oNX.save()
def updateType(oFN, wigDir, chrom, strand, rn = None, tn = None):
oNX = cgNexusFlat.Nexus(oFN, cgOriginRNAFlat.OriginRNA)
oNX.load(['tcc', 'transcriptType', 'transcriptTypes'], [rn, tn])
print 'loading wig'
coord_types = cgWig.loadSingleWigContext(wigDir, chrom, strand, 'tType')
print 'done loading'
domOrder = ['microRNA_noncoding',
'lincRNA_noncoding',
'longNC_noncoding',
'miRNA_pseudogene_noncoding',
'Mt_rRNA_noncoding',
'Mt_tRNA_noncoding',
'Mt_tRNA_pseudogene_noncoding',
'rRNA_noncoding',
'rRNA_pseudogene_noncoding',
'scRNA_pseudogene_noncoding',
'snoRNA_noncoding',
'snoRNA_pseudogene_noncoding',
'snRNA_noncoding',
'snRNA_pseudogene_noncoding',
'tRNA_pseudogene_noncoding',
'pseudogene_noncoding',
'protein_coding',
'None']
ds = cg.dominantSpotter(domOrder)
for oID in oNX.tcc:
oChrom, oStrand, start, end = cg.tccSplit(oNX.tcc[oID])
if oChrom == chrom and oStrand == strand:
tranTypes = coord_types.get(start, 'None').split(',')
types = [x.split(':')[1] if x != 'None' else 'None' for x in tranTypes]
types = list(set(types))
oNX.transcriptTypes[oID] = types
oNX.transcriptType[oID] = ds.spotItem(types)
oNX.save()
def updateType(oFN, wigDir, chrom, strand, rn=None, tn=None):
oNX = cgNexusFlat.Nexus(oFN, cgDegPeak.Peak)
oNX.load(['tcc', 'type'], [rn, tn])
if strand == '1':
strand = '-1'
else:
strand = '1'
print 'loading wig'
coord_types = cgWig.loadSingleWigContext(wigDir, chrom, strand, 'tType')
print 'done loading'
domOrder = [
'protein_coding', 'miRNA', 'rRNA', 'snoRNA', 'snRNA', 'lincRNA',
'longNC', 'misc_RNA', 'Mt_rRNA', 'Mt_tRNA', 'misc_RNA_pseudogene',
'Mt_tRNA_pseudogene', 'polymorphic_pseudogene', 'processed_transcript',
'miRNA_pseudogene', 'rRNA_pseudogene', 'scRNA_pseudogene',
'snoRNA_pseudogene', 'snRNA_pseudogene', 'tRNA_pseudogene',
'pseudogene', 'TR_C_gene', 'TR_J_gene', 'TR_V_gene', 'TR_V_pseudogene',
'IG_C_gene', 'IG_C_pseudogene', 'IG_D_gene', 'IG_J_gene',
'IG_J_pseudogene', 'IG_V_gene', 'IG_V_pseudogene', 'unknown', 'None'
]
ds = bioLibCG.dominantSpotter(domOrder)
for oID in oNX.tcc:
oChrom, oStrand, start, end = bioLibCG.tccSplit(oNX.tcc[oID])
#deg wigs is AS to actual clipping site
if oStrand == '1':
oStrand = '-1'
else:
oStrand = '1'
if oChrom == chrom and oStrand == strand:
tranTypes = coord_types.get(start, 'None').split(',')
print tranTypes
types = [
x.split(':')[1] if x != 'None' else ['None'] for x in tranTypes
]
oNX.type = oNX.transcriptType = ds.spotItem(types)
oNX.save()
def updateType(oFN, wigDir, chrom, strand, rn = None, tn = None):
oNX = cgNexusFlat.Nexus(oFN, cgOriginRNAFlat.OriginRNA)
oNX.load(['tcc', 'transcriptType', 'transcriptTypes'], [rn, tn])
print 'loading wig'
coord_types = cgWig.loadSingleWigContext(wigDir, chrom, strand, 'tType')
print 'done loading'
domOrder = ['microRNA_noncoding',
'lincRNA_noncoding',
'longNC_noncoding',
'miRNA_pseudogene_noncoding',
'Mt_rRNA_noncoding',
'Mt_tRNA_noncoding',
'Mt_tRNA_pseudogene_noncoding',
'rRNA_noncoding',
'rRNA_pseudogene_noncoding',
'scRNA_pseudogene_noncoding',
'snoRNA_noncoding',
'snoRNA_pseudogene_noncoding',
'snRNA_noncoding',
'snRNA_pseudogene_noncoding',
'tRNA_pseudogene_noncoding',
'pseudogene_noncoding',
'protein_coding',
'None']
ds = cg.dominantSpotter(domOrder)
for oID in oNX.tcc:
oChrom, oStrand, start, end = cg.tccSplit(oNX.tcc[oID])
if oChrom == chrom and oStrand == strand:
tranTypes = coord_types.get(start, 'None').split(',')
types = [x.split(':')[1] if x != 'None' else 'None' for x in tranTypes]
types = list(set(types))
oNX.transcriptTypes[oID] = types
oNX.transcriptType[oID] = ds.spotItem(types)
oNX.save()
def updateTypeAlignment(oFN, wigDir, chrom, strand, rn=None, tn=None):
'''This is for ALIGNMENTS...NOT DEG PEAKS!'''
oNX = cgNexusFlat.Nexus(oFN, cgAlignmentFlat.cgAlignment)
oNX.load(['tTcc', 'type'], [rn, tn])
if strand == '1':
strand = '-1'
else:
strand = '1'
print 'loading wig'
coord_types = cgWig.loadSingleWigContext(wigDir, chrom, strand, 'tType')
print 'done loading'
domOrder = [
'microRNA_noncoding', 'lincRNA_noncoding', 'longNC_noncoding',
'miRNA_pseudogene_noncoding', 'Mt_rRNA_noncoding', 'Mt_tRNA_noncoding',
'Mt_tRNA_pseudogene_noncoding', 'rRNA_noncoding',
'rRNA_pseudogene_noncoding', 'scRNA_pseudogene_noncoding',
'snoRNA_noncoding', 'snoRNA_pseudogene_noncoding', 'snRNA_noncoding',
'snRNA_pseudogene_noncoding', 'tRNA_pseudogene_noncoding',
'pseudogene_noncoding', 'protein_coding', 'None'
]
ds = bioLibCG.dominantSpotter(domOrder)
for oID in oNX.tTcc:
oChrom, oStrand, start, end = bioLibCG.tccSplit(oNX.tTcc[oID])
#deg wigs is AS to actual clipping site
if oStrand == '1':
oStrand = '-1'
else:
oStrand = '1'
if oChrom == chrom and oStrand == strand:
tranTypes = coord_types.get(start, 'None').split(',')
types = [
x.split(':')[1] if x != 'None' else 'None' for x in tranTypes
]
types = list(set(types))
oNX.type[oID] = ds.spotItem(types)
oNX.save()
def updateType(oFN, wigDir, chrom, strand, rn = None, tn = None):
oNX = cgNexusFlat.Nexus(oFN, cgDegPeak.Peak)
oNX.load(['tcc', 'type'], [rn, tn])
if strand == '1':
strand = '-1'
else:
strand = '1'
print 'loading wig'
coord_types = cgWig.loadSingleWigContext(wigDir, chrom, strand, 'tType')
print 'done loading'
domOrder = ['protein_coding', 'miRNA', 'rRNA', 'snoRNA', 'snRNA', 'lincRNA', 'longNC', 'misc_RNA',
'Mt_rRNA', 'Mt_tRNA', 'misc_RNA_pseudogene', 'Mt_tRNA_pseudogene', 'polymorphic_pseudogene',
'processed_transcript', 'miRNA_pseudogene', 'rRNA_pseudogene', 'scRNA_pseudogene',
'snoRNA_pseudogene', 'snRNA_pseudogene', 'tRNA_pseudogene', 'pseudogene', 'TR_C_gene',
'TR_J_gene', 'TR_V_gene', 'TR_V_pseudogene', 'IG_C_gene', 'IG_C_pseudogene', 'IG_D_gene',
'IG_J_gene', 'IG_J_pseudogene', 'IG_V_gene', 'IG_V_pseudogene', 'unknown', 'None']
ds = bioLibCG.dominantSpotter(domOrder)
for oID in oNX.tcc:
oChrom, oStrand, start, end = bioLibCG.tccSplit(oNX.tcc[oID])
#deg wigs is AS to actual clipping site
if oStrand == '1':
oStrand = '-1'
else:
oStrand = '1'
if oChrom == chrom and oStrand == strand:
tranTypes = coord_types.get(start, 'None').split(',')
print tranTypes
types = [x.split(':')[1] if x != 'None' else ['None'] for x in tranTypes]
oNX.type = oNX.transcriptType = ds.spotItem(types)
oNX.save()
def updateContext(oFN, wigDir, chrom, strand, rn = None, tn = None):
oNX = cgNexusFlat.Nexus(oFN, cgOriginRNAFlat.OriginRNA)
oNX.load(['tcc', 'context'], [rn, tn])
print 'loading wig'
coord_contexts = cgWig.loadSingleWigContext(wigDir, chrom, strand, 'context')
print 'done loading'
ds = cg.dominantSpotter(['C_EXON', 'C_3UTR', 'C_5UTR', 'NC_EXON', 'NC_3UTR', 'NC_5UTR', 'C_INTRON', 'NC_INTRON', 'INTER'])
for oID in oNX.tcc:
oChrom, oStrand, start, end = cg.tccSplit(oNX.tcc[oID])
if oChrom == chrom and oStrand == strand:
contexts = coord_contexts.get(start, 'INTER').split(',')
oNX.context[oID] = ds.spotItem(contexts)
oNX.save()
def updateContext(oFN, wigDir, chrom, strand, rn = None, tn = None):
oNX = cgNexusFlat.Nexus(oFN, cgOriginRNAFlat.OriginRNA)
oNX.load(['tcc', 'context'], [rn, tn])
print 'loading wig'
coord_contexts = cgWig.loadSingleWigContext(wigDir, chrom, strand, 'context')
print 'done loading'
ds = cg.dominantSpotter(['C_EXON', 'C_3UTR', 'C_5UTR', 'NC_EXON', 'NC_3UTR', 'NC_5UTR', 'C_INTRON', 'NC_INTRON', 'INTER'])
for oID in oNX.tcc:
oChrom, oStrand, start, end = cg.tccSplit(oNX.tcc[oID])
if oChrom == chrom and oStrand == strand:
contexts = coord_contexts.get(start, 'INTER').split(',')
oNX.context[oID] = ds.spotItem(contexts)
oNX.save()
def updateContext(oFN, wigDir, chrom, strand, switchStrand=False):
oNX = cgNexusFlat.Nexus(oFN, cgDegPeak.Peak)
oNX.load(['tcc', 'context'])
if switchStrand:
strand = str(-int(strand))
else:
strand = str(strand)
print 'loading wig'
coord_contexts = cgWig.loadSingleWigContext(wigDir, chrom, strand,
'context')
print 'done loading'
ds = bioLibCG.dominantSpotter([
'C_EXON', 'C_3UTR', 'C_5UTR', 'NC_EXON', 'NC_3UTR', 'NC_5UTR',
'C_INTRON', 'NC_INTRON', 'INTER'
])
for oID in oNX.tcc:
oChrom, oStrand, start, end = bioLibCG.tccSplit(oNX.tcc[oID])
#deg wigs is AS to actual clipping site
if switchStrand:
oStrand = str(-int(strand))
else:
oStrand = str(oStrand)
if oChrom == chrom and oStrand == strand:
contexts = coord_contexts.get(start, 'INTER').split(',')
oNX.context[oID] = ds.spotItem(contexts)
oNX.save()
def updateContext(oDir, geneSetFN):
print 'loading oRNA'
oDC = cgDB.dataController(oDir, cgOriginRNA.OriginRNA)
id_oRNA = oDC.load()
print 'loading gene set'
geneSet = cgGenes3.createGeneSetEditing(geneSetFN)
#Get in terms of tccs
print 'Joining'
oTcc_oRNA = oneToOne(id_oRNA.values(), 'tcc')
tTcc_transcripts = oneToMany(geneSet.transcripts, 'tcc')
#Overlap tccs
print 'overlapping'
oTcc_tTccs = compareData.getIndividualOverlaps(oTcc_oRNA.keys(), tTcc_transcripts.keys(), 1)
#create final dictionary containing {oRNA : [transcript, ..]}
oRNA_transcripts = {}
for oTcc in oTcc_tTccs:
oRNA = oTcc_oRNA[oTcc]
oRNA_transcripts[oRNA] = []
for tTcc in oTcc_tTccs[oTcc]:
oRNA_transcripts[oRNA].extend(tTcc_transcripts[tTcc])
print 'get context info'
#Go through each site and find out what it overlaps, and if it is in a coding region...
ds = bioLibCG.dominantSpotter(['EXON_INTRON', '3UTR', '5UTR', 'EXON', 'INTRON'])
for oRNA in oRNA_transcripts:
oRNA.transcriptIDs = []
oRNA.transcriptContexts = []
oRNA.transcriptTypes = []
oRNA.transcriptCodingTypes = []
if len(oRNA_transcripts[oRNA]) == 0:
continue
for transcript in oRNA_transcripts[oRNA]:
codingTranscript = '_coding' in transcript.tType
tType = None
codingFlag = None
tTypes = [x[1] for x in transcript.getOverlappingElements(oRNA.tcc)]
#categorize border types
tType = ds.spotItem(tTypes)
if tType == 'EXON' or 'EXON_INTRON':
if codingTranscript:
codingFlag = 'C'
else:
codingFlag = 'NC'
else:
codingFlag = 'NC'
oRNA.transcriptIDs.append(transcript.id)
oRNA.transcriptContexts.append(tType)
oRNA.transcriptTypes.append(transcript.tType)
oRNA.transcriptCodingTypes.append(codingFlag)
oDC.commit(id_oRNA)
