def updateContext(editFN, geneSetFN, outFN, refBase = 'A'):
print refBase
#Load Transcripts and Editing Sites
print 'loading editing sites'
eSites = cgEdit.loadEditingSites(editFN, refBase)
print 'loading gene set'
geneSet = cgGenes3.createGeneSetEditing(geneSetFN)
#make the eSites 0 based
for eSite in eSites:
#redo coordinate and tcc
eSite.coordinate = eSite.coordinate - 1
eSite.tcc = bioLibCG.makeTcc(eSite.chromosome, eSite.strand, eSite.coordinate, eSite.coordinate)
#Create Joint dictionaries
print 'creating joint dictionaries'
eJoint = {} #tcc : eSite
for eSite in eSites:
eJoint[eSite.tcc] = eSite
tJoint = {} # tcc : [transcript, ...]
for transcript in geneSet.transcripts:
if transcript.tcc in tJoint:
tJoint[transcript.tcc].append(transcript)
else:
tJoint[transcript.tcc] = [transcript]
#Overlap tccs
print 'overlapping joints'
##make new 0-based keys
tccOverlaps = compareData.getIndividualOverlaps(eJoint.keys(), tJoint.keys(), 1)
print 'creating final dictionary'
#create final dictionary containing {edit sites : [transcript, ..]}
eSiteTranscripts = {} # edit site: [transcript, ..]
for eTcc in tccOverlaps:
eSite = eJoint[eTcc]
eSiteTranscripts[eSite] = []
for tTcc in tccOverlaps[eTcc]:
eSiteTranscripts[eSite].extend(tJoint[tTcc])
print 'get context info'
#Go through each site and find out what it overlaps, and if it is in a coding region...
fOut = open(outFN, 'w')
for eSite in eSiteTranscripts:
if len(eSiteTranscripts[eSite]) == 0:
#label intergenic
tType = 'INTER'
codingFlag = 'NC'
fOut.write('%s\t%s\t%s\t%s\t%s\t%s\n' % (eSite.ID, 'NONE', 'NONE', tType, codingFlag, 'NONE'))
continue
for transcript in eSiteTranscripts[eSite]:
codingTranscript = '_coding' in transcript.tType
tType = None
codingFlag = None
tTypes = [ x[1] for x in transcript.getOverlappingElements(eSite.tcc)]
if '3UTR' in tTypes:
tType = '3UTR'
elif '5UTR' in tTypes:
tType = '5UTR'
else:
tType = tTypes[0] #has to be one thing...exon or intron
#This only works because UTR takes precedence over EXON in TYPE.
if tType == 'EXON':
if codingTranscript:
codingFlag = 'C'
else:
codingFlag = 'NC'
else:
codingFlag = 'NC'
fOut.write('%s\t%s\t%s\t%s\t%s\t%s\n' % (eSite.ID, transcript.parent, transcript.id, tType, codingFlag, transcript.tType))
#fOut.write('%s:%s:%s\t%s\t%s\t%s\t%s\n' % (eSite.chromosome, eSite.strand, eSite.coordinate, transcript.parent, transcript.id, tType, codingFlag))
fOut.close()
def updateContext(editFN, geneSetFN, outFN, refBase='A'):
print refBase
#Load Transcripts and Editing Sites
print 'loading editing sites'
eSites = cgEdit.loadEditingSites(editFN, refBase)
print 'loading gene set'
geneSet = cgGenes3.createGeneSetEditing(geneSetFN)
#make the eSites 0 based
for eSite in eSites:
#redo coordinate and tcc
eSite.coordinate = eSite.coordinate - 1
eSite.tcc = bioLibCG.makeTcc(eSite.chromosome, eSite.strand,
eSite.coordinate, eSite.coordinate)
#Create Joint dictionaries
print 'creating joint dictionaries'
eJoint = {} #tcc : eSite
for eSite in eSites:
eJoint[eSite.tcc] = eSite
tJoint = {} # tcc : [transcript, ...]
for transcript in geneSet.transcripts:
if transcript.tcc in tJoint:
tJoint[transcript.tcc].append(transcript)
else:
tJoint[transcript.tcc] = [transcript]
#Overlap tccs
print 'overlapping joints'
##make new 0-based keys
tccOverlaps = compareData.getIndividualOverlaps(eJoint.keys(),
tJoint.keys(), 1)
print 'creating final dictionary'
#create final dictionary containing {edit sites : [transcript, ..]}
eSiteTranscripts = {} # edit site: [transcript, ..]
for eTcc in tccOverlaps:
eSite = eJoint[eTcc]
eSiteTranscripts[eSite] = []
for tTcc in tccOverlaps[eTcc]:
eSiteTranscripts[eSite].extend(tJoint[tTcc])
print 'get context info'
#Go through each site and find out what it overlaps, and if it is in a coding region...
fOut = open(outFN, 'w')
for eSite in eSiteTranscripts:
if len(eSiteTranscripts[eSite]) == 0:
#label intergenic
tType = 'INTER'
codingFlag = 'NC'
fOut.write('%s\t%s\t%s\t%s\t%s\t%s\n' %
(eSite.ID, 'NONE', 'NONE', tType, codingFlag, 'NONE'))
continue
for transcript in eSiteTranscripts[eSite]:
codingTranscript = '_coding' in transcript.tType
tType = None
codingFlag = None
tTypes = [
x[1] for x in transcript.getOverlappingElements(eSite.tcc)
]
if '3UTR' in tTypes:
tType = '3UTR'
elif '5UTR' in tTypes:
tType = '5UTR'
else:
tType = tTypes[0] #has to be one thing...exon or intron
#This only works because UTR takes precedence over EXON in TYPE.
if tType == 'EXON':
if codingTranscript:
codingFlag = 'C'
else:
codingFlag = 'NC'
else:
codingFlag = 'NC'
fOut.write('%s\t%s\t%s\t%s\t%s\t%s\n' %
(eSite.ID, transcript.parent, transcript.id, tType,
codingFlag, transcript.tType))
#fOut.write('%s:%s:%s\t%s\t%s\t%s\t%s\n' % (eSite.chromosome, eSite.strand, eSite.coordinate, transcript.parent, transcript.id, tType, codingFlag))
fOut.close()
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)