def updateLocationBasedTargets(editFN, contextFN, miLocationFN, gFN):
eSites = cgEdit.loadEditingSites(editFN)
cgEdit.updateContextEditingSites(eSites, contextFN) #puts the UTR, EXON in eSite.context
geneSet = cgGenes3.createGeneSetEditing(gFN)
tName_t = {}
for t in geneSet.transcripts:
tName_t[t.id] = t
tName_miInfo = {}
f = open(miLocationFN, 'r')
for line in f:
ls = line.strip().split('\t')
tName = ls[0]
miName = ls[1]
loc = int(ls[2])
tName_miInfo.setdefault(tName, []).append([miName, loc])
for eSite in eSites:
if '3UTR' not in eSite.context:
continue
for tName in eSite.transcripts:
if tName in tName_miInfo:
t = tName_t[tName]
for info in tName_miInfo[tName]:
miName = info[0]
loc = info[1]
#get the position of e site in mrna for this transcript
ePosition = t.getRelativePositionMRNA(eSite.coordinate, coding = False)
print tName, miName, loc, ePosition
if loc - 22 <= ePosition <= loc:
print tName, miName, '%s:%s' % (eSite.chromosome, eSite.coordinate)
pass
def updateValidatedMicroTargets(editFN, microTargetFN, microSequenceFN, outFN, gFN):
flankAmount = 6
eSites = cgEdit.loadEditingSites(editFN)
cgEdit.updateContextEditingSites(eSites)
miNames_micros = cgMicroRNA.loadMicroRNAFromValidated(microTargetFN, microSequenceFN)
gf = GenomeFetch.GenomeFetch('hg19')
#update flanking region
for eSite in eSites:
chrom = eSite.chromosome
coord = eSite.coordinate
strand = eSite.strand
flankingSeq = gf.get_seq_from_to(chrom, coord - flankAmount, coord + flankAmount, strand)
eFlankingSeq = flankingSeq[:flankAmount] + 'G' + flankingSeq[flankAmount + 1:]
eSite.flank = flankingSeq.replace('T', 'U')
eSite.eFlank = eFlankingSeq.replace('T', 'U')
#joint
gName_micros = {}
for micro in miNames_micros.values():
for target in micro.targetGenes:
if micro not in gName_micros.setdefault(target, []): gName_micros[target].append(micro)
gene_m = {}
for eSite in eSites:
sharedMicros = gName_micros.get(eSite.gene)
if sharedMicros is None:
continue
for micro in sharedMicros:
print ''
print micro.name, eSite.gene, micro.sequence, micro.seed
print micro.comSeed
print eSite.flank, eSite.eFlank
print '%s:%s' % (eSite.chromosome, eSite.coordinate), eSite.flank, eSite.gene
if micro.comSeed == None:
#dumpObj.dumpObj(micro)
#print 'miR not in sequence file:', micro.name
#print micro.targetGenes
continue
if eSite.gene in gene_m:
if micro not in gene_m[eSite.gene]:
gene_m[eSite.gene].append(micro)
else:
gene_m[eSite.gene] = [micro]
#flanking
if micro.comSeed in eSite.flank:
eSite.before.append(micro.name)
if micro.comSeed in eSite.eFlank:
eSite.after.append(micro.name)
print len(gene_m)
count = 0
for g in gene_m:
print g
for m in gene_m[g]:
print '...', m.name
count += 1
print count
#check if these seeds are in the
checkIfSeedPresent(gene_m, gFN)
#write contents to file...
outF = open(outFN, 'w')
for eSite in eSites:
if len(eSite.before) == 0:
targets = 'None'
else:
targets = ','.join(eSite.before)
if len(eSite.after) == 0:
eTargets = 'None'
else:
eTargets = ','.join(eSite.after)
outF.write('%s\t%s:%s\t%s\t%s\t%s\n' % (eSite.ID, eSite.chromosome, eSite.coordinate, eSite.strand, targets, eTargets))
def checkSeeds(editFN, contextFN, miLocationFN, miSequenceFN, gFN):
eSites = cgEdit.loadEditingSites(editFN)
cgEdit.updateContextEditingSites(eSites, contextFN) #puts the UTR, EXON in eSite.context
geneSet = cgGenes3.createGeneSetEditing(gFN)
tName_t = {}
for t in geneSet.transcripts:
tName_t[t.id] = t
miName_miSequence = {}
f = open(miSequenceFN, 'r')
for line in f:
ls = line.strip().split('\t')
name = ls[0]
seq = ls[1]
name = 'hsa-' + name
miName_miSequence[name] = seq
tName_miInfo = {}
f = open(miLocationFN, 'r')
for line in f:
ls = line.strip().split('\t')
tName = ls[0]
miName = ls[1]
loc = int(ls[2])
tName_miInfo.setdefault(tName, []).append([miName, loc])
foundIt = []
notFoundIt = []
for tName in tName_miInfo:
try:
t = tName_t[tName]
except:
continue
checkSeq = get3UTRSeq(t)
try:
mRNA = t.getMRNA()
except:
continue
for miInfo in tName_miInfo[tName]:
miName = miInfo[0]
loc = miInfo[1]
try:
miSequence = miName_miSequence[miName]
miSeed = miSequence[1:8]
except:
continue
rcMiSeed = cgSeqMod.reverseComplementSequence(miSeed, True)
newLoc = loc - (len(mRNA) - len(checkSeq))
finding = checkSeq.find(rcMiSeed, newLoc - 25)
if finding != -1:
if (0 < newLoc - finding < 30):
newResult = '%s\t%s\t%s\t%s\t%s' % (miName, tName, finding, newLoc, loc)
if newResult not in foundIt: foundIt.append(newResult)
else:
if miName == 'hsa-miR-21':
print loc, len(checkSeq), len(mRNA)
print mRNA
print checkSeq
newResult = '%s\t%s\t%s\t%s\t%s' % (miName, tName, finding, newLoc, loc)
if newResult not in notFoundIt: notFoundIt.append(newResult)
print len(foundIt)
print len(notFoundIt)
print ''
for i in foundIt:
print i
print ''
for i in notFoundIt:
print i
