def countBySeed(editFN, microFN, flankAmount, outFN):
'''FlankF amount should be +/- 6'''
flankAmount = int(flankAmount)
eSites = cgEdit.loadEditingSites(editFN)
micros = cgMicroRNA.loadMicroRNAFromTargetScan(microFN, 'hsa')
gf = GenomeFetch.GenomeFetch('hg19')
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:]
flankingSeq.replace('T', 'U')
eFlankingSeq.replace('T','U')
checkID = 'hsa-miR-330-5p'
for microRNA in micros:
comSeed = cgSeqMod.reverseComplementSequence(microRNA.seed, True)
if comSeed in flankingSeq:
eSite.microTargets.append(microRNA.id)
if microRNA.id == checkID:
print '%s:%s' % (eSite.chromosome, eSite.coordinate), eSite.strand, eSite.gene
microRNA.numBefore += 1
#print '@', 'flank', eSite.ID, microRNA.id, flankingSeq, comSeed
if comSeed in eFlankingSeq:
microRNA.numAfter += 1
if microRNA.id == checkID:
print '%s:%s' % (eSite.chromosome, eSite.coordinate), eSite.strand, eSite.gene
eSite.eMicroTargets.append(microRNA.id)
#print '@', 'eFlank', eSite.ID, microRNA.id, eFlankingSeq, comSeed
for micro in micros:
if micro.numBefore > 0 or micro.numAfter > 0:
#print micro.id, micro.numBefore, micro.numAfter
pass
#write contents to file...
outF = open(outFN, 'w')
for eSite in eSites:
if len(eSite.microTargets) == 0:
targets = 'None'
else:
targets = ','.join(eSite.microTargets)
if len(eSite.eMicroTargets) == 0:
eTargets = 'None'
else:
eTargets = ','.join(eSite.eMicroTargets)
outF.write('%s\t%s:%s\t%s\t%s\t%s\n' % (eSite.ID, eSite.chromosome, eSite.coordinate, eSite.strand, targets, eTargets))
def updateMicroTargets(editFN, microFN, flankAmount, outFN):
'''FlankF amount should be +/- 6'''
flankAmount = int(flankAmount)
eSites = cgEdit.loadEditingSites(editFN)
micros = cgMicroRNA.loadMicroRNAFromTargetScan(microFN, 'hsa')
gf = GenomeFetch.GenomeFetch('hg19')
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:]
for microRNA in micros:
comSeed = cgSeqMod.reverseComplementSequence(microRNA.seed, True)
if comSeed in flankingSeq:
eSite.microTargets.append(microRNA.id)
print '@', 'flank', eSite.ID, microRNA.id, flankingSeq, comSeed
if comSeed in eFlankingSeq:
eSite.eMicroTargets.append(microRNA.id)
print '@', 'eFlank', eSite.ID, microRNA.id, eFlankingSeq, comSeed
#write contents to file...
outF = open(outFN, 'w')
for eSite in eSites:
if len(eSite.microTargets) == 0:
targets = 'None'
else:
targets = ','.join(eSite.microTargets)
if len(eSite.eMicroTargets) == 0:
eTargets = 'None'
else:
eTargets = ','.join(eSite.eMicroTargets)
outF.write('%s\t%s:%s\t%s\t%s\t%s\n' % (eSite.ID, eSite.chromosome, eSite.coordinate, eSite.strand, targets, eTargets))
