lpromotorMeth, rpromotorMeth, relativePromotorMethDiff, promotorMethDiff, promotorPvalue = methPercentageDiff(
methdata.getValuesInRange(genedata[ensembl].chr, promotorstart,
promotorstop))
lgenebodyMeth, rgenebodyMeth, relativeGeneBodyMethDiff, geneBodyMethDiff, geneBodyPvalue = methPercentageDiff(
methdata.getValuesInRange(genedata[ensembl].chr,
genedata[ensembl].start,
genedata[ensembl].end))
ltssMeth, rtssMeth, relativeTssMethDiff, tssMethDiff, tssPvalue = methPercentageDiff(
methdata.getValuesInRange(
genedata[ensembl].chr,
genedata[ensembl].start - tsssize / 2,
genedata[ensembl].start + tsssize / 2))
promotorClassification, promotorCpGRatio = classifyCpGContent(
genome.getSequence(genedata[ensembl].chr, promotorstart,
promotorstop).upper())
geneBodyClassification, genebodyCpGRatio = classifyCpGContent(
genome.getSequence(genedata[ensembl].chr,
genedata[ensembl].start,
genedata[ensembl].end).upper())
tssClassification, tssCpGRatio = classifyCpGContent(
genome.getSequence(genedata[ensembl].chr,
genedata[ensembl].start - tsssize / 2,
genedata[ensembl].start +
tsssize / 2).upper())
row = [ensembl, genedata[ensembl].name, "1" if incpg else "0"]
if exprfile != None:
row.extend([logFC, "1" if sig else "0"])
try:
chi2Tots[s][0].append(resultsDict[i][0])
chi2Tots[s][1].append(resultsDict[i][1])
except:
chi2Tots[s] = [[resultsDict[i][0]], [resultsDict[i][1]]]
for s in replicateTypes.split(","):
pooledMeths = chi2Tots[s]
chi2, p = methChiSquared(pooledMeths)
output.append(p)
for s in replicateTypes.split(","):
for i in replicateTypes.split(","):
if s != i:
output.append(str(methGetP(pooledTotals[s], pooledTotals[i])))
output.append(str(methPercentageDiff(pooledTotals[s], pooledTotals[i])))
for x in finalReplicateAnnotators:
firstRep = resultsDict[x]
for y in finalReplicateAnnotators:
if y != x:
secondRep = resultsDict[y]
output.append(str(methGetP(firstRep, secondRep)))
output.append(str(methPercentageDiff(firstRep, secondRep)))
seq = genome.getSequence(chrm,start,stop).upper()
classification, cpgs = classifyCpGContent(seq)
output.append(cpgs)
outputcsv.writerow(output)
except sequence.genome.UnknownChromosomeException:
continue