def testPeaks(degFN, dForm, allGeneInfo, gForm, switchStrand = False):
#load/configure gene Info
gNX = Nexus(allGeneInfo, gForm)
gNX.load(['geneName', 'numReads', 'numSpots'])
gName_numReads = {}
gName_numSpots = {}
while gNX.nextID():
gName_numReads[gNX.geneName] = gNX.numReads
gName_numSpots[gNX.geneName] = gNX.numSpots
#load degFN info
dNX = Nexus(degFN, dForm)
dNX.load(['tcc', 'eLevel', 'geneNames', 'pValBin'])
while dNX.nextID():
gNames, readsForPeak = dNX.geneNames, dNX.eLevel
chrom, strand, start, end = bioLibCG.tccSplit(dNX.tcc)
if switchStrand:
strand = -int(strand)
pVals = []
for gName in gNames:
#may have to change gene name cuz of multiple spans
try:
totGeneReads = gName_numReads[gName]
numSpotsForGene = gName_numSpots[gName]
except KeyError:
try:
gName = gName + '_RE_%s_%s' % (chrom, strand)
totGeneReads = gName_numReads[gName]
numSpotsForGene = gName_numSpots[gName]
except KeyError:
print "FIX THIS GENE NAME", gName
continue
#add psuedocount
totGeneReads += 1
numSpotsForGene += 1 # not sure whether to do this yet...
#check for hidden intron gene overlap
try:
q = 1.0/numSpotsForGene
except ZeroDivisionError:
continue #intron gene
#add p val
pVals.append(binom.sf(readsForPeak, totGeneReads, q))
dNX.pValBin = max(pVals) if pVals else -1.0
dNX.save()
