def updatePi(path, db, motifChrom="chr17"):
"""calculate nucleotide diversity for a given genomic region"""
mcollection = db["hg19"+motifChrom]
print 'updating pi'
#mcollection.ensure_index("pi",name="nucleotide_diversity",unique=False,background=True)
cursor = mcollection.find({"tf_name":{"$in": ["IRF3","MAFK","NFYA","SIN3A","ZNF384"]}})
#{"tf_name": tfName, "motif_genomic_regions_info.chr": motifChrom})
for infile in glob.glob(os.path.join(path,"*v5.20130502.sites.vcf.bw")):
(vcfpath,vcffile) = os.path.split(infile)
(vcffilename,vcfext) = os.path.splitext(vcffile)
#bwFile = os.path.join(path,vcffilename+'.bw')
bwFileSnp = os.path.join(path,vcffilename+'_snp.bw')
bwFileIndel = os.path.join(path,vcffilename+'_indel.bw')
expName = '1000genomes'
#countVcf.compressVcf(infile, expName, bwFile, bwFileSnp, bwFileIndel)
# coordDict, valuesDict = countVcf.getBinVarCoord(bwFile, expName)
# arrayDict = defaultdict(list)
coordDictSnp, valuesDictSnp = countVcf.getBinVarCoord(bwFileSnp, expName)
arrayDictSnp = defaultdict(list)
coordDictIndel, valuesDictIndel = countVcf.getBinVarCoord(bwFileIndel, expName)
arrayDictIndel = defaultdict(list)
for test in cursor:
#motifChrom = test["motif_genomic_regions_info"]["chr"]
motifStart = test["genomic_region"]["start"]
motifEnd = test["genomic_region"]["end"]
# if not motifChrom in arrayDict:
# arrayDict[motifChrom] = countVcf.buildVarHist(motifChrom, coordDict, valuesDict, expName)
if not motifChrom in arrayDictSnp:
arrayDictSnp[motifChrom] = countVcf.buildVarHist(motifChrom, coordDictSnp, valuesDictSnp, expName)
if not motifChrom in arrayDictIndel:
arrayDictIndel[motifChrom] = countVcf.buildVarHist(motifChrom, coordDictIndel, valuesDictIndel, expName)
# xs, xvals, sums = arrayDict[motifChrom]
# avg = countVcf.queryHist(xs,xvals,sums,motifStart,motifEnd)[0]
xs, xvals, sums = arrayDictSnp[motifChrom]
avgSnp = countVcf.queryHist(xs,xvals,sums,motifStart,motifEnd)[0]
xs, xvals, sums = arrayDictIndel[motifChrom]
avgIndel = countVcf.queryHist(xs,xvals,sums,motifStart,motifEnd)[0]
mcollection.update({"_id":test["_id"]},{"$set":{#"map.pi": avg,
"cons.piSnp": avgSnp,
"cons.piIndel": avgIndel}}, upsert = True)
#print "pi=", avgIndel#,motifEnd-motifStart
return 0
def updatePi(path, tfName, motifChrom):
"""calculate nucleotide diversity for a given genomic region"""
cursor = mcollection.find({"tf_name": tfName, "motif_genomic_regions_info.chr": motifChrom})
for infile in glob.glob(os.path.join(path,"*v5.20130502.sites.vcf.gz")):
(vcfpath,vcffile) = os.path.split(infile)
(vcffilename,vcfext) = os.path.splitext(vcffile)
bwFile = os.path.join(path,vcffilename+'.bw')
bwFileSnp = os.path.join(path,vcffilename+'_snp.bw')
bwFileIndel = os.path.join(path,vcffilename+'_indel.bw')
expName = '1000genomes'
#countVcf.compressVcf(infile, expName, bwFile, bwFileSnp, bwFileIndel)
#coordDict, valuesDict = countVcf.getBinVarCoord(bwFile, expName)
#arrayDict = defaultdict(list)
#coordDictSnp, valuesDictSnp = countVcf.getBinVarCoord(bwFileSnp, expName)
#arrayDictSnp = defaultdict(list)
coordDictIndel, valuesDictIndel = countVcf.getBinVarCoord(bwFileIndel, expName)
arrayDictIndel = defaultdict(list)
for test in cursor:
#motifChrom = test["motif_genomic_regions_info"]["chr"]
motifStart = test["motif_genomic_regions_info"]["start"]
motifEnd = test["motif_genomic_regions_info"]["end"]
#if not motifChrom in arrayDict:
#arrayDict[motifChrom] = countVcf.buildVarHist(motifChrom, coordDict, valuesDict, expName)
#if not motifChrom in arrayDictSnp:
#arrayDictSnp[motifChrom] = countVcf.buildVarHist(motifChrom, coordDictSnp, valuesDictSnp, expName)
if not motifChrom in arrayDictIndel:
arrayDictIndel[motifChrom] = countVcf.buildVarHist(motifChrom, coordDictIndel, valuesDictIndel, expName)
#xs, xvals, sums = arrayDict[motifChrom]
#avg = countVcf.queryHist(xs,xvals,sums,motifStart,motifEnd)[0]
#xs, xvals, sums = arrayDictSnp[motifChrom]
#avgSnp = countVcf.queryHist(xs,xvals,sums,motifStart,motifEnd)[0]
xs, xvals, sums = arrayDictIndel[motifChrom]
avgIndel = countVcf.queryHist(xs,xvals,sums,motifStart,motifEnd)[0]
mcollection.update({"_id":test["_id"]},{"$set":{#"motif_mapability_info.piTot": avg,
#"motif_mapability_info.piSnp": avgSnp,
"motif_mapability_info.piIndel": avgIndel}}, upsert = True)
print "pi=", avgIndel#,motifEnd-motifStart
return 0
