def updateChip(path,db,motifChrom="chr17",window=0):
"""mark motifs if it overlaps ENCODE excluded regions"""
mcollection = db["hg19"+motifChrom]
for infile in glob.glob(os.path.join(path,"*.bed.gz")):
(regpath,regfilename) = os.path.split(infile)
expName = regfilename.split(motifChrom)[0]
with gzip.open(infile,'rt') as bedFile:
bed = csv.reader(bedFile, delimiter = '\t')
annoIntvlDict = countBed.getBed4Anno(bed,expName)
intervalStartDict = countBed.sortStart(annoIntvlDict)
intervalEndDict = countBed.sortEnd(annoIntvlDict)
cursor = mcollection.find({"tf_name":{"$in": ["IRF3","MAFK","NFYA","SIN3A","ZNF384"]}})
#{"tf_name": tfName})
for test in cursor:
motifStart, motifEnd = test["genomic_region"]["start"], \
test["genomic_region"]["end"]
regionList, valueList = countBed.getMotifAnno(annoIntvlDict,
intervalStartDict,intervalEndDict,motifChrom,
motifStart,motifEnd,window)
if valueList != []:
#print regionList, valueList, motifChrom, motifStart, motifEnd
mcollection.update({"_id": test["_id"]},
{"$set": {"chip."+expName: valueList[0][1]}}, upsert = True)
return 0
def updateChip(path,db,motifChrom="chr17",window=0):
"""mark motifs if it overlaps ENCODE excluded regions"""
mcollection = db["hg19"+motifChrom]
for tf in ["CTCF"]:#os.listdir(path):#["CTCF","JUND","MAX","REST","SIN3A","SP1","USF1","YY1"]:
files = path+"/"+tf+"/wgEncodeBroadHistoneGm12878CtcfStdPkForma*"+motifChrom+".bed.gz"
for infile in glob.glob(files):
print "update", infile
(regpath,regfilename) = os.path.split(infile)
expName = regfilename.split(motifChrom)[0]
with gzip.open(infile,'rt') as bedFile:
bed = csv.reader(bedFile, delimiter = '\t')
annoIntvlDict = countBed.getBed4Anno(bed,expName)
intervalStartDict = countBed.sortStart(annoIntvlDict)
intervalEndDict = countBed.sortEnd(annoIntvlDict)
cursor = mcollection.find({"tf_name": tf})
for test in cursor:
motifStart, motifEnd = test["genomic_region"]["start"], \
test["genomic_region"]["end"]
regionList, valueList = countBed.getMotifAnno(annoIntvlDict,
intervalStartDict,intervalEndDict,motifChrom,
motifStart,motifEnd,window)
if valueList != []:
#print regionList, valueList, motifChrom, motifStart, motifEnd
mcollection.update({"_id": test["_id"]},
{"$set": {"chip."+expName: valueList[0][1]}}, upsert = True)
return 0