def updateCount(path, tfName):
"""update count data in discontinuous variableStep wiggle format"""
for infile in glob.glob(os.path.join(path,"*.wig")):
(wigpath,wigfilename) = os.path.split(infile)
##depends on the data type and source
expName = "Dnase"##or add an expName parser line
ctName = wigfilename.split('EncodeUwDnase')[-1].split('Aln')[0]
wigFile = open(infile,'rt')
wig = csv.reader(wigFile,delimiter='\t')
coordDict, valuesDict = countWig.getCoord(wig,ctName)
arrayDict = defaultdict(list)
cursor = mcollection.find({"tf_name": tfName})
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] = countWig.buildHist(motifChrom,coordDict,valuesDict,ctName)
xs, xvals, sums = arrayDict[motifChrom]
count = countWig.queryHist(xs, xvals, sums, motifStart, motifEnd)[0]
#print count
#mcollection.update({"_id":test["_id"]},{"$set":{expName: count}}, upsert = True)
test["ct_info"]["accessibility_score"][expName] = count
mcollection.save(test)
return 0
def getCount(path, tfName):
for infile in glob.glob(os.path.join(path,"*.wig")):
(wigpath,wigfilename) = os.path.split(infile)
##depends on the data type and source
methodName = "Dnase"
ctName = wigfilename.split('EncodeUwDnase')[-1].split('Aln')[0]
wigFile = open(infile,'rt')
wig = csv.reader(wigFile,delimiter='\t')
coordDict, valuesDict = countWig.getCoord(wig,ctName)
arrayDict = defaultdict(list)
cursor = mcollection.find({"tf_name": tfName})
for test in cursor:
motifChrom, motifStart, motifEnd = test["motif_genomic_regions_info"]["chr"], test["motif_genomic_regions_info"]["start"], test["motif_genomic_regions_info"]["end"]
if not motifChrom in arrayDict:
arrayDict[motifChrom] = countWig.buildHist(motifChrom,coordDict,valuesDict,ctName)
xs, xvals, sums = arrayDict[motifChrom]
count = countWig.queryHist(xs, xvals, sums, motifStart, motifEnd)[0]
#print count
test["ct_info"]["accessibility_score"][methodName] = count
mcollection.save(test)
return 0