def run(bidirfile,windowsize):
#Takes in a bidirectional file and outputs a dictionary of {chrom: [(start,stop)]}
#based on windowsize
bidirdict = dict()
bidirlist = Functions.parse_bidirfile(bidirfile)
for item in bidirlist:
chrom,start,stop = item[0:3]
if not chrom in bidirdict:
bidirdict[chrom] = list()
mid = (float(start)+float(stop))/2
bidirdict[chrom].append((int(mid-windowsize),int(mid+windowsize)))
return bidirdict
def run(bidirectionalfile, DNAseFile):
bidirlist = Functions.parse_bidirfile(bidirectionalfile)
bidirdict = dict()
datapoints = []
for item in bidirlist:
chrom, start, stop, parameters = item
if chrom not in bidirdict:
bidirdict[chrom] = []
else:
bidirdict[chrom].append((start,stop,parameters))
dnasedict = Functions.create_tup_dict(DNAseFile, False)
for chrom in dnasedict:
if chrom in bidirdict:
bidirtree = node.tree(bidirdict[chrom])
for item in dnasedict[chrom]:
bidirsite = bidirtree.searchInterval(item)
if len(bidirsite) != 0:
start = float(item[0])
stop = float(item[1])
size = stop - start
datapoints.append((bidirsite[2][6],size))
return datapoints
