Esempio n. 1
0
def loadHiC(expression):
    seen=set()
    with open(HIC,"rt") as IN:
        for line in IN:
            fields=line.rstrip().split()
            (chr1,begin1,end1,chr2,begin2,end2)=fields
            if(chr1!=chr2): continue
            array=expression.get(chr1,None)
            if(array is None): return
            anchor1=Interval(int(begin1),int(end1))
            anchor2=Interval(int(begin2),int(end2))
            anchor1.type=anchor2.type="anchor"
            anchor1.mate=anchor2
            anchor2.mate=anchor1
            anchor1.objects=[]; anchor2.objects=[]
            key1=chr1+" "+begin1+" "+end1
            key2=chr2+" "+begin2+" "+end2
            if(key1 not in seen): array.append(anchor1)
            if(key2 not in seen): array.append(anchor2)
            seen.add(key1); seen.add(key2)
Esempio n. 2
0
def loadHiC(expression):
    seen=set()
    with open(HIC,"rt") as IN:
        for line in IN:
            fields=line.rstrip().split()
            (chr1,begin1,end1,chr2,begin2,end2)=fields
            array=expression.get(chr1,None)
            if(array is None): return
            tad=Interval(int(begin1),int(end1))
            tad.type="anchor"
            tad.objects=[]
            key=chr1+" "+begin1+" "+end1
            if(key not in seen): array.append(tad)
            seen.add(key)