Readfile.py

# Returns a dictionary mapping node names to list of list of integers representing list of copy number list
def read(filename):
    nodes = {}
    charlist=[]
    chromosome=[]
    CNV={}
    for ele in range(1,23):
        chromosome.append("chr"+str(ele))
    chromosome.append("chrX")
    chromosome.append("chrY")
    data=open(filename)
    line=next(data)
    line=line[0:-1].split("\t")
    segDist={}
    k=0
    for ele in line:
        ele=ele.split("_")[0]
        segDist.setdefault(ele,[]).append(k)
        k=k+1
    for ele in chromosome:
        if segDist.has_key(ele):
            charlist.append((min(segDist[ele]),max(segDist[ele])+1))
    if segDist.has_key("chr23"):
        charlist.append((min(segDist["chr23"]),max(segDist["chr23"])+1))
    if segDist.has_key("chr24"):
        charlist.append((min(segDist["chr24"]),max(segDist["chr24"])+1))
    for line in data:
        array = line.split()
        name = array.pop(0)
        snip = []
        CNVvalue = []
        for (a,b) in charlist:
            snip.append(map(int, array[a:b]))
            CNVvalue.extend(map(int, array[a:b]))
        nodes[name] = snip
        CNV[name]=list(set(CNVvalue))
    data.close()
    root = 'NA'
    for ele in CNV.keys():
        if CNV[ele] == [2]:
            root=ele
    if root == "NA":
        snip=[]
        for (a,b) in charlist:
            snip.append([2]*(b-a))
        nodes['root']=snip
        root='root'
    return nodes,root