processing.py 文件源码

def construct_csr_matrix_from_data_and_nodes(f,nodes,blacklisted_nodes,remove_diag=True):
    print "GenomeDISCO | "+strftime("%c")+" | processing: Loading interaction data from "+f

    total_nodes=len(nodes.keys())
    i=[]
    j=[]
    v=[]

    #print strftime("%c")
    c=0
    for line in gzip.open(f):
        items=line.strip().split('\t')
        n1,n2,val=nodes[items[0]]['idx'],nodes[items[1]]['idx'],float(items[2])
        i.append(n1)
        j.append(n2)
        v.append(val)
        c+=1

    csr_m=csr_matrix( (v,(i,j)), shape=(total_nodes,total_nodes),dtype=float)
    if remove_diag:
        csr_m.setdiag(0)
    return filter_nodes(csr_m,blacklisted_nodes)