#PPI中癌基因子图

genesppi.py

#coding:UTF-8
#!/usr/bin/python

import networkx as nx
import matplotlib.pyplot as plt

def cancergenes(filename="cancer_gene_census.tsv"):
    doms,recs=[],[]
    for line in open(filename,'r').read().split('\r'):
        cons=line.split("\t")
        if(cons[11]=="Dom"):
            doms.append(cons[0])
        else:
            recs.append(cons[0])
        
    return doms,recs

def ppihave(genes,ppifile="BINARY_PROTEIN_PROTEIN_INTERACTIONS.txt"):
    ppis=[]
    for line in open(ppifile,'r').readlines():
        subs=line.split('\t')
        if subs[0] in genes and subs[3] in genes:
            ppis.append((subs[0],subs[3]))
    return ppis

def nxdraw():
    doms,res=cancergenes()
    ppis=ppihave(res+doms)
    G=nx.Graph()
    G.add_nodes_from(res+doms)
    G.add_edges_from(ppis)
    colors=[1]*len(res)+[2]*len(doms)
    pos=nx.spring_layout(G)
    nx.draw_networkx_nodes(G,pos,node_size=30,node_color=colors)
    nx.draw_networkx_edges(G,pos)
    plt.axis('off')
    plt.savefig("cancer_gene2ppi.png")

nxdraw()