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draw_nx.py
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draw_nx.py
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#!/usr/bin/python
# coding: UTF-8
import matplotlib
matplotlib.use('Agg')
try:
import matplotlib.pyplot as plt
except:
raise
import networkx as nx
import re
import get_compounds_from_gene2
def make_dic():
f = open("data/compound_id_converter.txt")
data = f.readlines()
dict = {}
for x in data:
tmp = x.split('\t')
dict.update({tmp[1].strip("\n"):tmp[0].strip("\n")})
return dict
def search_id(name):
f = open("data/compound_id_converter.txt")
data = f.readlines()
res = 0
for x in data:
tmp = x.split('\t')
if name == tmp[1].strip("\n"):
res = tmp[0].strip("\n")
print "found"
return res
def search_compound(id):
f = open("data/compound_id_converter.txt")
data = f.readlines()
res = 0
for x in data:
tmp = x.split('\t')
if id == tmp[0].strip("\n"):
res = tmp[1].strip("\n")
return res
def read_data(filename):
f = open(filename)
data = f.readlines()
f.close()
res = []
#If csv "," or "\t"
for x in data:
tmp = x.split(',')
arr = []
for y in tmp:
if y:
arr.append(y.strip('\r'))
res.append(arr)
return res
def Graph_info(G):
print "Number of nodes is %d"%G.number_of_nodes()
print "Number of edges is %d"%G.number_of_edges()
def show_data(pos,neg,id):
for x in pos:
if str(id) == str(x[0]):
return x
for x in neg:
if str(id) == str(x[0]):
return x
def show_connections(G,pos,neg):
for x in pos:
try:
tmp = nx.all_neighbors(G,x[0])
for y in tmp:
print y
except:
print "Not Found"
for y in neg:
try:
tmp = nx.all_neighbors(G,x[0])
for y in tmp:
print y
except:
print "Not Found"
def read_gene(compound_id):
f = open("data/gene_compound_all.txt")
lines = f.readlines()
f.close()
for x in lines:
tmp = x.split("\t")
if compound_id == tmp[2]:
#print "Find GENE"
return tmp[0]
def gene_foldchange(gene):
f = open("data/gene_foldchange.csv")
lines = f.readlines()
f.close()
for x in lines:
tmp = x.split(",")
if tmp[0].upper() == gene:
return tmp[1]
def Draw_Graph(file_name):
f = open(file_name)
lines2 = f.readlines()
f.close()
G = nx.Graph()
for line in lines2:
tmp = line.split('\t')
G.add_edge(tmp[0].strip('\n'),tmp[1].strip('\n'))
return G
def Find_Neighbors(G, pos, neg):
#Write Result
f1 = open('result2.txt','w')
for x in pos:
try:
tmp = nx.all_neighbors(G,x[0])
for t in x:
f1.write(t.strip('\r\n'))
f1.write('\t')
#All neighbors
for x1 in tmp:
tmp_data = show_data(pos,neg,x1)
for z in tmp_data:
f1.write(z.strip('\r\n'))
f1.write('\t')
f1.close()
#Neighbors of query compound try to find related gene
tmp_gene = read_gene(tmp_data[0])
if tmp_gene:
f1.write(tmp_gene.strip('\r\n'))
f1.write('\t')
f1.write(gene_foldchange(tmp_gene).strip('\n'))
f1.write('\t')
res_gene = read_gene(x[0])
#Query Compound Related Gene
if res_gene:
f1.write(res_gene.strip('\r\n'))
f1.write("\t")
f1.write(gene_foldchange(res_gene).strip('\n'))
f1.write('\n')
except:
#print "not found"
#f1.write(x[1])
f1.write('\n')
for y in neg:
try:
tmp = nx.all_neighbors(G,y[0])
for t in y:
f1.write(t.strip('\r\n'))
f1.write('\t')
for y1 in tmp:
tmp_data = show_data(pos,neg,y1)
for z in tmp_data:
f1.write(z.strip('\r\n'))
f1.write('\t')
#Neighbors of query compound try to find related gene
tmp_gene = read_gene(tmp_data[0])
if tmp_gene:
f1.write(tmp_gene.strip('\n'))
f1.write('\t')
f1.write(gene_foldchange(tmp_gene).strip('\n'))
f1.write('\t')
res_gene = read_gene(y[0])
#Query Compound Related Gene
if res_gene:
f1.write(res_gene.strip('\r\n'))
f1.write('\t')
f1.write(gene_foldchange(res_gene).strip('\n'))
f1.write('\n')
except:
#print "not found"
#f1.write(y[1])
f1.write('\n')
f1.close()
def Find_Neighbors2(pos, neg):
#Write Result
f1 = open('result2.txt','w')
for x in pos:
try:
tmp = get_neighbor2(x[0])
for t in x:
print "WRITE"
f1.write(t.strip('\r\n'))
f1.write('\t')
#All neighbors
for x1 in tmp:
tmp_data = show_data(pos,neg,x1)
for z in tmp_data:
f1.write(z.strip('\r\n'))
f1.write('\t')
#Neighbors of query compound try to find related gene
tmp_gene = read_gene(tmp_data[0])
if tmp_gene:
f1.write(tmp_gene.strip('\r\n'))
f1.write('\t')
f1.write(gene_foldchange(tmp_gene).strip('\n'))
f1.write('\t')
res_gene = read_gene(x[0])
#Query Compound Related Gene
if res_gene:
f1.write(res_gene.strip('\r\n'))
f1.write("\t")
f1.write(gene_foldchange(res_gene).strip('\n'))
f1.write('\n')
except:
#print "not found"
#f1.write(x[1])
f1.write('\n')
for y in neg:
try:
tmp = get_neighbor2(y[0])
for t in y:
print "write"
f1.write(t.strip('\r\n'))
f1.write('\t')
for y1 in tmp:
tmp_data = show_data(pos,neg,y1)
if y1.find("hsa") != -1:
f1.write(x1)
f1.write("\t")
for z in tmp_data:
f1.write(z.strip('\r\n'))
f1.write('\t')
#Neighbors of query compound try to find related gene
tmp_gene = read_gene(tmp_data[0])
if tmp_gene:
f1.write(tmp_gene.strip('\n'))
f1.write('\t')
f1.write(gene_foldchange(tmp_gene).strip('\n'))
f1.write('\t')
res_gene = read_gene(y[0])
#Query Compound Related Gene
if res_gene:
f1.write(res_gene.strip('\r\n'))
f1.write('\t')
f1.write(gene_foldchange(res_gene).strip('\n'))
f1.write('\n')
except:
#print "not found"
#f1.write(y[1])
f1.write('\n')
f1.close()
def get_neighbor2(id):
f = open("data/hsa_list.txt")
line = f.readlines()
f.close()
res = []
for x in line:
tmp = get_compounds_from_gene2.get_compound(x[5:13])
for y in tmp:
#If id is in the passway
if id == y:
res.extend(tmp)
res.append(x[5:13])
break
print "neighbor2"
print res
return res
if __name__ == "__main__":
#Read Compound
pos = read_data("data/metabo_data_1126_pos_ave.csv")
neg = read_data("data/metabo_data_1126_neg_ave.csv")
#G = Draw_Graph("data/node_neo.txt")
#Test
"""
tmp = nx.all_neighbors(G,"C00311")
for x in tmp:
print x
tmp = get_neighbor2("C00311")
print tmp
"""
Find_Neighbors2(pos,neg)