diff rpviz/Test with Ecoli ntwk/E coli PPI network.py @ 16:fe78fd6b315a draft

planemo upload commit 87db86a34f2d92eb2c9756bf9ee53ae2970554d5

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpviz/Test with Ecoli ntwk/E coli PPI network.py	Tue Jun 11 11:42:40 2019 -0400
@@ -0,0 +1,31 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Tue May 28 11:38:34 2019
+
+@author: Anaelle
+"""
+
+
+import networkx as nx
+import numpy as np
+import matplotlib.pyplot as plt 
+import requests
+
+
+tab=np.loadtxt('HT.PMID-15690043.EcoliNet.303gene.3446link.txt',dtype='str',delimiter='\t') #Network file
+smartab=np.loadtxt('Copy_of_All_genes_of_E._coli_K-12_substr._MG1655.txt', dtype='str',delimiter='\t',usecols=(0,1)) #Smart table to assign a link to each node
+
+reseau=nx.Graph() 
+dic_links={}
+for i in range(len(tab)):
+    reseau.add_edge(tab[i][0],tab[i][1],weight=tab[i][2]) #network construction
+for nodes in range(len(list(reseau.nodes))):
+    for j in range(len(smartab)):
+        if smartab[j][1][1:-1]==list(reseau.nodes)[nodes]: 
+            url=smartab[j][0][1:-1]
+            left, right = url.split(':') 
+            url_new = ':'.join( [left, requests.utils.quote(right)] ) #to avoid encoding problems
+            dic_links[list(reseau.nodes)[nodes]]= url_new#each link is assigned to each node
+            
+nx.set_node_attributes(reseau,name='link',values=dic_links)
+nx.write_gml(reseau,'reseau.gml') 
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