diff rpviz/csv_network.py @ 16:fe78fd6b315a draft

planemo upload commit 87db86a34f2d92eb2c9756bf9ee53ae2970554d5

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpviz/csv_network.py	Tue Jun 11 11:42:40 2019 -0400
@@ -0,0 +1,60 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Wed May 29 17:23:04 2019
+
+@author: anael
+Read the output of retropath
+To visualize a csv file
+"""
+
+import csv
+import argparse
+import os
+
+def arguments():
+    parser = argparse.ArgumentParser(description='Visualizing a network from csv')
+    parser.add_argument('infile', 
+                        help='Input csv file.')
+    #parser.add_argument('outfile', 
+                       # help='Input some file.')
+    return parser
+
+parser = arguments()
+arg = parser.parse_args()
+
+assert os.path.exists('infile/'+arg.infile)
+file='infile/'+arg.infile
+data=csv.reader(open(file))
+tab=[]
+for ligne in data :
+    tab.append(ligne)
+    
+List=[] #List of different number of pathways in the file
+for i in range(1,len(tab)):
+    List.append(int(tab[i][0]))
+    List=list(set(List))
+    List.sort()
+for i in range(len(List)) :
+    nb=int(List[i])
+    name=file+str(nb)
+    LR=[]
+    Lreact=[]
+    Lprod=[]
+    for i in range(len(tab)):
+        if tab[i][0]==str(nb) :#we chose the pathway
+            LR.append(tab[i][2]) #reaction = Unique ID
+            Lreact.append(tab[i][3].split(":"))
+            Lprod.append([tab[i][4]])
+    #print('LR = '+ str(LR))
+    #print('Lreact = '+ str(Lreact))
+    #print('Lprod = '+ str(Lprod))
+    #from nxvisualizer import network
+    #network(LR,Lreact,Lprod,name)   
+    from network2json import  network2 #to convert the lists in a json network
+    network2(LR,Lreact,Lprod,name)
+    
+
+   
+
+    
+    
\ No newline at end of file