diff rpviz/main.py @ 16:fe78fd6b315a draft

planemo upload commit 87db86a34f2d92eb2c9756bf9ee53ae2970554d5

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rpviz/main.py	Tue Jun 11 11:42:40 2019 -0400
@@ -0,0 +1,56 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Jun 10 11:48:55 2019
+
+@author: anael
+"""
+
+import argparse
+import os
+from .sbml2lists import sbml2list
+from .network2json import network2
+from .py2html2 import html2
+
+def arguments():
+    parser = argparse.ArgumentParser(description='Visualizing a network from sbml')
+    parser.add_argument('inputfolder', 
+                        help='Input folder with sbml files.')
+    parser.add_argument('outfile',
+                        help='html file.')
+    return parser
+
+def run(infolder,outfile,test=True):
+    
+    if test:
+        folders=[infolder]
+    else:
+        folders=os.listdir(infolder)
+    json_elements={}
+    for f in folders:
+        if test:
+            file=f
+        else:
+            file=os.path.join(infolder,f)   
+        output=sbml2list(file)
+        LR=output[0]
+        Lreact=output[1]
+        Lprod=output[2]
+        name=output[3]
+        species_smiles=output[4]
+        images=output[5]
+        species_names=output[6]
+        species_links=output[7]
+
+        #from smile2picture import picture
+        #image=picture(species_smiles)
+
+        
+        json_elements[name]=network2(LR,Lreact,Lprod,name,species_smiles,images,species_names,species_links)
+
+    
+    html2(json_elements,outfile)
+
+if __name__ == '__main__':
+    parser = arguments()
+    arg = parser.parse_args()
+    run(arg.inputfolder,arg.outfile)