diff toolOptBioDes.py @ 24:8f42eba7e2eb draft

planemo upload commit 2414e76bee8adbe48fee12b14b13a743a03b9748-dirty

--- a/toolOptBioDes.py	Fri Jul 05 06:26:22 2019 -0400
+++ b/toolOptBioDes.py	Fri Jul 05 17:18:26 2019 -0400
@@ -15,14 +15,20 @@
 
 def arguments():
     parser = argparse.ArgumentParser(description='toolOptBioDes: Optimal SynBio Design. Pablo Carbonell, SYNBIOCHEM, 2019')
-    parser.add_argument('infile', 
-                        help='Input csv file (DoE specificiations).')
     parser.add_argument('size', 
                         help='Library size.')
     parser.add_argument('outfile', 
                         help='Output csv design file.')
     parser.add_argument('diagfile', 
                         help='Output csv diagnostics file.')
+    parser.add_argument('-infile', default=None,
+                        help='Input csv file (DoE specifications sheet).')
+    parser.add_argument('-partsfile', default=None,
+                        help='Input csv file (Regulartory parts).')
+    parser.add_argument('-genesfile', default=None,
+                        help='Input csv file (Genetic parts).')
+    parser.add_argument('-sbolOut', default=None,
+                        help='Output design in SBOL format.')
     parser.add_argument('-server', default='http://optbiodes.synbiochem.co.uk/REST',
                         help='OptBioDes server.')
     return parser
@@ -49,10 +55,33 @@
         cw.writerow( [res['data']['libsize'], res['data']['J']] )
     print( 'Size:', res['data']['libsize'], 'Efficiency:', res['data']['J'] )
 
+def partsUploadSbol( partsfile, genesfile, size, outfile, diagfile, sbolOut, server ):
+    files = { 
+        'parts': open(partsfile, 'rb' ),
+        'genes': open(genesfile, 'rb')
+    }
+    values = {'size': size}
+    r = requests.post( os.path.join(url, 'Parts' ), files=files, data=values )
+    res = json.loads( r.content.decode('utf-8') )
+    M = res['data']['M']
+    with open(outfile, 'w') as h:
+        cw = csv.writer(h)      
+        cw.writerow( res['data']['names'] )
+        for row in M:
+            cw.writerow( row )
+    with open(diagfile, 'w') as h:
+        cw = csv.writer(h)
+        cw.writerow( ['Size', 'Efficiency'] )
+        cw.writerow( [res['data']['libsize'], res['data']['J']] )
+    open(sbolOut, 'w').write(res['data']['sbol'])
+    print( 'Size:', res['data']['libsize'], 'Efficiency:', res['data']['J'] )
 
 
 if __name__ == "__main__":
     parser = arguments()
     arg = parser.parse_args()
     assert os.path.exists(arg.infile)
-    sheetUpload( arg.infile, arg.size, arg.outfile, arg.diagfile, arg.server )
+    if arg.sbolOut is None:
+        sheetUpload( arg.infile, arg.size, arg.outfile, arg.diagfile, arg.server )
+    else:
+        partsUploadSbol(  arg.partsfile, arg.genesfile, arg.size, arg.outfile, arg.diagfile, arg.sbolOut, arg.server )