diff toolSelenzyme.py @ 0:ac027c9ace4d draft

planemo upload commit 9e24fae395aeaca30c5bcdef80a21b7decb04042-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolSelenzyme.py	Mon Apr 29 09:49:36 2019 -0400
@@ -0,0 +1,48 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Mar 19
+
+@author: Pablo Carbonell
+@description: Query Selenzme: Enzyme sequence selection.
+
+"""
+import requests
+import argparse
+import csv
+import os
+import json
+
+def arguments():
+    parser = argparse.ArgumentParser(description='toolSelenzyme: Enzyme sequence selection. Pablo Carbonell, SYNBIOCHEM, 2019')
+    parser.add_argument('infile', 
+                        help='Input csv file.')
+    parser.add_argument('outfile', 
+                        help='Input csv file.')
+    parser.add_argument('-server', default='http://selenzyme.synbiochem.co.uk/REST',
+                        help='Selenzyme server.')
+    return parser
+
+# Output columns, to be improved
+columns = ['Seq. ID', 'Score', 'Organism Source', 'Description']
+
+if __name__ == "__main__":
+    parser = arguments()
+    arg = parser.parse_args()
+    assert os.path.exists(arg.infile)
+    with open(arg.infile) as handler:
+        cv = csv.DictReader(handler)
+        row = next(cv)
+        url = arg.server
+        assert 'smarts' in row
+        r = requests.post( os.path.join(url, 'Query') , json={'smarts': row['smarts']} )
+        res = json.loads( r.content.decode('utf-8') )
+        assert res['data'] is not None
+        val = json.loads( res['data'] )
+        assert 'Seq. ID' in val and len(val['Seq. ID'])>0
+        with open(arg.outfile, 'w' ) as writer:
+            cw = csv.writer( writer )
+            cw.writerow( columns )
+            for ix in sorted(val['Seq. ID'], key=lambda z: int(z)):
+                cw.writerow( [val[j][ix] for j in columns] )
+