Mercurial > repos > pablocarb > synbiodesign
view toolOptBioDes.py @ 2:856bd14e6e96 draft
planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty
author | pablocarb |
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date | Thu, 02 May 2019 07:16:40 -0400 |
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children | f3771c0a2327 |
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#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Created on Mar 19 @author: Pablo Carbonell @description: Query OptBioDes: optimal synbio design. """ import requests import argparse import csv import os import json def arguments(): parser = argparse.ArgumentParser(description='toolOptBioDes: Optimal SynBio Design. Pablo Carbonell, SYNBIOCHEM, 2019') parser.add_argument('infile', help='Input xlsx file (DoE specificiations).') parser.add_argument('outfile', help='Output csv design file.') parser.add_argument('diagfile', help='Output csv diagnostics file.') parser.add_argument('-server', default='http://doe.synbiochem.co.uk/REST', help='OptBioDes server.') return parser def testApp(url): r = requests.get( url ) res = json.loads( r.content.decode('utf-8') ) print( res ) def sheetUpload(doefile, outfile, diagfile, url): files = { 'file': open(doefile, 'rb' ) } values = {'size': 64} r = requests.post( os.path.join(url, 'Query' ), 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 ) 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.outfile, arg.diagfile, arg.url )