Mercurial > repos > pablocarb > synbiodesign
view toolOptBioDes.py @ 19:dbc40b306014 draft
planemo upload commit 87db86a34f2d92eb2c9756bf9ee53ae2970554d5-dirty
author | pablocarb |
---|---|
date | Thu, 13 Jun 2019 08:56:51 -0400 |
parents | 6a1fbacdfaf5 |
children | 8f42eba7e2eb |
line wrap: on
line source
#!/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 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('-server', default='http://optbiodes.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, size, outfile, diagfile, url): files = { 'file': open(doefile, 'rb' ) } values = {'size': int(size), 'format': 'csv'} 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 ) with open(diagfile, 'w') as h: cw = csv.writer(h) cw.writerow( ['Size', 'Efficiency'] ) cw.writerow( [res['data']['libsize'], res['data']['J']] ) 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 )