comparison toolOptBioDes.py @ 8:6572347b3e1a draft

planemo upload commit 6a252d04f4b2f79606ab6679b6a91f957e33da7b-dirty

7:e328a5f60135

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('size', 
                        help='Library size.')
    parser.add_argument('outfile', 
                        help='Output csv design file.')
    parser.add_argument('diagfile', 

    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)}
    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__":

8:6572347b3e1a

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', 

    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__":