Mercurial > repos > pablocarb > synbiodesign
comparison toolOptBioDes.py @ 24:8f42eba7e2eb draft
planemo upload commit 2414e76bee8adbe48fee12b14b13a743a03b9748-dirty
| author | pablocarb |
|---|---|
| date | Fri, 05 Jul 2019 17:18:26 -0400 |
| parents | 6a1fbacdfaf5 |
| children | 0ad6fda90f41 |
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| 23:635b76a9bd7a | 24:8f42eba7e2eb |
|---|---|
| 13 import os | 13 import os |
| 14 import json | 14 import json |
| 15 | 15 |
| 16 def arguments(): | 16 def arguments(): |
| 17 parser = argparse.ArgumentParser(description='toolOptBioDes: Optimal SynBio Design. Pablo Carbonell, SYNBIOCHEM, 2019') | 17 parser = argparse.ArgumentParser(description='toolOptBioDes: Optimal SynBio Design. Pablo Carbonell, SYNBIOCHEM, 2019') |
| 18 parser.add_argument('infile', | |
| 19 help='Input csv file (DoE specificiations).') | |
| 20 parser.add_argument('size', | 18 parser.add_argument('size', |
| 21 help='Library size.') | 19 help='Library size.') |
| 22 parser.add_argument('outfile', | 20 parser.add_argument('outfile', |
| 23 help='Output csv design file.') | 21 help='Output csv design file.') |
| 24 parser.add_argument('diagfile', | 22 parser.add_argument('diagfile', |
| 25 help='Output csv diagnostics file.') | 23 help='Output csv diagnostics file.') |
| 24 parser.add_argument('-infile', default=None, | |
| 25 help='Input csv file (DoE specifications sheet).') | |
| 26 parser.add_argument('-partsfile', default=None, | |
| 27 help='Input csv file (Regulartory parts).') | |
| 28 parser.add_argument('-genesfile', default=None, | |
| 29 help='Input csv file (Genetic parts).') | |
| 30 parser.add_argument('-sbolOut', default=None, | |
| 31 help='Output design in SBOL format.') | |
| 26 parser.add_argument('-server', default='http://optbiodes.synbiochem.co.uk/REST', | 32 parser.add_argument('-server', default='http://optbiodes.synbiochem.co.uk/REST', |
| 27 help='OptBioDes server.') | 33 help='OptBioDes server.') |
| 28 return parser | 34 return parser |
| 29 | 35 |
| 30 def testApp(url): | 36 def testApp(url): |
| 47 cw = csv.writer(h) | 53 cw = csv.writer(h) |
| 48 cw.writerow( ['Size', 'Efficiency'] ) | 54 cw.writerow( ['Size', 'Efficiency'] ) |
| 49 cw.writerow( [res['data']['libsize'], res['data']['J']] ) | 55 cw.writerow( [res['data']['libsize'], res['data']['J']] ) |
| 50 print( 'Size:', res['data']['libsize'], 'Efficiency:', res['data']['J'] ) | 56 print( 'Size:', res['data']['libsize'], 'Efficiency:', res['data']['J'] ) |
| 51 | 57 |
| 58 def partsUploadSbol( partsfile, genesfile, size, outfile, diagfile, sbolOut, server ): | |
| 59 files = { | |
| 60 'parts': open(partsfile, 'rb' ), | |
| 61 'genes': open(genesfile, 'rb') | |
| 62 } | |
| 63 values = {'size': size} | |
| 64 r = requests.post( os.path.join(url, 'Parts' ), files=files, data=values ) | |
| 65 res = json.loads( r.content.decode('utf-8') ) | |
| 66 M = res['data']['M'] | |
| 67 with open(outfile, 'w') as h: | |
| 68 cw = csv.writer(h) | |
| 69 cw.writerow( res['data']['names'] ) | |
| 70 for row in M: | |
| 71 cw.writerow( row ) | |
| 72 with open(diagfile, 'w') as h: | |
| 73 cw = csv.writer(h) | |
| 74 cw.writerow( ['Size', 'Efficiency'] ) | |
| 75 cw.writerow( [res['data']['libsize'], res['data']['J']] ) | |
| 76 open(sbolOut, 'w').write(res['data']['sbol']) | |
| 77 print( 'Size:', res['data']['libsize'], 'Efficiency:', res['data']['J'] ) | |
| 52 | 78 |
| 53 | 79 |
| 54 if __name__ == "__main__": | 80 if __name__ == "__main__": |
| 55 parser = arguments() | 81 parser = arguments() |
| 56 arg = parser.parse_args() | 82 arg = parser.parse_args() |
| 57 assert os.path.exists(arg.infile) | 83 assert os.path.exists(arg.infile) |
| 58 sheetUpload( arg.infile, arg.size, arg.outfile, arg.diagfile, arg.server ) | 84 if arg.sbolOut is None: |
| 85 sheetUpload( arg.infile, arg.size, arg.outfile, arg.diagfile, arg.server ) | |
| 86 else: | |
| 87 partsUploadSbol( arg.partsfile, arg.genesfile, arg.size, arg.outfile, arg.diagfile, arg.sbolOut, arg.server ) |