annotate toolSelenzyme.py @ 0:ac027c9ace4d draft

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author pablocarb
date Mon, 29 Apr 2019 09:49:36 -0400
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children 635b76a9bd7a
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1 #!/usr/bin/env python3
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2 # -*- coding: utf-8 -*-
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3 """
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4 Created on Mar 19
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6 @author: Pablo Carbonell
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7 @description: Query Selenzme: Enzyme sequence selection.
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8
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9 """
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10 import requests
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11 import argparse
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12 import csv
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13 import os
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14 import json
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15
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16 def arguments():
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17 parser = argparse.ArgumentParser(description='toolSelenzyme: Enzyme sequence selection. Pablo Carbonell, SYNBIOCHEM, 2019')
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18 parser.add_argument('infile',
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19 help='Input csv file.')
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20 parser.add_argument('outfile',
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21 help='Input csv file.')
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22 parser.add_argument('-server', default='http://selenzyme.synbiochem.co.uk/REST',
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23 help='Selenzyme server.')
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24 return parser
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25
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26 # Output columns, to be improved
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27 columns = ['Seq. ID', 'Score', 'Organism Source', 'Description']
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29 if __name__ == "__main__":
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30 parser = arguments()
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31 arg = parser.parse_args()
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32 assert os.path.exists(arg.infile)
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33 with open(arg.infile) as handler:
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34 cv = csv.DictReader(handler)
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35 row = next(cv)
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36 url = arg.server
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37 assert 'smarts' in row
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38 r = requests.post( os.path.join(url, 'Query') , json={'smarts': row['smarts']} )
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39 res = json.loads( r.content.decode('utf-8') )
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40 assert res['data'] is not None
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41 val = json.loads( res['data'] )
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42 assert 'Seq. ID' in val and len(val['Seq. ID'])>0
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43 with open(arg.outfile, 'w' ) as writer:
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44 cw = csv.writer( writer )
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45 cw.writerow( columns )
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46 for ix in sorted(val['Seq. ID'], key=lambda z: int(z)):
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47 cw.writerow( [val[j][ix] for j in columns] )
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48