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1 import sys, csv, argparse, os
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2
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3 from bl.vl.kb import KnowledgeBase as KB
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4 import bl.vl.utils.ome_utils as vlu
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5 from bl.vl.utils import get_logger, LOG_LEVELS
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6
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7
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8 def make_parser():
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9 parser = argparse.ArgumentParser(description='set parents of the selected individuals to None')
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10 parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
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11 parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
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12 help='logging level (default=INFO)', default='INFO')
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13 parser.add_argument('-H', '--host', type=str, help='omero hostname')
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14 parser.add_argument('-U', '--user', type=str, help='omero user')
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15 parser.add_argument('-P', '--passwd', type=str, help='omero password')
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16 parser.add_argument('--in_file', type=str, required=True,
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17 help='list of the individuals')
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18 parser.add_argument('--out_file', type=str, required=True,
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19 help='output file')
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20 return parser
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21
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22
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23 def main(argv):
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24 parser = make_parser()
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25 args = parser.parse_args(argv)
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26
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27 logger = get_logger('drop_parental_info', level=args.loglevel,
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28 filename=args.logfile)
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29
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30 try:
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31 host = args.host or vlu.ome_host()
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32 user = args.user or vlu.ome_user()
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33 passwd = args.passwd or vlu.ome_passwd()
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34 except ValueError, ve:
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35 logger.critical(ve)
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36 sys.exit(ve)
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37
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38 kb = KB(driver='omero')(host, user, passwd)
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39
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40 logger.info('Retrieving individuals')
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41 inds = kb.get_objects(kb.Individual)
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42 logger.info('Retrieved %d individuals' % len(inds))
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43 inds_lookup = {}
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44 for i in inds:
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45 inds_lookup[i.id] = i
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46
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47 with open(args.in_file) as in_file:
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48 reader = csv.DictReader(in_file, delimiter='\t')
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49 records = []
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50 for row in reader:
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51 try:
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52 # The 'individual' : inds_lookup[row['individual']].id
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53 # is quite redundant but is a usefull check in order
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54 # to filter wrong VIDs
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55 record = {'individual' : inds_lookup[row['individual']].id,
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56 'father' : 'None',
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57 'mother' : 'None'}
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58 records.append(record)
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59 except KeyError, ke:
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60 logger.warning('Individual with VID %s does not exist, skipping line' % ke)
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61
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62 with open(args.out_file, 'w') as out_file:
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63 writer = csv.DictWriter(out_file, ['individual', 'father', 'mother'],
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64 delimiter = '\t')
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65 writer.writeheader()
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66 writer.writerows(records)
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67
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68 if __name__ == '__main__':
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69 main(sys.argv[1:])
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