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3
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1 '''
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2 From a file like this
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3 individual sibling
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4 V08E18411BC66F4987BCA43EFC6F636224 V0AE5660BF4A7149589BE9DB3308B50327
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5 V0FAE2B10F690041509739A3F4B314DC8F V00875417B31684EC2A62EE37717913445
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6 V0382EF862AA4B475697C95D3777043239 V08E376727ED8E4B369DAA3B62A9395E1B
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7 ....
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8
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9 retrieve indivual's parents using sibling informations and build a file like
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10
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11 individual father mother
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12 V08E18411BC66F4987BCA43EFC6F636224 V027DE334753424F07B81A70053EF5B873 V035222CAEE0474AFEBB9A161D4B64914E
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13 V0FAE2B10F690041509739A3F4B314DC8F V0E966B53BDCC942C09D6B6D96DE98F4F4 V0F7B6926C6FBE4F0BB38BBC6CFB13A825
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14 ....
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15
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16 '''
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17
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18 import sys, csv, argparse, logging, os
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19
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20 from bl.vl.kb import KnowledgeBase as KB
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21 import bl.vl.utils.ome_utils as vlu
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22 from bl.vl.utils import get_logger, LOG_LEVELS
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23
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24
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25 def make_parser():
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26 parser = argparse.ArgumentParser(description='retrieve parents information using sibling')
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27 parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
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28 parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
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29 help='logging level (default=INFO)', default='INFO')
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30 parser.add_argument('-H', '--host', type=str, help='omero hostname')
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31 parser.add_argument('-U', '--user', type=str, help='omero user')
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32 parser.add_argument('-P', '--passwd', type=str, help='omero passwd')
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33 parser.add_argument('--in_file', type=str, required=True,
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34 help='input file with individual-sibling couples')
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35 parser.add_argument('--out_file', type=str, required=True,
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36 help='output file with parents information')
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37 return parser
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38
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39
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40 def main(argv):
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41 parser = make_parser()
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42 args = parser.parse_args(argv)
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43
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44 logger = get_logger('get_parents_from_sibling', level=args.loglevel,
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45 filename=args.logfile)
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46
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47 try:
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48 host = args.host or vlu.ome_host()
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49 user = args.user or vlu.ome_user()
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50 passwd = args.passwd or vlu.ome_passwd()
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51 except ValueError, ve:
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52 logger.critical(ve)
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53 sys.exit(ve)
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54
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55 kb = KB(driver='omero')(host, user, passwd)
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56
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57 logger.info('Retrieving individuals')
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58 inds = kb.get_objects(kb.Individual)
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59 logger.info('Retrieved %d individuals' % len(inds))
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60 inds_lookup = {}
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61 for ind in inds:
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62 inds_lookup[ind.id] = ind
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63
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64 with open(args.in_file) as infile:
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65 reader = csv.DictReader(infile, delimiter='\t')
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66 records = []
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67 for row in reader:
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68 try:
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69 sib = inds_lookup[row['sibling']]
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70 rec = {'individual' : row['individual'],
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71 'father' : sib.father.id if sib.father else 'None',
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72 'mother' : sib.mother.id if sib.mother else 'None'}
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73 logger.info('Individual %s, father: %s - mother: %s' % (row['individual'],
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74 rec['father'],
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75 rec['mother']))
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76 records.append(rec)
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77 except KeyError:
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78 logger.error('Unable to find individual %s' % row['sibling'])
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79
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80 logger.info('Retrieved parents for %d individuals' % len(records))
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81
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82 with open(args.out_file, 'w') as outfile:
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83 writer = csv.DictWriter(outfile, ['individual', 'father', 'mother'],
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84 delimiter='\t')
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85 writer.writeheader()
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86 writer.writerows(records)
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87
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88 if __name__ == '__main__':
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89 main(sys.argv[1:])
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