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3
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1 """
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2 Split a file like::
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3
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4 source enrollment
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5 V044DE795E7F9F42FEB9855288CF577A77 ASTUDY:2141
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6 V06C59B915C0FD47DABE6AE02C731780AF BSTUDY:390
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7
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8 into two separated a new TSV files
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9
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10 source study label
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11 V044DE795E7F9F42FEB9855288CF577A77 ASTUDY 2141
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12 V06C59B915C0FD47DABE6AE02C731780AF BSTUDY 390
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13
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14 """
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15
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16 import sys, argparse, csv
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17 from bl.vl.utils import LOG_LEVELS, get_logger
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18
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19
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20 def get_parser():
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21 parser = argparse.ArgumentParser('Prepare input files for enrollments import workflow')
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22 parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
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23 parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
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24 help='logging level', default='INFO')
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25 parser.add_argument('--in-file', type=str, required=True,
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26 help='input TSV file')
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27 parser.add_argument('--out-enrollments', type=str, required=True,
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28 help='input file with Enrollments definitions')
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29 return parser
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30
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31
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32 def get_enrollments_definitions(records, logger):
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33 logger.info('Creating enrollment definitions')
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34 enr_defs = []
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35 for rec in records:
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36 try:
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37 edef = {}
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38 edef['source'] = rec['source']
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39 try:
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40 edef['study'], edef['label'] = rec['enrollment'].split(':')
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41 except ValueError:
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42 logger.error('Skipped record %r, wrong label format for %s', rec, rec['enrollment'])
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43 continue
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44 except KeyError, ke:
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45 logger.error('Skipped record %r, missing key %s', rec, ke)
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46 continue
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47 enr_defs.append(edef)
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48 logger.info('Retrieved %d enrollment definitions', len(enr_defs))
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49 return enr_defs
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50
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51
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52 def get_parents_definitions(records, logger):
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53 logger.info('Creating parents definitions')
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54 parents_defs = []
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55 for rec in records:
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56 try:
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57 pdef = dict()
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58 pdef['individual'] = rec['individual']
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59 if rec['father'] != 'None' or rec['mother'] != 'None':
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60 pdef['father'] = rec['father']
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61 pdef['mother'] = rec['mother']
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62 parents_defs.append(pdef)
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63 else:
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64 continue
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65 except KeyError, ke:
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66 logger.error('Skipped record %r, missing key %s', rec, ke)
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67 continue
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68 logger.info('Retrieved %d parents definitions', len(parents_defs))
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69 return parents_defs
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70
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71
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72 def main(argv):
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73 parser = get_parser()
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74 args = parser.parse_args(argv)
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75
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76 logger = get_logger('prepare_enrollments_import', level=args.loglevel,
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77 filename=args.logfile)
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78
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79 logger.info('Start processing file %s', args.in_file)
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80
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81 with open(args.in_file) as in_file:
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82 reader = csv.DictReader(in_file, delimiter='\t')
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83 records = [row for row in reader]
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84 logger.info('Loaded %d records', len(records))
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85
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86 enrollment_defs = get_enrollments_definitions(records, logger)
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87 with open(args.out_enrollments, 'w') as enr_out:
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88 enr_writer = csv.DictWriter(enr_out,
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89 ['source', 'study', 'label'],
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90 delimiter='\t')
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91 enr_writer.writeheader()
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92 enr_writer.writerows(enrollment_defs)
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93
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94 logger.info('Job completed')
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95
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96 if __name__ == '__main__':
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97 main(sys.argv[1:])
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