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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 individual gender father mother
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5 ASTUDY:2141 MALE ASTUDY:12 ASTUDY:12341
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6 ASTUDY:415 MALE ASTUDY:3562 ASTUDY:13612
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7
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8 into two separated TSV files, the first one will be used to import new individuals and enrollments,
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9 the second one will be used to update father and mother informations for the individuals in the first
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10 file.
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11 """
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12
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13 import sys, argparse, csv
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14 from bl.vl.utils import LOG_LEVELS, get_logger
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15
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16
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17 def get_parser():
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18 parser = argparse.ArgumentParser('Prepare input files for individuals import workflow')
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19 parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
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20 parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
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21 help='logging level', default='INFO')
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22 parser.add_argument('--in-file', type=str, required=True,
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23 help='input TSV file')
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24 parser.add_argument('--out-individuals', type=str, required=True,
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25 help='input file with Individuals definitions')
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26 parser.add_argument('--out-parents', type=str, required=True,
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27 help='input file with parents definitions')
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28 return parser
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29
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30
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31 def get_individual_definitions(records, logger):
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32 logger.info('Creating individual definitions')
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33 ind_defs = []
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34 for rec in records:
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35 try:
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36 idef = {'father': 'None', 'mother': 'None'}
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37 idef['gender'] = rec['gender']
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38 try:
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39 idef['study'], idef['label'] = rec['individual'].split(':')
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40 except ValueError:
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41 logger.error('Skipped record %r, wrong label format for %s', rec, rec['individual'])
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42 continue
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43 except KeyError, ke:
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44 logger.error('Skipped record %r, missing key %s', rec, ke)
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45 continue
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46 ind_defs.append(idef)
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47 logger.info('Retrieved %d individual definitions', len(ind_defs))
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48 return ind_defs
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49
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50
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51 def get_parents_definitions(records, logger):
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52 logger.info('Creating parents definitions')
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53 parents_defs = []
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54 for rec in records:
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55 try:
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56 pdef = dict()
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57 pdef['individual'] = rec['individual']
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58 if rec['father'] != 'None' or rec['mother'] != 'None':
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59 pdef['father'] = rec['father']
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60 pdef['mother'] = rec['mother']
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61 parents_defs.append(pdef)
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62 else:
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63 continue
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64 except KeyError, ke:
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65 logger.error('Skipped record %r, missing key %s', rec, ke)
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66 continue
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67 logger.info('Retrieved %d parents definitions', len(parents_defs))
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68 return parents_defs
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69
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70
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71 def main(argv):
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72 parser = get_parser()
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73 args = parser.parse_args(argv)
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74
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75 logger = get_logger('prepare_individuals_import', level=args.loglevel,
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76 filename=args.logfile)
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77
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78 logger.info('Start processing file %s', args.in_file)
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79
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80 with open(args.in_file) as in_file:
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81 reader = csv.DictReader(in_file, delimiter='\t')
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82 records = [row for row in reader]
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83 logger.info('Loaded %d records', len(records))
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84
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85 individual_defs = get_individual_definitions(records, logger)
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86 with open(args.out_individuals, 'w') as inds_out:
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87 inds_writer = csv.DictWriter(inds_out,
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88 ['study', 'label', 'gender', 'father', 'mother'],
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89 delimiter='\t')
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90 inds_writer.writeheader()
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91 inds_writer.writerows(individual_defs)
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92
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93 parents_defs = get_parents_definitions(records, logger)
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94 with open(args.out_parents, 'w') as parents_out:
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95 parents_writer = csv.DictWriter(parents_out, ['individual', 'father', 'mother'],
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96 delimiter='\t')
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97 parents_writer.writeheader()
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98 parents_writer.writerows(parents_defs)
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99
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100 logger.info('Job completed')
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101
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102 if __name__ == '__main__':
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103 main(sys.argv[1:])
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104
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105
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