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1 """
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2 Map PlateWell labels written as PLATE_BARCODE:WELL_LABEL to labels written as
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3 PLATE_LABEL:WELL_LABEL which is the PlateWell label format required by the map_vid
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4 application.
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5 The inputs are a TSV file and the label of the column of this file containing the
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6 PlateWell labels that are going to be mapped.
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7 """
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8
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9 import csv, argparse, sys, copy
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10
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11 from bl.vl.kb import KnowledgeBase as KB
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12 from bl.vl.utils import LOG_LEVELS, get_logger
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13 import bl.vl.utils.ome_utils as vlu
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14
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15
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16 def get_wells_map(kb, plate_barcodes, logger):
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17 wells_map = {}
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18 logger.info('Start building PlateWells map')
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19 res = kb.get_by_field(kb.TiterPlate, 'barcode', plate_barcodes)
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20 logger.debug('Plates %r --- Results: %r', plate_barcodes, res)
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21 for _, pl in res.iteritems():
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22 if pl.OME_TABLE == 'TiterPlate':
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23 if pl.barcode:
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24 for w in kb.get_wells_by_plate(pl):
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25 logger.debug('Mapping well %s of plate %s', w.label, w.container.label)
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26 wells_map['%s:%s' % (w.container.barcode, w.label)] = '%s:%s' % (w.container.label,
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27 w.label)
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28 else:
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29 logger.debug('TiterPlate %s has no barcode', pl.label)
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30 else:
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31 logger.debug('Object is a %r, skipping it', pl.OME_TABLE)
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32 logger.info('Mapped %d PlateWells', len(wells_map))
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33 return wells_map
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34
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35
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36 def get_plates_list(records, plates_column, logger):
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37 plates = set()
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38 logger.info('Retrieving TiterPlate barcodes from %d records', len(records))
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39 for r in records:
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40 plates.add(r[plates_column].split(':')[0])
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41 logger.info('Found %d TiterPlate objects', len(plates))
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42 return list(plates)
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43
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44
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45 def make_parser():
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46 parser = argparse.ArgumentParser('Map barcodes in PlateWell labels to TiterPlate labels')
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47 parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
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48 parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
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49 help='logging level', default='INFO')
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50 parser.add_argument('-H', '--host', type=str, help='OMERO host')
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51 parser.add_argument('-U', '--user', type=str, help='OMERO user')
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52 parser.add_argument('-P', '--passwd', type=str, help='OMERO password')
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53 parser.add_argument('--in-file', type=str, required=True,
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54 help='input TSV file')
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55 parser.add_argument('--column-label', type=str, required=True,
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56 help='the label of the columun containing the values that will be mapped')
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57 parser.add_argument('--out-file', type=str, required=True,
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58 help='output TSV file')
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59 parser.add_argument('--strict-mapping', action='store_true',
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60 help='if output records are less than the input ones, raise an error')
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61 return parser
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62
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63
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64 def main(argv):
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65 parser = make_parser()
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66 args = parser.parse_args(argv)
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67
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68 logger = get_logger('wells_barcode_to_label', level=args.loglevel,
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69 filename=args.logfile)
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70 try:
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71 host = args.host or vlu.ome_host()
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72 user = args.user or vlu.ome_user()
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73 passwd = args.passwd or vlu.ome_passwd()
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74 except ValueError, ve:
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75 logger.critical(ve)
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76 sys.exit(ve)
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77
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78 logger.info('Starting job')
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79
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80 kb = KB(driver='omero')(host, user, passwd)
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81 # wells_map = get_wells_map(kb, logger)
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82
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83 with open(args.in_file) as in_file, open(args.out_file, 'w') as out_file:
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84 reader = csv.DictReader(in_file, delimiter='\t')
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85 if args.column_label not in reader.fieldnames:
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86 msg = 'No column %s in file %s' % (args.column_label, args.in_file)
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87 logger.critical(msg)
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88 raise RuntimeError(msg)
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89 records = [row for row in reader]
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90 plates = get_plates_list(records, args.column_label, logger)
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91 wells_map = get_wells_map(kb, plates, logger)
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92 logger.info('Mapping %d records', len(records))
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93 writer = csv.DictWriter(out_file, reader.fieldnames, delimiter='\t')
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94 writer.writeheader()
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95 mapped_records = []
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96 for rec in records:
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97 mapped = copy.deepcopy(rec)
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98 logger.debug('Mapping value %s', mapped[args.column_label])
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99 if mapped[args.column_label] in wells_map:
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100 mapped[args.column_label] = wells_map[mapped[args.column_label]]
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101 mapped_records.append(mapped)
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102 if args.strict_mapping and len(mapped_records) < len(records):
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103 msg = 'Mapped %d record of %d' % (len(mapped_records), len(records))
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104 logger.critical(msg)
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105 sys.exit(msg)
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106 logger.info('%d records mapped', len(mapped_records))
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107 writer.writerows(mapped_records)
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108 logger.info('Job completed')
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109
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110
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111 if __name__ == '__main__':
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112 main(sys.argv[1:]) |
