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1 import sys, argparse, csv
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2
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3 from bl.vl.kb import KnowledgeBase as KB
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4 from bl.vl.utils import get_logger, LOG_LEVELS
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5 import bl.vl.utils.ome_utils as vlu
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6 from bl.vl.graph.drivers.neo4j import Neo4JDriver
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7
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8
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9 def make_parser():
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10 parser = argparse.ArgumentParser(description='map wells label to illumina bead chip measures')
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11 parser.add_argument('--logfile', type=str, help='log file (deafult=stderr)')
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12 parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
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13 help='logging level (default=INFO)', default='INFO')
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14 parser.add_argument('-H', '--host', type=str, help='OMERO server hostname')
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15 parser.add_argument('-U', '--user', type=str, help='OMERO user')
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16 parser.add_argument('-P', '--passwd', type=str, help='OMERO password')
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17 parser.add_argument('--in_file', type=str, help='input file',
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18 required=True)
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19 parser.add_argument('--out_file', type=str, help='output file',
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20 required=True)
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21 parser.add_argument('--well_column', type=str, help='label of the column that will be mapped',
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22 default='source')
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23 return parser
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24
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25
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26 def get_wells_map(plate, kb, logger):
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27 logger.info('Mapping wells for plate %s', plate.label)
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28 wells_map = {}
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29 for w in kb.get_wells_by_plate(plate):
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30 wells_map[w.label] = w
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31 logger.info('Mapped %d wells', len(wells_map))
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32 return wells_map
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33
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34
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35 def get_plates_map(plates_list, kb, logger):
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36 logger.info('Loading TiterPlates map')
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37 plates_map = {}
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38 for pl in kb.get_objects(kb.TiterPlate):
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39 if isinstance(pl, kb.TiterPlate) and pl.barcode in plates_list:
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40 plates_map[pl.barcode] = get_wells_map(pl, kb, logger)
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41 logger.info('Mapped %d plates', len(plates_map))
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42 return plates_map
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43
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44
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45 def get_connected_illumina_measures(well, kb, logger):
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46 logger.debug('Loading connected IlluminaBeadChipMeasures for well %s:%s', well.label,
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47 well.container.label)
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48 return kb.dt.get_connected(well, aklass = kb.IlluminaBeadChipMeasures,
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49 direction = Neo4JDriver.DIRECTION_OUTGOING)
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50
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51
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52 def wells_to_illumina(in_file, out_file, column_label, kb, logger):
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53 with open(in_file) as ifile, open(out_file, 'w') as ofile:
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54 reader = csv.DictReader(ifile, delimiter='\t')
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55 in_records = [r for r in reader]
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56 plates_barcodes = set([x[column_label].split(':')[0] for x in in_records])
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57 plates_map = get_plates_map(plates_barcodes, kb, logger)
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58 writer = csv.DictWriter(ofile, reader.fieldnames, delimiter='\t')
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59 writer.writeheader()
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60 logger.info('Mapping wells to illumina bead chip measures')
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61 for rec in in_records:
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62 barcode, well = rec[column_label].split(':')
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63 measures = get_connected_illumina_measures(plates_map[barcode][well], kb,
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64 logger)
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65 if len(measures) != 1:
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66 logger.warning('Found %d measures for well %s:%s, skipping line', len(measures),
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67 barcode, well)
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68 continue
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69 rec[column_label] = measures[0].label
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70 writer.writerow(rec)
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71
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72
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73 def main(argv):
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74 parser = make_parser()
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75 args = parser.parse_args(argv)
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76
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77 logger = get_logger('from_well_to_illumina_measures', level=args.loglevel,
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78 filename=args.logfile)
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79
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80 try:
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81 host = args.host or vlu.ome_host()
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82 user = args.user or vlu.ome_user()
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83 passwd = args.passwd or vlu.ome_passwd()
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84 except ValueError, ve:
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85 logger.critical(ve)
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86 sys.exit(ve)
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87
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88 kb = KB(driver='omero')(host, user, passwd)
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89 wells_to_illumina(args.in_file, args.out_file, args.well_column,
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90 kb, logger)
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91 logger.info('Job completed')
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92
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93
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94 if __name__ == '__main__':
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95 main(sys.argv[1:])
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