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3
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1 """
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2 """
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3 import csv, sys, argparse, logging
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4
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5
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6 LOG_FORMAT = '%(asctime)s|%(levelname)-8s|%(message)s'
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7 LOG_DATEFMT = '%Y-%m-%d %H:%M:%S'
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8 LOG_LEVELS = ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL']
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9
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10 def make_parser():
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11 parser = argparse.ArgumentParser(description='prepare inputs for VLUTIL.prepare_seq_dsample_inputs')
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12 parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
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13 parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
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14 help='logging level', default='INFO')
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15 parser.add_argument('--in-file', '-i', type=str, required=True,
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16 help='input file')
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17 return parser
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18
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19 def read_samplesheet(in_file):
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20 with open(in_file, 'rU') as f:
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21 reader = csv.DictReader(f, delimiter='\t')
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22 recs = [r for r in reader]
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23 fieldnames = reader.fieldnames
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24 return recs, fieldnames
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25
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26 def is_header_different(titer_plate_header, header_to_be_checked):
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27 result = set(header_to_be_checked).difference(frozenset(titer_plate_header))
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28 if len(result) > 0:
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29 return True
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30 else:
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31 return False
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32
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33 def main(argv):
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34 parser = make_parser()
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35 args = parser.parse_args(argv)
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36
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37 log_level = getattr(logging, args.loglevel)
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38 kwargs = {'format': LOG_FORMAT,
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39 'datefmt': LOG_DATEFMT,
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40 'level': log_level}
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41 if args.logfile:
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42 kwargs['filename'] = args.logfile
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43 logging.basicConfig(**kwargs)
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44 logger = logging.getLogger('check tsv header')
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45
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46 logger.info('Loading data from file %s' % args.in_file)
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47 recs, file_header = read_samplesheet(args.in_file)
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48 logger.debug('Retrieved %d records', len(recs))
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49
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50 titer_plate_header = ['study', 'label', 'barcode', 'rows', 'columns']
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51
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52 if is_header_different(titer_plate_header, file_header):
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53 logger.info("Tsv file header has to have this elements: {}".format(titer_plate_header))
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54 # hack to support old galaxy
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55 sys.stderr.write("Headers not compliant to: {}".format(titer_plate_header))
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56 sys.exit(2)
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57 else:
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58 logger.info("Header check passed")
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59
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60 if __name__ == '__main__':
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61 main(sys.argv[1:])
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