diff galaxy-tools/biobank/utils/prepare_aligned_seq_dsample_import.py @ 0:ba6cf6ede027 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/utils/prepare_aligned_seq_dsample_import.py	Wed Sep 28 06:03:30 2016 -0400
@@ -0,0 +1,76 @@
+import csv, sys, argparse, logging
+
+LOG_FORMAT = '%(asctime)s|%(levelname)-8s|%(message)s'
+LOG_DATEFMT = '%Y-%m-%d %H:%M:%S'
+LOG_LEVELS = ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL']
+
+
+def make_parser():
+    parser = argparse.ArgumentParser(description='build aligned seq data sample import files')
+    parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
+    parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
+                        help='logging level', default='INFO')
+    parser.add_argument('--study',  type=str, required=True,
+                        help='study')
+    parser.add_argument('--label',  type=str, required=True,
+                        help='label')
+    parser.add_argument('--source',  type=str, required=True,
+                        help='source')
+    parser.add_argument('--device',  type=str, required=True,
+                        help='device')
+    parser.add_argument('--path',  type=str, required=True,
+                        help='path')
+    parser.add_argument('--sample',  type=str, required=True,
+                        help='sample')
+    parser.add_argument('--genome_reference',  type=str, required=True,
+                        help='genome reference')
+    parser.add_argument('--dsample_ofile', type=str, default='./genome_variations_dsample.tsv',
+                        help='output file containing data samples definitions')
+    parser.add_argument('--dobject_ofile', type=str, default='./genome_variations_dobject.tsv',
+                        help='output file containing data samples definitions')
+
+    return parser
+
+def main(argv):
+    parser = make_parser()
+    args = parser.parse_args(argv)
+
+    log_level = getattr(logging, args.loglevel)
+    kwargs = {'format': LOG_FORMAT,
+              'datefmt': LOG_DATEFMT,
+              'level': log_level}
+    if args.logfile:
+        kwargs['filename'] = args.logfile
+    logging.basicConfig(**kwargs)
+    logger = logging.getLogger('prepare_aligned_seq_dsample_inport')
+
+
+    with open(args.dsample_ofile, 'w') as ofile:
+        out_file_header = ['study', 'label', 'source', 'source_type', 'seq_dsample_type', 'status', 'device', 'sample', 'genome_reference']
+        writer = csv.DictWriter(ofile, out_file_header, delimiter='\t')
+        writer.writeheader()
+        writer.writerow({'study': args.study,
+                        'label': args.label,
+                        'source': args.source,
+                        'device': args.device,
+                        'source_type' : 'Tube',
+                        'seq_dsample_type': 'AlignedSeqDataSample',
+                        'status': 'USABLE',
+                        'sample' : args.sample,
+                        'genome_reference': args.genome_reference})
+    logger.info('Done writing file %s' % args.dsample_ofile)
+
+    with open(args.dobject_ofile, 'w') as ofile:
+        out_file_header = ['study', 'path', 'data_sample', 'mimetype', 'size', 'sha1']
+        writer = csv.DictWriter(ofile, out_file_header, delimiter='\t')
+        writer.writeheader()
+        writer.writerow({'study': args.study,
+                        'path': args.path,
+                        'data_sample': args.label,
+                        'mimetype': 'x-vl/bam',
+                        'size': '-1',
+                        'sha1': 'N.A.'})
+    logger.info('Done writing file %s' % args.dobject_ofile)
+
+if __name__ == '__main__':
+    main(sys.argv[1:])