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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/utils/wells_barcode_to_label.py	Wed Sep 28 06:03:30 2016 -0400
@@ -0,0 +1,112 @@
+"""
+Map PlateWell labels written as PLATE_BARCODE:WELL_LABEL to labels written as
+PLATE_LABEL:WELL_LABEL which is the PlateWell label format required by the map_vid
+application.
+The inputs are a TSV file and the label of the column of this file containing the
+PlateWell labels that are going to be mapped.
+"""
+
+import csv, argparse, sys, copy
+
+from bl.vl.kb import KnowledgeBase as KB
+from bl.vl.utils import LOG_LEVELS, get_logger
+import bl.vl.utils.ome_utils as vlu
+
+
+def get_wells_map(kb, plate_barcodes, logger):
+    wells_map = {}
+    logger.info('Start building PlateWells map')
+    res = kb.get_by_field(kb.TiterPlate, 'barcode', plate_barcodes)
+    logger.debug('Plates %r --- Results: %r', plate_barcodes, res)
+    for _, pl in res.iteritems():
+        if pl.OME_TABLE == 'TiterPlate':
+            if pl.barcode:
+                for w in kb.get_wells_by_plate(pl):
+                    logger.debug('Mapping well %s of plate %s', w.label, w.container.label)
+                    wells_map['%s:%s' % (w.container.barcode, w.label)] = '%s:%s' % (w.container.label,
+                                                                                     w.label)
+            else:
+                logger.debug('TiterPlate %s has no barcode', pl.label)
+        else:
+            logger.debug('Object is a %r, skipping it', pl.OME_TABLE)
+    logger.info('Mapped %d PlateWells', len(wells_map))
+    return wells_map
+
+
+def get_plates_list(records, plates_column, logger):
+    plates = set()
+    logger.info('Retrieving TiterPlate barcodes from %d records', len(records))
+    for r in records:
+        plates.add(r[plates_column].split(':')[0])
+    logger.info('Found %d TiterPlate objects', len(plates))
+    return list(plates)
+
+
+def make_parser():
+    parser = argparse.ArgumentParser('Map barcodes in PlateWell labels to TiterPlate labels')
+    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('-H', '--host', type=str, help='OMERO host')
+    parser.add_argument('-U', '--user', type=str, help='OMERO user')
+    parser.add_argument('-P', '--passwd', type=str, help='OMERO password')
+    parser.add_argument('--in-file', type=str, required=True,
+                        help='input TSV file')
+    parser.add_argument('--column-label', type=str, required=True,
+                        help='the label of the columun containing the values that will be mapped')
+    parser.add_argument('--out-file', type=str, required=True,
+                        help='output TSV file')
+    parser.add_argument('--strict-mapping', action='store_true',
+                        help='if output records are less than the input ones, raise an error')
+    return parser
+
+
+def main(argv):
+    parser = make_parser()
+    args = parser.parse_args(argv)
+
+    logger = get_logger('wells_barcode_to_label', level=args.loglevel,
+                        filename=args.logfile)
+    try:
+        host = args.host or vlu.ome_host()
+        user = args.user or vlu.ome_user()
+        passwd = args.passwd or vlu.ome_passwd()
+    except ValueError, ve:
+        logger.critical(ve)
+        sys.exit(ve)
+
+    logger.info('Starting job')
+
+    kb = KB(driver='omero')(host, user, passwd)
+    # wells_map = get_wells_map(kb, logger)
+
+    with open(args.in_file) as in_file, open(args.out_file, 'w') as out_file:
+        reader = csv.DictReader(in_file, delimiter='\t')
+        if args.column_label not in reader.fieldnames:
+            msg = 'No column %s in file %s' % (args.column_label, args.in_file)
+            logger.critical(msg)
+            raise RuntimeError(msg)
+        records = [row for row in reader]
+        plates = get_plates_list(records, args.column_label, logger)
+        wells_map = get_wells_map(kb, plates, logger)
+        logger.info('Mapping %d records', len(records))
+        writer = csv.DictWriter(out_file, reader.fieldnames, delimiter='\t')
+        writer.writeheader()
+        mapped_records = []
+        for rec in records:
+            mapped = copy.deepcopy(rec)
+            logger.debug('Mapping value %s', mapped[args.column_label])
+            if mapped[args.column_label] in wells_map:
+                mapped[args.column_label] = wells_map[mapped[args.column_label]]
+                mapped_records.append(mapped)
+        if args.strict_mapping and len(mapped_records) < len(records):
+            msg = 'Mapped %d record of %d' % (len(mapped_records), len(records))
+            logger.critical(msg)
+            sys.exit(msg)
+        logger.info('%d records mapped', len(mapped_records))
+        writer.writerows(mapped_records)
+    logger.info('Job completed')
+
+
+if __name__ == '__main__':
+    main(sys.argv[1:])
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