diff galaxy-tools/biobank/updater/drop_parental_info.py @ 0:ba6cf6ede027 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/updater/drop_parental_info.py	Wed Sep 28 06:03:30 2016 -0400
@@ -0,0 +1,69 @@
+import sys, csv, argparse, os
+
+from bl.vl.kb import KnowledgeBase as KB
+import bl.vl.utils.ome_utils as vlu
+from bl.vl.utils import get_logger, LOG_LEVELS
+
+
+def make_parser():
+    parser = argparse.ArgumentParser(description='set parents of the selected individuals to None')
+    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)', default='INFO')
+    parser.add_argument('-H', '--host', type=str, help='omero hostname')
+    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='list of the individuals')
+    parser.add_argument('--out_file', type=str, required=True,
+                        help='output file')
+    return parser
+
+
+def main(argv):
+    parser = make_parser()
+    args = parser.parse_args(argv)
+
+    logger = get_logger('drop_parental_info', 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)
+
+    kb = KB(driver='omero')(host, user, passwd)
+
+    logger.info('Retrieving individuals')
+    inds = kb.get_objects(kb.Individual)
+    logger.info('Retrieved %d individuals' % len(inds))
+    inds_lookup = {}
+    for i in inds:
+        inds_lookup[i.id] = i
+
+    with open(args.in_file) as in_file:
+        reader = csv.DictReader(in_file, delimiter='\t')
+        records = []
+        for row in reader:
+            try:
+                # The 'individual' : inds_lookup[row['individual']].id
+                # is quite redundant but is a usefull check in order
+                # to filter wrong VIDs
+                record = {'individual' : inds_lookup[row['individual']].id,
+                          'father' : 'None',
+                          'mother' : 'None'}
+                records.append(record)
+            except KeyError, ke:
+                logger.warning('Individual with VID %s does not exist, skipping line' % ke)
+
+    with open(args.out_file, 'w') as out_file:
+        writer = csv.DictWriter(out_file, ['individual', 'father', 'mother'],
+                                delimiter = '\t')
+        writer.writeheader()
+        writer.writerows(records)
+
+if __name__ == '__main__':
+    main(sys.argv[1:])