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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/tools/get_parents_from_sibling.py	Wed Sep 28 06:03:30 2016 -0400
@@ -0,0 +1,89 @@
+'''
+From a file like this
+individual                           sibling
+V08E18411BC66F4987BCA43EFC6F636224   V0AE5660BF4A7149589BE9DB3308B50327
+V0FAE2B10F690041509739A3F4B314DC8F   V00875417B31684EC2A62EE37717913445
+V0382EF862AA4B475697C95D3777043239   V08E376727ED8E4B369DAA3B62A9395E1B
+....
+
+retrieve indivual's parents using sibling informations and build a file like
+
+individual                           father                               mother
+V08E18411BC66F4987BCA43EFC6F636224   V027DE334753424F07B81A70053EF5B873   V035222CAEE0474AFEBB9A161D4B64914E
+V0FAE2B10F690041509739A3F4B314DC8F   V0E966B53BDCC942C09D6B6D96DE98F4F4   V0F7B6926C6FBE4F0BB38BBC6CFB13A825
+....
+
+'''
+
+import sys, csv, argparse, logging, 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='retrieve parents information using sibling')
+    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 passwd')
+    parser.add_argument('--in_file', type=str, required=True,
+                        help='input file with individual-sibling couples')
+    parser.add_argument('--out_file', type=str, required=True,
+                        help='output file with parents information')
+    return parser
+
+
+def main(argv):
+    parser = make_parser()
+    args = parser.parse_args(argv)
+
+    logger = get_logger('get_parents_from_sibling', 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 ind in inds:
+        inds_lookup[ind.id] = ind
+
+    with open(args.in_file) as infile:
+        reader = csv.DictReader(infile, delimiter='\t')
+        records = []
+        for row in reader:
+            try:
+                sib = inds_lookup[row['sibling']]
+                rec = {'individual' : row['individual'],
+                       'father'     : sib.father.id if sib.father else 'None',
+                       'mother'     : sib.mother.id if sib.mother else 'None'}
+                logger.info('Individual %s, father: %s - mother: %s' % (row['individual'],
+                                                                        rec['father'],
+                                                                        rec['mother']))
+                records.append(rec)
+            except KeyError:
+                logger.error('Unable to find individual %s' % row['sibling'])
+
+    logger.info('Retrieved parents for %d individuals' % len(records))
+
+    with open(args.out_file, 'w') as outfile:
+        writer = csv.DictWriter(outfile, ['individual', 'father', 'mother'],
+                                delimiter='\t')
+        writer.writeheader()
+        writer.writerows(records)
+
+if __name__ == '__main__':
+    main(sys.argv[1:])