diff renumber.py @ 0:6002cc0df04e draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4e5a5af7689f1713c34a6ad9a9594c205e762fdd

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/renumber.py	Tue May 03 13:38:55 2016 -0400
@@ -0,0 +1,57 @@
+#!/usr/bin/env python
+import json
+import copy
+import argparse
+from webapollo import WebApolloInstance
+import logging
+logging.basicConfig(level=logging.INFO)
+log = logging.getLogger(__name__)
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
+    parser.add_argument('apollo', help='Complete Apollo URL')
+    parser.add_argument('username', help='WA Admin Username')
+    parser.add_argument('password', help='WA Admin Password')
+
+    parser.add_argument('cn', help='Organism Common Name')
+
+    parser.add_argument('--email')
+    parser.add_argument('--prefix', default='gene_')
+    parser.add_argument('--leading', default='3')
+
+    args = parser.parse_args()
+
+
+    wa = WebApolloInstance(args.apollo, args.username, args.password)
+    # User must have an account
+    gx_user = wa.users.loadUsers(email=args.email)
+    if len(gx_user) == 0:
+        raise Exception("Unknown user. Please register first")
+
+    # Must find the organism
+    org = wa.organisms.findOrganismByCn(args.cn)
+    # TODO: verify user has permissions on the organism
+    wa.annotations.setSequence(args.cn, org['id'])
+    raw_data =  wa.annotations.getFeatures()['features']
+
+    data = sorted([
+        (x['parent_id'], x['uniquename'], x['location']['fmin'], x['name'])
+        for x in raw_data
+    ], key=lambda x: x[2])
+
+    format_string = args.prefix + '%0' + args.leading + 'd'
+    format_string_mrna = format_string + '.mRNA'
+
+    outData = copy.copy(org)
+    outData['changes'] = []
+
+    for i, feat in enumerate(data):
+        idx = i + 1
+        log.info('Renaming %s to %s', feat[3], format_string % idx)
+        outData['changes'].append((feat[0], format_string % idx))
+        wa.annotations.setName(feat[0], format_string % idx)
+        outData['changes'].append((feat[1], format_string_mrna % idx))
+        wa.annotations.setName(feat[1], format_string_mrna % idx)
+
+    print json.dumps(outData, indent=2)