diff create_features_from_gff3.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/create_features_from_gff3.py	Tue May 03 13:38:55 2016 -0400
@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+import argparse
+from webapollo import WebApolloInstance, featuresToFeatureSchema
+from BCBio import GFF
+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', help='User Email')
+    parser.add_argument('gff3', type=file, help='GFF3 file')
+    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")
+
+    # TODO: Check user perms on org.
+
+    org = wa.organisms.findOrganismByCn(args.cn)
+    wa.annotations.setSequence(args.cn, org['id'])
+
+    for rec in GFF.parse(args.gff3):
+        featureData = featuresToFeatureSchema(rec.features)
+        wa.annotations.addFeature(
+            {
+                'features': featureData
+            }, trustme=True
+        )