diff delete_features.py @ 0:1f2e360f7554 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/delete_features.py	Mon Sep 11 05:48:05 2017 -0400
@@ -0,0 +1,66 @@
+#!/usr/bin/env python
+from __future__ import print_function
+
+import argparse
+import logging
+import random
+
+from webapollo import AssertUser, GuessOrg, OrgOrGuess, WAAuth, WebApolloInstance, retry
+logging.basicConfig(level=logging.INFO)
+log = logging.getLogger(__name__)
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Sample script to delete all features from an organism')
+    WAAuth(parser)
+    parser.add_argument('email', help='User Email')
+    parser.add_argument('--type', help='Feature type filter')
+    OrgOrGuess(parser)
+
+    args = parser.parse_args()
+
+    wa = WebApolloInstance(args.apollo, args.username, args.password)
+    # User must have an account
+    gx_user = AssertUser(wa.users.loadUsers(email=args.email))
+
+    # Get organism
+    org_cn = GuessOrg(args, wa)
+    if isinstance(org_cn, list):
+        org_cn = org_cn[0]
+
+    # TODO: Check user perms on org.
+    org = wa.organisms.findOrganismByCn(org_cn)
+
+    sequences = wa.organisms.getSequencesForOrganism(org['id'])
+    for sequence in sequences['sequences']:
+        log.info("Processing %s %s", org['commonName'], sequence['name'])
+        # Call setSequence to tell apollo which organism we're working with
+        wa.annotations.setSequence(sequence['name'], org['id'])
+        # Then get a list of features.
+        features = wa.annotations.getFeatures()
+        # For each feature in the features
+        for feature in sorted(features['features'], key=lambda x: random.random()):
+            if args.type:
+                if args.type == 'tRNA':
+                    if feature['type']['name'] != 'tRNA':
+                        continue
+
+                elif args.type == 'terminator':
+                    if feature['type']['name'] != 'terminator':
+                        continue
+
+                elif args.type == 'mRNA':
+                    if feature['type']['name'] != 'mRNA':
+                        continue
+
+                else:
+                    raise Exception("Unknown type")
+
+            # We see that deleteFeatures wants a uniqueName, and so we pass
+            # is the uniquename field in the feature.
+            def fn():
+                wa.annotations.deleteFeatures([feature['uniquename']])
+                print('Deleted %s [type=%s]' % (feature['uniquename'], feature['type']['name']))
+
+            if not retry(fn, limit=3):
+                print('Error %s' % feature['uniquename'])