{"action":"opened","issue":{"url":"https://api.github.com/repos/hammerlab/varcode/issues/70","labels_url":"https://api.github.com/repos/hammerlab/varcode/issues/70/labels{/name}","comments_url":"https://api.github.com/repos/hammerlab/varcode/issues/70/comments","events_url":"https://api.github.com/repos/hammerlab/varcode/issues/70/events","html_url":"https://github.com/hammerlab/varcode/issues/70","id":71699457,"number":70,"title":"AttributeError: 'FrameShiftTruncation' object has no attribute 'aa_alt'","user":{"login":"tavinathanson","id":322932,"avatar_url":"https://avatars.githubusercontent.com/u/322932?v=3","gravatar_id":"","url":"https://api.github.com/users/tavinathanson","html_url":"https://github.com/tavinathanson","followers_url":"https://api.github.com/users/tavinathanson/followers","following_url":"https://api.github.com/users/tavinathanson/following{/other_user}","gists_url":"https://api.github.com/users/tavinathanson/gists{/gist_id}","starred_url":"https://api.github.com/users/tavinathanson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tavinathanson/subscriptions","organizations_url":"https://api.github.com/users/tavinathanson/orgs","repos_url":"https://api.github.com/users/tavinathanson/repos","events_url":"https://api.github.com/users/tavinathanson/events{/privacy}","received_events_url":"https://api.github.com/users/tavinathanson/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/hammerlab/varcode/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-04-28T20:53:02Z","updated_at":"2015-04-28T20:53:02Z","closed_at":null,"body":"Issue with multiple inheritance of `FrameShiftTruncation`, where `mutant_protein_sequence` uses the definition in `PrematureStop`?\r\n\r\n```\r\n/Users/tavi/drive/work/repos/cancer/topiary/topiary/mutant_epitope_predictor.pyc in predict(self, variant_collection, mhc_alleles, gene_expression_dict, min_gene_expresion_value, transcript_expression_dict, min_transcript_expresion_value, raise_on_variant_effect_error)\r\n    145         fasta_dict = create_fasta_dict(\r\n    146             effects=variant_effects.values(),\r\n--> 147             padding_around_mutation=self.padding_around_mutation)\r\n    148         return mhc_model.predict(fasta_dict)\r\n\r\n/Users/tavi/drive/work/repos/cancer/topiary/topiary/mutant_epitope_predictor.pyc in create_fasta_dict(effects, padding_around_mutation)\r\n     20         # TODO: will mhctools take an object key?\r\n     21         key = effect.variant\r\n---> 22         seq = effect.mutant_protein_sequence\r\n     23         # some effects will lack a mutant protein sequence since\r\n     24         # they are either silent or unpredictable\r\n\r\n/Users/tavi/.virtualenvs/nejm/lib/python2.7/site-packages/memoized_property.pyc in fget_memoized(self)\r\n     38     def fget_memoized(self):\r\n     39         if not hasattr(self, attr_name):\r\n---> 40             setattr(self, attr_name, fget(self))\r\n     41         return getattr(self, attr_name)\r\n     42 \r\n\r\n/Users/tavi/drive/work/repos/cancer/varcode/varcode/effects.py in mutant_protein_sequence(self)\r\n    546     def mutant_protein_sequence(self):\r\n    547         prefix = self.original_protein_sequence[:self.aa_mutation_start_offset]\r\n--> 548         return prefix + self.aa_alt\r\n    549 \r\n    550 \r\n\r\nAttributeError: 'FrameShiftTruncation' object has no attribute 'aa_alt'\r\n```"}}