{"action":"created","comment":{"url":"https://api.github.com/repos/mutalyzer/mutalyzer/pulls/comments/67193045","id":67193045,"diff_hunk":"@@ -83,9 +83,19 @@ class Grammar():\n     # BNF: GeneName -> ([a-Z] | [0-9] | `-')+\n     GeneName = Word(unicode(alphanums) + '-', min=1)\n \n-    # BNF: GeneSymbol -> `(' Name (TransVar | ProtIso)? `)'\n-    GeneSymbol = Suppress('(') + Group(GeneName('GeneSymbol') + \\\n-                 Optional(TransVar ^ ProtIso))('Gene') + Suppress(')')\n+    # BNF: GeneProductID -> GeneName (TransVar | ProtIso)\n+    GeneProductID = Group(GeneName('GeneSymbol') + \\\n+                          Optional(TransVar ^ ProtIso))('Gene')\n+\n+    # BNF: AccNoStem -> ([a-Z] Number `_')+\n+    AccNoStem = NotAny('LRG_') + Combine(Word(unicode(alphas) + '_') + Number)\n+\n+    # BNF: AccNoFull -> AccNoStem `.' Number\n+    AccNoFull = AccNoStem + Suppress('.') + Number\n+\n+    # BNF: GeneSymbol -> `(' (GeneProductID | AccNoFull) `)'\n+    GeneSymbol = Suppress('(') + (GeneProductID ^ AccNoFull('AccNoTransVar')) \\\n+                 + Suppress(')')","path":"mutalyzer/grammar.py","position":19,"original_position":19,"commit_id":"c3c0bd7dd8379c96427486f6d5f02f336ed817d6","original_commit_id":"c3c0bd7dd8379c96427486f6d5f02f336ed817d6","user":{"login":"mkroon1","id":17007949,"avatar_url":"https://avatars.githubusercontent.com/u/17007949?v=3","gravatar_id":"","url":"https://api.github.com/users/mkroon1","html_url":"https://github.com/mkroon1","followers_url":"https://api.github.com/users/mkroon1/followers","following_url":"https://api.github.com/users/mkroon1/following{/other_user}","gists_url":"https://api.github.com/users/mkroon1/gists{/gist_id}","starred_url":"https://api.github.com/users/mkroon1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mkroon1/subscriptions","organizations_url":"https://api.github.com/users/mkroon1/orgs","repos_url":"https://api.github.com/users/mkroon1/repos","events_url":"https://api.github.com/users/mkroon1/events{/privacy}","received_events_url":"https://api.github.com/users/mkroon1/received_events","type":"User","site_admin":false},"body":"I'm not sure. Being agnostic here would make the code that handles the parsing output more complex or more inefficient I think. E.g. if the input is some unknown string, we'd have to treat it as a possible protein isoform, transcript variant and transcript accession number and then still fail if we can't find the string as any of these options.","created_at":"2016-06-15T16:09:09Z","updated_at":"2016-06-15T16:09:09Z","html_url":"https://github.com/mutalyzer/mutalyzer/pull/405#discussion_r67193045","pull_request_url":"https://api.github.com/repos/mutalyzer/mutalyzer/pulls/405","_links":{"self":{"href":"https://api.github.com/repos/mutalyzer/mutalyzer/pulls/comments/67193045"},"html":{"href":"https://github.com/mutalyzer/mutalyzer/pull/405#discussion_r67193045"},"pull_request":{"href":"https://api.github.com/repos/mutalyzer/mutalyzer/pulls/405"}}},"pull_request":{"url":"https://api.github.com/repos/mutalyzer/mutalyzer/pulls/405","id":73890528,"html_url":"https://github.com/mutalyzer/mutalyzer/pull/405","diff_url":"https://github.com/mutalyzer/mutalyzer/pull/405.diff","patch_url":"https://github.com/mutalyzer/mutalyzer/pull/405.patch","issue_url":"https://api.github.com/repos/mutalyzer/mutalyzer/issues/405","number":405,"state":"open","locked":false,"title":"Accept transcript accession number as transcript variant 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