{"action":"created","issue":{"url":"https://api.github.com/repos/griffithlab/pVACtools/issues/135","repository_url":"https://api.github.com/repos/griffithlab/pVACtools","labels_url":"https://api.github.com/repos/griffithlab/pVACtools/issues/135/labels{/name}","comments_url":"https://api.github.com/repos/griffithlab/pVACtools/issues/135/comments","events_url":"https://api.github.com/repos/griffithlab/pVACtools/issues/135/events","html_url":"https://github.com/griffithlab/pVACtools/pull/135","id":332899924,"node_id":"MDExOlB1bGxSZXF1ZXN0MTk1MjcxNzU4","number":135,"title":"Add MHCnuggets prediction algorithm","user":{"login":"susannasiebert","id":6617192,"node_id":"MDQ6VXNlcjY2MTcxOTI=","avatar_url":"https://avatars1.githubusercontent.com/u/6617192?v=4","gravatar_id":"","url":"https://api.github.com/users/susannasiebert","html_url":"https://github.com/susannasiebert","followers_url":"https://api.github.com/users/susannasiebert/followers","following_url":"https://api.github.com/users/susannasiebert/following{/other_user}","gists_url":"https://api.github.com/users/susannasiebert/gists{/gist_id}","starred_url":"https://api.github.com/users/susannasiebert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/susannasiebert/subscriptions","organizations_url":"https://api.github.com/users/susannasiebert/orgs","repos_url":"https://api.github.com/users/susannasiebert/repos","events_url":"https://api.github.com/users/susannasiebert/events{/privacy}","received_events_url":"https://api.github.com/users/susannasiebert/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-06-15T20:10:20Z","updated_at":"2018-07-03T18:40:34Z","closed_at":null,"author_association":"COLLABORATOR","pull_request":{"url":"https://api.github.com/repos/griffithlab/pVACtools/pulls/135","html_url":"https://github.com/griffithlab/pVACtools/pull/135","diff_url":"https://github.com/griffithlab/pVACtools/pull/135.diff","patch_url":"https://github.com/griffithlab/pVACtools/pull/135.patch"},"body":"The current mhcnuggets package is not python3 compatible but a PR with the necessary changes has been merged into master on the MHCnuggets-2.0 repository. I added a line in the .travis.yml to install mhcnuggets from master, which can be taken out once a new package with the changes has been released.\r\n\r\nThe allele format required my MHCnuggets is quite different from IEDB so if someone wants to run allele HLA-A*02:01 on NetMHC and MHCnuggets they would need to specify this allele twice, once in the format `HLA-A*02:01` (for NetMHC) and once as HLA-A0201 (MHCnugget). We should consider defining a standardized set of alleles for pVACtools and handling the conversion internally.\r\n\r\nCloses #67 "},"comment":{"url":"https://api.github.com/repos/griffithlab/pVACtools/issues/comments/402255068","html_url":"https://github.com/griffithlab/pVACtools/pull/135#issuecomment-402255068","issue_url":"https://api.github.com/repos/griffithlab/pVACtools/issues/135","id":402255068,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMjI1NTA2OA==","user":{"login":"huang-ying","id":1408456,"node_id":"MDQ6VXNlcjE0MDg0NTY=","avatar_url":"https://avatars0.githubusercontent.com/u/1408456?v=4","gravatar_id":"","url":"https://api.github.com/users/huang-ying","html_url":"https://github.com/huang-ying","followers_url":"https://api.github.com/users/huang-ying/followers","following_url":"https://api.github.com/users/huang-ying/following{/other_user}","gists_url":"https://api.github.com/users/huang-ying/gists{/gist_id}","starred_url":"https://api.github.com/users/huang-ying/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/huang-ying/subscriptions","organizations_url":"https://api.github.com/users/huang-ying/orgs","repos_url":"https://api.github.com/users/huang-ying/repos","events_url":"https://api.github.com/users/huang-ying/events{/privacy}","received_events_url":"https://api.github.com/users/huang-ying/received_events","type":"User","site_admin":false},"created_at":"2018-07-03T18:40:34Z","updated_at":"2018-07-03T18:40:34Z","author_association":"NONE","body":"I ran following command\r\n```bash\r\npvacfuse run pvacfuse_example_data/fusions.bedpe.annot Test HLA-A0201 MHCnuggetsI pvacfuse_example_data/mhcnuggets -e 9\r\n```\r\nand got following error message\r\n```\r\nBuilding model\r\nInvalid human allele\r\nClosest allele found None\r\n```\r\nIt seems mhcnuggets requires HLA-A02:01, change it in `pVACtools/tools/pvacseq/iedb_alleles/class_i/MHCnuggets.txt` works"}}
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