{"action":"created","issue":{"url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/65","repository_url":"https://api.github.com/repos/BioJulia/Bio.jl","labels_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/65/labels{/name}","comments_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/65/comments","events_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/65/events","html_url":"https://github.com/BioJulia/Bio.jl/pull/65","id":94309991,"number":65,"title":"Blastwrapper","user":{"login":"kescobo","id":3502975,"avatar_url":"https://avatars.githubusercontent.com/u/3502975?v=3","gravatar_id":"","url":"https://api.github.com/users/kescobo","html_url":"https://github.com/kescobo","followers_url":"https://api.github.com/users/kescobo/followers","following_url":"https://api.github.com/users/kescobo/following{/other_user}","gists_url":"https://api.github.com/users/kescobo/gists{/gist_id}","starred_url":"https://api.github.com/users/kescobo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kescobo/subscriptions","organizations_url":"https://api.github.com/users/kescobo/orgs","repos_url":"https://api.github.com/users/kescobo/repos","events_url":"https://api.github.com/users/kescobo/events{/privacy}","received_events_url":"https://api.github.com/users/kescobo/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/BioJulia/Bio.jl/labels/stage:%20RTR","name":"stage: RTR","color":"bfe5bf"},{"url":"https://api.github.com/repos/BioJulia/Bio.jl/labels/stage:%20WIP","name":"stage: WIP","color":"d4c5f9"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":16,"created_at":"2015-07-10T13:42:48Z","updated_at":"2016-03-31T08:26:26Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/BioJulia/Bio.jl/pulls/65","html_url":"https://github.com/BioJulia/Bio.jl/pull/65","diff_url":"https://github.com/BioJulia/Bio.jl/pull/65.diff","patch_url":"https://github.com/BioJulia/Bio.jl/pull/65.patch"},"body":"## Blast Tools module for Bio.jl - Spec and Roadmap\r\n\r\nBio.jl needs a way to run BLAST and other command line tools commonly used in biology applications, taking inputs and capturing outputs in Bio.jl formats. \r\n\r\n### Minimum requirements for BLAST module\r\nWith Blast+ installed on users' system:\r\n\r\n**Input**\r\n\r\n- [x] accept seq object~~, string~~ or file as query and subject\r\n    - [x] accept single sequence objects\r\n    - [x] accept multi-sequence objects\r\n- [x] blastn, blastp, blastall\r\n    - [ ] others?\r\n- [x] accept flags for search modification\r\n- [x] take/parse blast xml output\r\n\r\n**Output**\r\n\r\n- [x] return alignment object or strings for alignment\r\n- [x] return stats object w/other information\r\n- [ ] allow return of other blast outputs (tsv, csv etc)\r\n\r\n### Other Useful Features\r\n\r\n- [ ] bundle blast package from within Bio.jl (is this possible?)\r\n- [ ] pull queries/subjects from NCBI\r\n    - [ ] incorporate into Bio.jl formats\r\n- [ ] run Blast through NCBI servers instead of locally\r\n- [ ] ... others?"},"comment":{"url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/comments/203817275","html_url":"https://github.com/BioJulia/Bio.jl/pull/65#issuecomment-203817275","issue_url":"https://api.github.com/repos/BioJulia/Bio.jl/issues/65","id":203817275,"user":{"login":"Ward9250","id":3399309,"avatar_url":"https://avatars.githubusercontent.com/u/3399309?v=3","gravatar_id":"","url":"https://api.github.com/users/Ward9250","html_url":"https://github.com/Ward9250","followers_url":"https://api.github.com/users/Ward9250/followers","following_url":"https://api.github.com/users/Ward9250/following{/other_user}","gists_url":"https://api.github.com/users/Ward9250/gists{/gist_id}","starred_url":"https://api.github.com/users/Ward9250/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Ward9250/subscriptions","organizations_url":"https://api.github.com/users/Ward9250/orgs","repos_url":"https://api.github.com/users/Ward9250/repos","events_url":"https://api.github.com/users/Ward9250/events{/privacy}","received_events_url":"https://api.github.com/users/Ward9250/received_events","type":"User","site_admin":false},"created_at":"2016-03-31T08:26:26Z","updated_at":"2016-03-31T08:26:26Z","body":"Actually yes very good point @ScottPJones, @kescobo  that might be easier than trying to rebase, whilst you are still getting used to Git."}}