{"action":"created","issue":{"url":"https://api.github.com/repos/grunwaldlab/Microbe-ID/issues/1","labels_url":"https://api.github.com/repos/grunwaldlab/Microbe-ID/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/grunwaldlab/Microbe-ID/issues/1/comments","events_url":"https://api.github.com/repos/grunwaldlab/Microbe-ID/issues/1/events","html_url":"https://github.com/grunwaldlab/Microbe-ID/pull/1","id":80668941,"number":1,"title":"MLST: swapping muscle for mafft add","user":{"login":"alexweisberg","id":12143265,"avatar_url":"https://avatars.githubusercontent.com/u/12143265?v=3","gravatar_id":"","url":"https://api.github.com/users/alexweisberg","html_url":"https://github.com/alexweisberg","followers_url":"https://api.github.com/users/alexweisberg/followers","following_url":"https://api.github.com/users/alexweisberg/following{/other_user}","gists_url":"https://api.github.com/users/alexweisberg/gists{/gist_id}","starred_url":"https://api.github.com/users/alexweisberg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/alexweisberg/subscriptions","organizations_url":"https://api.github.com/users/alexweisberg/orgs","repos_url":"https://api.github.com/users/alexweisberg/repos","events_url":"https://api.github.com/users/alexweisberg/events{/privacy}","received_events_url":"https://api.github.com/users/alexweisberg/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"Tabima","id":897426,"avatar_url":"https://avatars.githubusercontent.com/u/897426?v=3","gravatar_id":"","url":"https://api.github.com/users/Tabima","html_url":"https://github.com/Tabima","followers_url":"https://api.github.com/users/Tabima/followers","following_url":"https://api.github.com/users/Tabima/following{/other_user}","gists_url":"https://api.github.com/users/Tabima/gists{/gist_id}","starred_url":"https://api.github.com/users/Tabima/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Tabima/subscriptions","organizations_url":"https://api.github.com/users/Tabima/orgs","repos_url":"https://api.github.com/users/Tabima/repos","events_url":"https://api.github.com/users/Tabima/events{/privacy}","received_events_url":"https://api.github.com/users/Tabima/received_events","type":"User","site_admin":false},"milestone":null,"comments":6,"created_at":"2015-05-25T21:11:45Z","updated_at":"2015-06-05T05:01:13Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/grunwaldlab/Microbe-ID/pulls/1","html_url":"https://github.com/grunwaldlab/Microbe-ID/pull/1","diff_url":"https://github.com/grunwaldlab/Microbe-ID/pull/1.diff","patch_url":"https://github.com/grunwaldlab/Microbe-ID/pull/1.patch"},"body":"I switched out using muscle for the MLST analysis to using MAFFT add to add to existing alignments which get concatenated together. In this new method, the user can add any number of individual gene sequences, up to the size of the dataset, rather than pre-concatenated genes in a specific order.\r\nI also set it up so that each dataset of gene alignments has its own folder, that way datasets with overlapping genes but different taxa don't conflict. I did not add datasets for the Housekeeping genes and  Virulence genes as I don't have the original gene alignments. We will also have to change the help message on the MLST page so that it matches this new method."},"comment":{"url":"https://api.github.com/repos/grunwaldlab/Microbe-ID/issues/comments/109162277","html_url":"https://github.com/grunwaldlab/Microbe-ID/pull/1#issuecomment-109162277","issue_url":"https://api.github.com/repos/grunwaldlab/Microbe-ID/issues/1","id":109162277,"user":{"login":"Tabima","id":897426,"avatar_url":"https://avatars.githubusercontent.com/u/897426?v=3","gravatar_id":"","url":"https://api.github.com/users/Tabima","html_url":"https://github.com/Tabima","followers_url":"https://api.github.com/users/Tabima/followers","following_url":"https://api.github.com/users/Tabima/following{/other_user}","gists_url":"https://api.github.com/users/Tabima/gists{/gist_id}","starred_url":"https://api.github.com/users/Tabima/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Tabima/subscriptions","organizations_url":"https://api.github.com/users/Tabima/orgs","repos_url":"https://api.github.com/users/Tabima/repos","events_url":"https://api.github.com/users/Tabima/events{/privacy}","received_events_url":"https://api.github.com/users/Tabima/received_events","type":"User","site_admin":false},"created_at":"2015-06-05T05:01:13Z","updated_at":"2015-06-05T05:01:13Z","body":"Cool, I think that's the best way to do it.\r\n\r\nTaking all of that on account:\r\n\r\n* We don't need to add the datasets for the Housekeeping genes and Virulence genes as the help page explains well with one is which, and your method creates a concatenated alignment for any mix-and-match set of genes the user wants to use.\r\n\r\n* I'll fix the help message on the MLST page so that it matches the new method ASAP.\r\n\r\nIf you are fine with this, I'll just merge it!\r\n\r\nThanks again for all your help."}}