{"action":"created","issue":{"url":"https://api.github.com/repos/nextstrain/augur/issues/166","repository_url":"https://api.github.com/repos/nextstrain/augur","labels_url":"https://api.github.com/repos/nextstrain/augur/issues/166/labels{/name}","comments_url":"https://api.github.com/repos/nextstrain/augur/issues/166/comments","events_url":"https://api.github.com/repos/nextstrain/augur/issues/166/events","html_url":"https://github.com/nextstrain/augur/pull/166","id":340187071,"node_id":"MDExOlB1bGxSZXF1ZXN0MjAwNjU3NjM3","number":166,"title":"Find & Annotate DRM Sites","user":{"login":"emmahodcroft","id":14290674,"node_id":"MDQ6VXNlcjE0MjkwNjc0","avatar_url":"https://avatars1.githubusercontent.com/u/14290674?v=4","gravatar_id":"","url":"https://api.github.com/users/emmahodcroft","html_url":"https://github.com/emmahodcroft","followers_url":"https://api.github.com/users/emmahodcroft/followers","following_url":"https://api.github.com/users/emmahodcroft/following{/other_user}","gists_url":"https://api.github.com/users/emmahodcroft/gists{/gist_id}","starred_url":"https://api.github.com/users/emmahodcroft/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/emmahodcroft/subscriptions","organizations_url":"https://api.github.com/users/emmahodcroft/orgs","repos_url":"https://api.github.com/users/emmahodcroft/repos","events_url":"https://api.github.com/users/emmahodcroft/events{/privacy}","received_events_url":"https://api.github.com/users/emmahodcroft/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":9,"created_at":"2018-07-11T10:40:27Z","updated_at":"2018-07-27T15:15:25Z","closed_at":null,"author_association":"CONTRIBUTOR","pull_request":{"url":"https://api.github.com/repos/nextstrain/augur/pulls/166","html_url":"https://github.com/nextstrain/augur/pull/166","diff_url":"https://github.com/nextstrain/augur/pull/166.diff","patch_url":"https://github.com/nextstrain/augur/pull/166.patch"},"body":"This adds `find_drm.py` which finds specified DRM sites (including on ancestral seqs if provided), annotates them onto nodes, and generates colours for them.\r\nAt the moment this is pretty TB specific (expecting a non-standard file format and only TB drug names) but can be modified to apply to HIV (or anything else). However, it's of big interest in TB datasets, so important to have.\r\n\r\nA couple of notes:\r\n- Colours are generated by the script. At the moment this works by passing in your `color.tsv` file (with country & other trait colours) and the colours generated for DRM are added to this file, with a new version being written out. This is then what should be passed to `export`\r\n- This currently only works with VCF input but should be modified to work with Fasta\r\n- At the moment this requires annoying modification of `config.py` to include all the fields generated by the script in order to colour by them. I didn't bother changing this; if the plan is to bundle generation of `config.py` into export it can be tackled once there. However if it would be better to deal with now, I can change it to modify and write out a new version of `config.py` as it currently does with `color.tsv`. \r\n\r\nUnfortunately the Lee et al. data (the TB dataset currently on github) has no DRMs and so running this does nothing. I'll try and trim my Walker et al. dataset down to published sequences which I can then provide for testing this bit."},"comment":{"url":"https://api.github.com/repos/nextstrain/augur/issues/comments/408449575","html_url":"https://github.com/nextstrain/augur/pull/166#issuecomment-408449575","issue_url":"https://api.github.com/repos/nextstrain/augur/issues/166","id":408449575,"node_id":"MDEyOklzc3VlQ29tbWVudDQwODQ0OTU3NQ==","user":{"login":"rneher","id":8379168,"node_id":"MDQ6VXNlcjgzNzkxNjg=","avatar_url":"https://avatars3.githubusercontent.com/u/8379168?v=4","gravatar_id":"","url":"https://api.github.com/users/rneher","html_url":"https://github.com/rneher","followers_url":"https://api.github.com/users/rneher/followers","following_url":"https://api.github.com/users/rneher/following{/other_user}","gists_url":"https://api.github.com/users/rneher/gists{/gist_id}","starred_url":"https://api.github.com/users/rneher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rneher/subscriptions","organizations_url":"https://api.github.com/users/rneher/orgs","repos_url":"https://api.github.com/users/rneher/repos","events_url":"https://api.github.com/users/rneher/events{/privacy}","received_events_url":"https://api.github.com/users/rneher/received_events","type":"User","site_admin":false},"created_at":"2018-07-27T15:15:25Z","updated_at":"2018-07-27T15:15:25Z","author_association":"MEMBER","body":"I feel `mapping` is a pretty bad name for this as it has a very well defined meaning in bioinformatics that is very different from what is happening here. my proposal is `sequence-traits` in analogy to `traits`. these really are traits derived from sequence based on a list of mutations that correspond to particular features. happy to consider other names though.\r\n\r\nother than that, I stream-lined this and made generic. "}}
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