{"action":"created","issue":{"url":"https://api.github.com/repos/hammerlab/pyensembl/issues/68","labels_url":"https://api.github.com/repos/hammerlab/pyensembl/issues/68/labels{/name}","comments_url":"https://api.github.com/repos/hammerlab/pyensembl/issues/68/comments","events_url":"https://api.github.com/repos/hammerlab/pyensembl/issues/68/events","html_url":"https://github.com/hammerlab/pyensembl/pull/68","id":63299394,"number":68,"title":"DB for transcripts","user":{"login":"iskandr","id":48441,"avatar_url":"https://avatars.githubusercontent.com/u/48441?v=3","gravatar_id":"","url":"https://api.github.com/users/iskandr","html_url":"https://github.com/iskandr","followers_url":"https://api.github.com/users/iskandr/followers","following_url":"https://api.github.com/users/iskandr/following{/other_user}","gists_url":"https://api.github.com/users/iskandr/gists{/gist_id}","starred_url":"https://api.github.com/users/iskandr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/iskandr/subscriptions","organizations_url":"https://api.github.com/users/iskandr/orgs","repos_url":"https://api.github.com/users/iskandr/repos","events_url":"https://api.github.com/users/iskandr/events{/privacy}","received_events_url":"https://api.github.com/users/iskandr/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"tavinathanson","id":322932,"avatar_url":"https://avatars.githubusercontent.com/u/322932?v=3","gravatar_id":"","url":"https://api.github.com/users/tavinathanson","html_url":"https://github.com/tavinathanson","followers_url":"https://api.github.com/users/tavinathanson/followers","following_url":"https://api.github.com/users/tavinathanson/following{/other_user}","gists_url":"https://api.github.com/users/tavinathanson/gists{/gist_id}","starred_url":"https://api.github.com/users/tavinathanson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tavinathanson/subscriptions","organizations_url":"https://api.github.com/users/tavinathanson/orgs","repos_url":"https://api.github.com/users/tavinathanson/repos","events_url":"https://api.github.com/users/tavinathanson/events{/privacy}","received_events_url":"https://api.github.com/users/tavinathanson/received_events","type":"User","site_admin":false},"milestone":null,"comments":1,"created_at":"2015-03-20T20:14:59Z","updated_at":"2015-03-23T23:54:46Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/hammerlab/pyensembl/pulls/68","html_url":"https://github.com/hammerlab/pyensembl/pull/68","diff_url":"https://github.com/hammerlab/pyensembl/pull/68.diff","patch_url":"https://github.com/hammerlab/pyensembl/pull/68.patch"},"body":"Instead of using `pyfaidx` to wrap a FASTA index file for reference transcripts, instead using `biopython` to create a `sqlite3` database of transcripts. This is preferable since we don't have to convert between `Bio.Seq` objects (used in Varcode), Python strings, and `pyfaidx` sequences (which have a different API than BioPython). This should, theoretically, eventually be faster (though the performance is currently dominated by other code).\r\n\r\nAlso, I pulled out the benchmarking code used by `test_timings.py` into a small library called `tinytimer` (which I can reuse in Varcode). \r\n\r\n<!-- Reviewable:start -->\r\n[<img src=\"https://reviewable.io/review_button.png\" height=40 alt=\"Review on Reviewable\"/>](https://reviewable.io/reviews/hammerlab/pyensembl/68)\r\n<!-- Reviewable:end -->\r\n"},"comment":{"url":"https://api.github.com/repos/hammerlab/pyensembl/issues/comments/85251218","html_url":"https://github.com/hammerlab/pyensembl/pull/68#issuecomment-85251218","issue_url":"https://api.github.com/repos/hammerlab/pyensembl/issues/68","id":85251218,"user":{"login":"tavinathanson","id":322932,"avatar_url":"https://avatars.githubusercontent.com/u/322932?v=3","gravatar_id":"","url":"https://api.github.com/users/tavinathanson","html_url":"https://github.com/tavinathanson","followers_url":"https://api.github.com/users/tavinathanson/followers","following_url":"https://api.github.com/users/tavinathanson/following{/other_user}","gists_url":"https://api.github.com/users/tavinathanson/gists{/gist_id}","starred_url":"https://api.github.com/users/tavinathanson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tavinathanson/subscriptions","organizations_url":"https://api.github.com/users/tavinathanson/orgs","repos_url":"https://api.github.com/users/tavinathanson/repos","events_url":"https://api.github.com/users/tavinathanson/events{/privacy}","received_events_url":"https://api.github.com/users/tavinathanson/received_events","type":"User","site_admin":false},"created_at":"2015-03-23T23:54:46Z","updated_at":"2015-03-23T23:54:46Z","body":"Started commenting this up on Friday but didn't finish. I'll shoot be done tomorrow AM, sorry for the delay."}}