{"action":"created","issue":{"url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/21","labels_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/21/labels{/name}","comments_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/21/comments","events_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/21/events","html_url":"https://github.com/trinityrnaseq/trinityrnaseq/issues/21","id":66002350,"number":21,"title":"New FASTA header format breaks parsers","user":{"login":"Blahah","id":836040,"avatar_url":"https://avatars.githubusercontent.com/u/836040?v=3","gravatar_id":"","url":"https://api.github.com/users/Blahah","html_url":"https://github.com/Blahah","followers_url":"https://api.github.com/users/Blahah/followers","following_url":"https://api.github.com/users/Blahah/following{/other_user}","gists_url":"https://api.github.com/users/Blahah/gists{/gist_id}","starred_url":"https://api.github.com/users/Blahah/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Blahah/subscriptions","organizations_url":"https://api.github.com/users/Blahah/orgs","repos_url":"https://api.github.com/users/Blahah/repos","events_url":"https://api.github.com/users/Blahah/events{/privacy}","received_events_url":"https://api.github.com/users/Blahah/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-04-02T20:12:04Z","updated_at":"2015-04-03T10:48:12Z","closed_at":null,"body":"Our users (of transrate) have reported that Trinity has moved to using a hew FASTA header format that looks like:\r\n`>TR18|c0_g1_i1 len=387 path=[365:0-386] [-1, 365, -2]`. (see issue https://github.com/Blahah/transrate/issues/127, some of which I have copied below).\r\n\r\nIn the example above, it's clear that `TR18|c0_g1_i1` is supposed to be the entry ID. However, many bio-library parsers will not interpret it that way. In 2003 or so, NCBI claimed that using the `>db_name|sequence_identifier` format was standard, but that system is very non-standard in practise, outside of the NCBI. Almost every other system uses `>sequence_identifier|other description`.\r\n\r\ntransrate uses the BioRuby FASTA parser, which has a pretty sensible design - it interprets everything before the first `|` or space as the sequence identifier, except in special cases for the NCBI databases. This accurately captures the FASTA header information for hundreds of pieces of bioinformatics software, but currently not for Trinity.\r\n\r\nWith this new Trinity setup we are forced to decide between adding another special case to BioRuby for Trinity, or hacking around this change in any software that wants to read Trinity sequence IDs. However, the third option is for the change in Trinity to be reverted. I would argue for this third option on the basis that it requires the least changes throughout the community. Would you consider this?"},"comment":{"url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/comments/89251697","html_url":"https://github.com/trinityrnaseq/trinityrnaseq/issues/21#issuecomment-89251697","issue_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/21","id":89251697,"user":{"login":"Blahah","id":836040,"avatar_url":"https://avatars.githubusercontent.com/u/836040?v=3","gravatar_id":"","url":"https://api.github.com/users/Blahah","html_url":"https://github.com/Blahah","followers_url":"https://api.github.com/users/Blahah/followers","following_url":"https://api.github.com/users/Blahah/following{/other_user}","gists_url":"https://api.github.com/users/Blahah/gists{/gist_id}","starred_url":"https://api.github.com/users/Blahah/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Blahah/subscriptions","organizations_url":"https://api.github.com/users/Blahah/orgs","repos_url":"https://api.github.com/users/Blahah/repos","events_url":"https://api.github.com/users/Blahah/events{/privacy}","received_events_url":"https://api.github.com/users/Blahah/received_events","type":"User","site_admin":false},"created_at":"2015-04-03T10:48:12Z","updated_at":"2015-04-03T10:48:12Z","body":"Great! Moving to `TR_c_g_i` would solve the issue."}}