{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/122","labels_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/122/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/122/comments","events_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/122/events","html_url":"https://github.com/broadinstitute/viral-ngs/pull/122","id":67382341,"number":122,"title":"Added multichr_mafft","user":{"login":"tomkinsc","id":53064,"avatar_url":"https://avatars.githubusercontent.com/u/53064?v=3","gravatar_id":"","url":"https://api.github.com/users/tomkinsc","html_url":"https://github.com/tomkinsc","followers_url":"https://api.github.com/users/tomkinsc/followers","following_url":"https://api.github.com/users/tomkinsc/following{/other_user}","gists_url":"https://api.github.com/users/tomkinsc/gists{/gist_id}","starred_url":"https://api.github.com/users/tomkinsc/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tomkinsc/subscriptions","organizations_url":"https://api.github.com/users/tomkinsc/orgs","repos_url":"https://api.github.com/users/tomkinsc/repos","events_url":"https://api.github.com/users/tomkinsc/events{/privacy}","received_events_url":"https://api.github.com/users/tomkinsc/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-04-09T15:08:55Z","updated_at":"2015-04-09T15:36:01Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/broadinstitute/viral-ngs/pulls/122","html_url":"https://github.com/broadinstitute/viral-ngs/pull/122","diff_url":"https://github.com/broadinstitute/viral-ngs/pull/122.diff","patch_url":"https://github.com/broadinstitute/viral-ngs/pull/122.patch"},"body":"Added argparse function multichr_mafft to perform alignment on multiple\r\nchromosomes stored in sample-specific FASTA files. Added a helper\r\nfunction used as a pre-processing step to MAFFT that transposes\r\nchromosome info from separate sample-specific FASTA files into FASTA\r\nfiles each containing respective-records"},"comment":{"url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/comments/91266418","html_url":"https://github.com/broadinstitute/viral-ngs/pull/122#issuecomment-91266418","issue_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/122","id":91266418,"user":{"login":"dpark01","id":8513746,"avatar_url":"https://avatars.githubusercontent.com/u/8513746?v=3","gravatar_id":"","url":"https://api.github.com/users/dpark01","html_url":"https://github.com/dpark01","followers_url":"https://api.github.com/users/dpark01/followers","following_url":"https://api.github.com/users/dpark01/following{/other_user}","gists_url":"https://api.github.com/users/dpark01/gists{/gist_id}","starred_url":"https://api.github.com/users/dpark01/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dpark01/subscriptions","organizations_url":"https://api.github.com/users/dpark01/orgs","repos_url":"https://api.github.com/users/dpark01/repos","events_url":"https://api.github.com/users/dpark01/events{/privacy}","received_events_url":"https://api.github.com/users/dpark01/received_events","type":"User","site_admin":false},"created_at":"2015-04-09T15:36:01Z","updated_at":"2015-04-09T15:36:01Z","body":"The description leads me to believe that this function requires identical sequence IDs in each input file (e.g. \"chr1\", \"chr2\"), and then it performs a renaming of each sequence ID (in the FASTA header lines) in the output file (appending the filename or something to each), but that doesn't appear to be the case, looking at the code.\r\n\r\nI was thinking about this a bit last night and was realizing that there are some cases where we might want to do some renaming of sequence IDs (because the inputs might be identically named) and other scenarios where we wouldn't want to touch it at all (because everything was handled upstream just fine) and we wouldn't want to impose the renaming by default.. maybe just optionally, but we can deal with that later.\r\n\r\nBut I think what would be a good idea is to add a sanity check (this can be in the MAFFT Tool.execute itself, after it concatenates its input files) that errors out if the FASTA that serves as input to MAFFT has non-unique sequence IDs.  I don't even know if MAFFT would error anyway, but we certainly wouldn't know how to interpret its output even if it didn't error."}}