{"action":"created","issue":{"url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/121","labels_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/121/labels{/name}","comments_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/121/comments","events_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/121/events","html_url":"https://github.com/broadinstitute/viral-ngs/issues/121","id":67381378,"number":121,"title":"Make MAFFT alignment tool work with multiple samples containing multiple chromosomes","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":1,"created_at":"2015-04-09T15:04:17Z","updated_at":"2015-04-09T15:10:01Z","closed_at":null,"body":"In the case where MAFFT is being used to align sequences stored in sample-specific FASTA files, MAFFT should be able to do an alignment among the respective chromosomes from the FASTA files, such that the output is a series of chromosome-specific alignments in FASTA files.\r\n\r\nIn the case of two samples from organisms with two chromosomes, the input and output would be as follows:\r\n\r\n```\r\nInput: \r\n    sample1.fasta would contain chr1, chr2\r\n    sample2.fasta would also contain chr1, chr2\r\nOutput:\r\n    chr1.fasta would contain chr1_sample1, chr1_sample2, chr1_sample3\r\n    chr2.fasta would contain chr2_sample1, chr2_sample2, chr2_sample3\r\n```\r\n\r\nBefore MAFFT, an intermediate step would be needed to transpose the chromosomes from their respective FASTA files to chromosome-specific FASTA files prior to alignment. This can be done via ```itertools.izip```(Python2)/```zip```(Python3) and ```Bio.SeqIO.parse()```, which returns an iterable."},"comment":{"url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/comments/91258905","html_url":"https://github.com/broadinstitute/viral-ngs/issues/121#issuecomment-91258905","issue_url":"https://api.github.com/repos/broadinstitute/viral-ngs/issues/121","id":91258905,"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},"created_at":"2015-04-09T15:10:01Z","updated_at":"2015-04-09T15:10:01Z","body":"Added in commit represented in pull request #122 "}}