{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1608","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1608/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1608/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1608/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1608","id":185407943,"number":1608,"title":"gb2genome.py produces a fasta file with all N's","user":{"login":"lfaller","id":7854149,"avatar_url":"https://avatars.githubusercontent.com/u/7854149?v=3","gravatar_id":"","url":"https://api.github.com/users/lfaller","html_url":"https://github.com/lfaller","followers_url":"https://api.github.com/users/lfaller/followers","following_url":"https://api.github.com/users/lfaller/following{/other_user}","gists_url":"https://api.github.com/users/lfaller/gists{/gist_id}","starred_url":"https://api.github.com/users/lfaller/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lfaller/subscriptions","organizations_url":"https://api.github.com/users/lfaller/orgs","repos_url":"https://api.github.com/users/lfaller/repos","events_url":"https://api.github.com/users/lfaller/events{/privacy}","received_events_url":"https://api.github.com/users/lfaller/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-10-26T14:21:41Z","updated_at":"2016-10-26T15:50:26Z","closed_at":null,"body":"Hi all,\r\n\r\nI would like to use `gb2genome.py` to generate a set of new reference files for E. coli MG1655.\r\n\r\nI downloaded the genbank file from here: https://www.ncbi.nlm.nih.gov/nuccore/U00096.3?report=gbwithparts&log$=seqview\r\n\r\nI selected \"full\" Genbank format and \"show GIs\".\r\n\r\nUnfortunately, when I run `gb2genome.py`, I get a fasta file full of N's. The gtf file looks fine at first glance.\r\n\r\nI called the command as follows:\r\n\r\n```\r\n~/bin/gb2genome.py --gbk ecoli_mg1655.gb --prefix ecoli_mg1655\r\n\r\nU00096.3        Skipped 417 entries having types: rep_origin, source, misc_feature, mobile_element, repeat_region.\r\n#Time elapsed: 0:00:01.247412\r\n```\r\n\r\nThanks for any advice you might have!\r\n~Lina"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/256391691","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1608#issuecomment-256391691","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1608","id":256391691,"user":{"login":"lpantano","id":1621788,"avatar_url":"https://avatars.githubusercontent.com/u/1621788?v=3","gravatar_id":"","url":"https://api.github.com/users/lpantano","html_url":"https://github.com/lpantano","followers_url":"https://api.github.com/users/lpantano/followers","following_url":"https://api.github.com/users/lpantano/following{/other_user}","gists_url":"https://api.github.com/users/lpantano/gists{/gist_id}","starred_url":"https://api.github.com/users/lpantano/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lpantano/subscriptions","organizations_url":"https://api.github.com/users/lpantano/orgs","repos_url":"https://api.github.com/users/lpantano/repos","events_url":"https://api.github.com/users/lpantano/events{/privacy}","received_events_url":"https://api.github.com/users/lpantano/received_events","type":"User","site_admin":false},"created_at":"2016-10-26T15:50:26Z","updated_at":"2016-10-26T15:50:26Z","body":"Hi,\n\nnormally the genbank that they showed is the small version. There should be an option to get the full genbank file, that would make easier to have a consistent annotation, but I guess that downloading the FASTA should make the trick.\n\nI think you should go to the link Send, and then choose File, And then full genbank. That is how I normally do.\n\nlet us know if any of the option worked.\n\nthanks\n\n> On Oct 26, 2016, at 11:21 AM, lfaller <notifications@github.com> wrote:\n> \n> Ah, makes sense! I don't know how to get the Genbank file with the fasta sequence in it, but there is a link to \"FASTA\" on the top of the page that shows the whole chromosome, it seems.\n> \n> So I will try to run the script to generate the GTF file and then download the separate fasta file.\n> \n> Thanks!\n> \n> —\n> You are receiving this because you are subscribed to this thread.\n> Reply to this email directly, view it on GitHub <https://github.com/chapmanb/bcbio-nextgen/issues/1608#issuecomment-256380648>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABi_HDJVYec4Glm2jqDEVQ3u0DOemmLNks5q32_rgaJpZM4KhOwR>.\n> \n\n"}}
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