{"action":"created","issue":{"url":"https://api.github.com/repos/MadsAlbertsen/mmgenome/issues/21","labels_url":"https://api.github.com/repos/MadsAlbertsen/mmgenome/issues/21/labels{/name}","comments_url":"https://api.github.com/repos/MadsAlbertsen/mmgenome/issues/21/comments","events_url":"https://api.github.com/repos/MadsAlbertsen/mmgenome/issues/21/events","html_url":"https://github.com/MadsAlbertsen/mmgenome/issues/21","id":81135629,"number":21,"title":"Importing FASTA data using Biostrings into mmgenome ","user":{"login":"jrherr","id":2516381,"avatar_url":"https://avatars.githubusercontent.com/u/2516381?v=3","gravatar_id":"","url":"https://api.github.com/users/jrherr","html_url":"https://github.com/jrherr","followers_url":"https://api.github.com/users/jrherr/followers","following_url":"https://api.github.com/users/jrherr/following{/other_user}","gists_url":"https://api.github.com/users/jrherr/gists{/gist_id}","starred_url":"https://api.github.com/users/jrherr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jrherr/subscriptions","organizations_url":"https://api.github.com/users/jrherr/orgs","repos_url":"https://api.github.com/users/jrherr/repos","events_url":"https://api.github.com/users/jrherr/events{/privacy}","received_events_url":"https://api.github.com/users/jrherr/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-05-26T21:03:39Z","updated_at":"2015-05-27T04:51:22Z","closed_at":"2015-05-27T04:51:22Z","body":"Just wanting to give the package a try and I'm having a hard time getting past loading the example data.  I'm getting this error in Biostrings -- might not have to do with the `mmgenome` package, but I can't find any solutions via google.\r\n```\r\n> assembly <- readDNAStringSet(\"data/assembly.fa\", format = \"fasta\")\r\nError in .Call2(\"new_input_ExternalFilePtr\", fp, PACKAGE = \"Biostrings\") : \r\n  cannot open file 'data/assembly.fa'\r\n```\r\n\r\nHere's my R information:\r\n```\r\n> sessionInfo()\r\nR version 3.2.0 (2015-04-16)\r\nPlatform: x86_64-apple-darwin13.4.0 (64-bit)\r\nRunning under: OS X 10.10.4 (Yosemite)\r\n\r\nlocale:\r\n[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8\r\n\r\nattached base packages:\r\n [1] stats4    parallel  grid      stats     graphics  grDevices utils     datasets \r\n [9] methods   base     \r\n\r\nother attached packages:\r\n [1] mmgenome_0.6.1       dplyr_0.4.1          reshape2_1.4.1       igraph_0.7.1        \r\n [5] Biostrings_2.36.1    XVector_0.8.0        IRanges_2.2.1        S4Vectors_0.6.0     \r\n [9] BiocGenerics_0.14.0  vegan_2.3-0          lattice_0.20-31      permute_0.8-4       \r\n[13] knitr_1.10.5         ggplot2_1.0.1        gridExtra_0.9.1      sp_1.1-0            \r\n[17] BiocInstaller_1.18.2\r\n```\r\nHow best do you recommend importing FASTA files?\r\n\r\nThanks so much for your time and developing a needed tool."},"comment":{"url":"https://api.github.com/repos/MadsAlbertsen/mmgenome/issues/comments/105755037","html_url":"https://github.com/MadsAlbertsen/mmgenome/issues/21#issuecomment-105755037","issue_url":"https://api.github.com/repos/MadsAlbertsen/mmgenome/issues/21","id":105755037,"user":{"login":"MadsAlbertsen","id":988600,"avatar_url":"https://avatars.githubusercontent.com/u/988600?v=3","gravatar_id":"","url":"https://api.github.com/users/MadsAlbertsen","html_url":"https://github.com/MadsAlbertsen","followers_url":"https://api.github.com/users/MadsAlbertsen/followers","following_url":"https://api.github.com/users/MadsAlbertsen/following{/other_user}","gists_url":"https://api.github.com/users/MadsAlbertsen/gists{/gist_id}","starred_url":"https://api.github.com/users/MadsAlbertsen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MadsAlbertsen/subscriptions","organizations_url":"https://api.github.com/users/MadsAlbertsen/orgs","repos_url":"https://api.github.com/users/MadsAlbertsen/repos","events_url":"https://api.github.com/users/MadsAlbertsen/events{/privacy}","received_events_url":"https://api.github.com/users/MadsAlbertsen/received_events","type":"User","site_admin":false},"created_at":"2015-05-27T04:51:22Z","updated_at":"2015-05-27T04:51:22Z","body":"It seems like it can't find the `assembly.fa` file.\r\n\r\nHave you downloaded the [example data](http://figshare.com/articles/Rocco_an_example_metagenome_dataset_for_the_mmgenome_R_package/1149981) and put it in the folder `data` within your current workspace?\r\n\r\nIf you wan't a fast try of the `mmgenome` package you can also just load the example data directly using `data(Rocco)`.."}}