Importing FASTA data using Biostrings into mmgenome

[jrherr]

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.

> assembly <- readDNAStringSet("data/assembly.fa", format = "fasta")
Error in .Call2("new_input_ExternalFilePtr", fp, PACKAGE = "Biostrings") : 
  cannot open file 'data/assembly.fa'

Here's my R information:

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.4 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
 [1] stats4    parallel  grid      stats     graphics  grDevices utils     datasets 
 [9] methods   base     

other attached packages:
 [1] mmgenome_0.6.1       dplyr_0.4.1          reshape2_1.4.1       igraph_0.7.1        
 [5] Biostrings_2.36.1    XVector_0.8.0        IRanges_2.2.1        S4Vectors_0.6.0     
 [9] BiocGenerics_0.14.0  vegan_2.3-0          lattice_0.20-31      permute_0.8-4       
[13] knitr_1.10.5         ggplot2_1.0.1        gridExtra_0.9.1      sp_1.1-0            
[17] BiocInstaller_1.18.2

How best do you recommend importing FASTA files?

Thanks so much for your time and developing a needed tool.

[MadsAlbertsen]

It seems like it can't find the assembly.fa file.

Have you downloaded the example data and put it in the folder data within your current workspace?

If you wan't a fast try of the mmgenome package you can also just load the example data directly using data(Rocco).

[jrherr]

Thanks, I tried using data too -- I don't think this is a mmgenome issue after doing some investigation -- I think it's an issue with Biostrings.

Do you recommend using your new package instead? It also relies on Biostrings?

[Kirk3gaard]

The "multi-metagenome" package is no longer under development as it was replaced with the "mmgenome" package