[R] How to load fasta file with openPrimeR?

[Bill Dunlap]

> but if I give these commands to a local file:
> ```
> fasta.file <- system.file("extdata", "IMGT_data", "templates",
>                 "stx.fa", package = "openPrimeR")
> fasta.file <- system.file("stx.fa", package = "openPrimeR")
> ```
> where stx.fa il the file I wanted to open and that is present in the
> working directly. I get only an empty object.

If "stx.fa" is in fact in the current working directory then use
   fasta.file <- "stx.fa"
system.file() is for accessing files in installed packages.

-Bill

On Mon, Feb 15, 2021 at 10:11 AM Luigi Marongiu
<marongiu.luigi using gmail.com> wrote:
>
> Hello,
> I am trying to load a fast file with the package 'openPrimeR'. The
> manual (https://www.bioconductor.org/packages/release/bioc/vignettes/openPrimeR/inst/doc/openPrimeR_vignette.html)
> says to use:
> ```
> fasta.file <- system.file("extdata", "IMGT_data", "templates",
>                 "Homo_sapiens_IGH_functional_exon.fasta", package =
> "openPrimeR")
> # Load the template sequences from 'fasta.file'
> seq.df.simple <- read_templates(fasta.file)
> ```
> but if I give these commands to a local file:
> ```
> fasta.file <- system.file("extdata", "IMGT_data", "templates",
>                 "stx.fa", package = "openPrimeR")
> fasta.file <- system.file("stx.fa", package = "openPrimeR")
> ```
> where stx.fa il the file I wanted to open and that is present in the
> working directly. I get only an empty object.
> What am I getting wrong?
> Thank you
>
>
> --
> Best regards,
> Luigi
>
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.