[R] How to load fasta file with openPrimeR?

[Bert Gunter]

As this is a Bioconductor package, why not ask on their support page:

https://support.bioconductor.org/



Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


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
>
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