[R] How to load fasta file with openPrimeR?

[Luigi Marongiu]

I think the problem is system.file, which is R base, but I'll go for
bioconductor. Thanks

On Mon, Feb 15, 2021 at 7:18 PM Bert Gunter <bgunter.4567 using gmail.com> wrote:
>
> 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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-- 
Best regards,
Luigi