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
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 at 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 at 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. >[[alternative HTML version deleted]]
> 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 at 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 at 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.