[R] write.dna command

[William Michels]

We'll need more information on the packages you're using. Can you post the
output of:

> sessionInfo()

Finally, is this a Bioconductor question? They have their own support site:

https://support.bioconductor.org

HTH,

William Michels, Ph.D.


On Sat, Jun 17, 2017 at 11:05 AM, Jeff Newmiller <jdnewmil at dcn.davis.ca.us>
wrote:

> I suspect you meant
>
> WD <- "~/Documents/Scripting/R_Studio/Sequences/"
>
> but I am entirely unfamiliar with the packages you are using, and know
> nothing about what is on your hard drive.
>
> For future reference:
>
> A) Read the Posting Guide.  This is a plain text email list, and your html
> formatting gets removed leaving a mess that is not always readable.
>
> B) Most frequent users of R change their working directory to where their
> project files are before they start R. If you are using RStudio, the use of
> Projects will take care of this for you. Then you don't have to put in your
> whole working path in the script and you can copy/move your R and data
> files elsewhere without breaking everything.
> --
> Sent from my phone. Please excuse my brevity.
>
> On June 17, 2017 7:26:42 AM PDT, Mogjib Salek <mogjibs at gmail.com> wrote:
> >Hi all,
> >
> >I am learning R by "doing". And this is my first post.
> >
> >I want to use R: 1- to fetch a DNA sequence from a databank (see
> >bellow)
> >and 2- store it as FASTA file.
> >
> >The problem: neither an error is prompted nor the fasta file is
> >created.
> >Testing the code (see bellow), I notice that everything works until
> >the *"write.dna"
> >*command - which is not creating the fasta file.
> >
> >Here is my code:
> >
> >####Get gene sequence from GenBank and store it as fasta file
> >####16 June 2017
> >
> >#1- Set the working directory and make sure the right libraries are
> >installed
> >(make sure 'ape' and 'seqinr' packages are installed)
> >
> >WD <- "~Documents/Scripting/R_Studio/Sequences/"
> >setwd <- (WD)
> >
> >#2- Fetch a sequence ( bellow, "enter  manually the desired DNA ID")
> >from
> >GenBank and store it as fasta file.
> >
> >      DNAid <- "JF806202"
> >
> >    # Store the sequence in lst (a list)
> >      lst <- read.GenBank(DNAid, as.character = T)
> >
> >      # convert the sequence to fasta format
> >      write.dna (lst, file = "DNAseq.fasta", format = "fasta", append =
> >FALSE,
> >           nbcol= 6, colsep= " ", colw= 10)
> >
> >
> >Any help will be appreciated.
> >Thank you.
> >
> >Kelas
> >
> >       [[alternative HTML version deleted]]
> >
> >______________________________________________
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> >PLEASE do read the posting guide
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> >and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> 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.
>

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