[R] write.dna command

[William Michels]

Hi Mogjib,

Does the following solve your issue?

> setwd(WD)



On Sat, Jun 17, 2017 at 7:26 AM, 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]]
>
> ______________________________________________
> 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]]