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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