write.dna command

sessionInfo()

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]]

setwd(WD)

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]]