[R] write.dna command

Mogjib Salek mogjibs at gmail.com
Sat Jun 17 16:26:42 CEST 2017

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
(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 =
           nbcol= 6, colsep= " ", colw= 10)

Any help will be appreciated.
Thank you.


	[[alternative HTML version deleted]]

More information about the R-help mailing list