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
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