How to convert DNAbin to FASTA in R?

Question

I am trying to convert my_dnabin1, a DNAbin file of 55 samples, to fasta format. I am using the following code to convert it into a fasta file.

dnabin_to_fasta <- lapply(my_dnabin1, function(x) as.character(x[1:length(x)])) This generates a list of 55 samples which looks like:

$SS.11.01

[1] "t" "t" "a" "c" "c" "t" "a" "a" "a" "a" "a" "g" "c" "c" "g" "c" "t" "t" "c" "c" "c" "t" "c" "c" "a" "a" [27] "c" "c" "c" "t" "a" "g" "a" "a" "g" "c" "a" "a" "a" "c" "c" "t" "t" "t" "c" "a" "a" "c" "c" "c" "c" "a"

$SS.11.02

[1] "t" "t" "a" "c" "c" "t" "a" "a" "a" "a" "a" "g" "c" "c" "g" "c" "t" "t" "c" "c" "c" "t" "c" "c" "a" "a" [27] "c" "c" "c" "t" "a" "g" "a" "a" "g" "c" "a" "a" "a" "c" "c" "t" "t" "t" "c" "a" "a" "c" "c" "c" "c" "a"

and so on...

However, I want a fasta formatted file as the output that may look something like:

>SS.11.01 ttacctga

>SS.11.02 ttacctga

Answer 1

you can try this

lapply(my_dnabin1, function(x) paste0(x, collapse = ''))