Hello everyone!

I need to perform a function on several fasta files located in the same folder. I first created a file object which lists the files names present in the Rtest folder.

files <- list.files(path="~/R/Rtest")

Then I put my script into a function called genWS. The first step of this function is to import the files one by one to perform a series of actions on them.

genWS <- function(input) {
x<-readDNAStringSet(file="input", format="fasta")
...
}

At the end of the script I put a FOR loop to go on the next fasta file.

for (j in 1:length(files)) {
  genWS(files[j])
}

My problem is that I got this error when I try to run the whole script despite it works fine when I import fasta file one by one manually.

Error in .Call2("new_input_ExternalFilePtr", fp, PACKAGE = "Biostrings") : 
  cannot open file 'input'
Called from: .Call2("new_input_ExternalFilePtr", fp, PACKAGE = "Biostrings")

Any idea of what happen and how to solve it ?

Thanks!

Use readDNAStringSet(file=input, ...) i.e., the variable, rather than a character string "input".

Unrelated to your problem, but R knows how to iterate over vectors, so the loop can be written

for (file in files)
    genWS(file)

Usually 1:length(x) is the wrong thing to do -- it produces surprising results when length(x) equals 0 -- and a better practice would use seq_along()  or seq_len().