loop over all files in folder in R

Question

I would like to import all files from a folder, convert the files and then export them with the same name, but with a different extension. In my specific case I want to convert 150 nexus files (.nex) to fasta files (.fasta)

This is how the code looks if I do it one by one:

library(ape)
gen1 <- read.nexus.data("gen1.nex") #import nexus file
write.dna(gen1, file = "./fastas/gen1.fasta", format = "fasta") #export fastafile

But now I fail to make a working for-loop to do all 150 files in one run. This is what I tried:

library(ape)
filenames = dir(pattern="*.nex")
for (i in filenames){
i <- read.nexus.data(i)
write.dna(i, file = "./fastas/i.fasta", format = "fasta")
}

When I run this code, I get only one file named "i.fasta" and not 150 files named gen1.fasta, gen2.fasta, DNAsequence1.fasta, DNAsequence2.fasta, etc. How should I change the for-loop to make it work correct?

thank you both for your comments. With "paste0" I get the error: non-string argument to internal 'paste'; while with sprintf, I get the error: unsupported type — PaulH, Oct 03 '16 at 09:44
Yes the issue is that you're rewriting `i` at each iteration. Try `for (i in filenames){dat <- read.nexus.data(i); write.dna(dat, file = sprintf("./fastas/%s.fasta", i), format = "fasta")}` — plannapus, Oct 03 '16 at 09:49
wonderful, the script is working. This saves me a lot of time. — PaulH, Oct 03 '16 at 09:52

score 1 · Answer 1 · answered Oct 03 '16 at 09:53

1

solution is quite simple when using paste function:

library(ape)
filenames = dir(pattern="*.nex")
for (f in filenames){
  i <- read.nexus.data(f)
  write.dna(i, file = paste0("./fastas/",f,".fasta"), format = "fasta")
}

answered Oct 03 '16 at 09:53

Wietze314

5,942
2
21
40

score 1 · Accepted Answer · answered Oct 03 '16 at 09:54

You need to 1) include the value of i inside the character string giving the fasta filename, 2) not rewrite i when you're loading your nexus file.

library(ape)
filenames = dir(pattern="*.nex")
for (i in filenames){
    dat <- read.nexus.data(i)
    write.dna(dat, file = sprintf("./fastas/%s.fasta", i), format = "fasta")
}

score 0 · Answer 3 · answered Sep 06 '18 at 16:11

0

something not stylish, but it works well

library(ape)
tmp <- list.files(pattern = "*.nex")
genes <- lapply(tmp, read.nexus.data)
for (i in 1:length(tmp))
  write.dna(genes[[i]], file = paste(tmp[i], ".fasta"), format = "fasta")

answered Sep 06 '18 at 16:11

Oscar Inostroza

23
5

loop over all files in folder in R

3 Answers3