Hi Jarrett,
read.FASTA() always returns a list. So you may do something (quite general)
like:
fls <- dir(pattern = "\\.fas$|\\.fasta$", ignore.case = TRUE) # add more file
extensions if needed
X <- lapply(fls, read.FASTA)
seqlen <- lengths(X)
if (length(unique(seqlen)) == 1) X <- as.matrix(X)
If the sequences are not of the same length, you can use the vector 'seqlen'
for further processing, for instance to remove the shortest ones (if this makes
sense):
X[seqlen > 100]
Also I found the function fasta.index (in Biostrings on BioConductor) to be
very useful for this kind of tasks: it scans a bunch of FASTA files (possibly
in different directories) and returns a data frame with each row describing
each sequence (length, label, path, ...).
HTH
Best,
Emmanuel
----- Le 12 Mar 20, à 22:18, Jarrett Phillips phillipsjarre...@gmail.com a
écrit :
> Hi All,
>
> I have a folder with multiple FASTA files which need to be read into R.
>
> To avoid file overwriting, I use ape::rbind.DNAbin() as follows:
>
> file.names <- list.files(path = envr$filepath, pattern = ".fas")
> tmp <- matrix()
> for (i in 1:length(file.names)) {
> seqs <- read.dna(file = file.names[i], format = "fasta")
> seqs <- rbind.DNAbin(tmp, seqs)
> }
>
> When run however, I get an error saying that the files do not have the same
> number of columns (i.e., alignments are all not of the same length).
>
> How can I avoid this error. I feel that it's a basic fix, but one that is
> not immediately obvious to me.
>
> Thanks!
>
> [[alternative HTML version deleted]]
>
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