Re: [R-sig-phylo] Iterating though multiple FASTA files via rbind.DNAbin

[Liam J. Revell]

Dear Jarrett.

I haven't checked to see if this works, but "DNAbin" objects can either 
be a matrix (the default if all the sequences have the same length) or a 
list.

For your code to work as a list you might change it to be something like:

seqs <- list()
class(seqs) <- "DNAbin"
for(...) { ## your for loop
        seqs <- c(seqs,
                read.dna(file = ..., format="fasta", as.matrix=FALSE))
}

(In which you substitute ... for your original code.)

In theory, I believe that this (or something like this) should do what 
you want.

All the best, Liam

Liam J. Revell
Associate Professor, University of Massachusetts Boston
Profesor Asistente, Universidad Católica de la Ssma Concepción
web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org

Academic Director UMass Boston Chile Abroad:
https://www.umb.edu/academics/caps/international/biology_chile

On 3/12/2020 11:18 AM, Jarrett Phillips wrote:
[EXTERNAL SENDER]

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!

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