It will be more efficient if you pre-specify the length of the list, I
understand. Depending on the size of the data, this may or may not be
important. I have not tested this code either.
seqs <- vector(mode = "list", length = DESIRED_LENGTH) ## replace
DESIRED_LENGTH with the appropriate number
class(seqs) <- "DNAbin"
for( i in seq_along(seqs) ) { ## your for loop
seqs[[i]] <- read.dna(file = ..., format="fasta", as.matrix=FALSE))
}
- Bret
________________________________
From: R-sig-phylo <r-sig-phylo-boun...@r-project.org> on behalf of Liam J.
Revell <liam.rev...@umb.edu>
Sent: Thursday, March 12, 2020 10:26 AM
To: Jarrett Phillips <phillipsjarre...@gmail.com>; r-sig-phylo@r-project.org
<r-sig-phylo@r-project.org>
Subject: Re: [R-sig-phylo] Iterating though multiple FASTA files via
rbind.DNAbin
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 Cat�lica de la Ssma Concepci�n
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!
>
> [[alternative HTML version deleted]]
>
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