Hi Jarrett,
This has been working for me using the package ‘apex':
x <- read.multiFASTA(files) # creates a multiDNA object
genes <- x@dna[] # creates a list with your loci.
I hope this helps.
Best
Gustavo
Em qui., 12 de mar. de 2020 às 11:18, Jarrett Phillips <
phillipsjarre...@gmail.com> escreveu:
> 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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>
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--
*Gustavo Silva de Miranda*
Peter Buck Postdoctoral Fellow - GGI <https://ggi.si.edu/>
Department of Entomology
National Museum of Natural History
Smithsonian Institution
Personal website <http://gustavomiranda.weebly.com/> | Google Scholar
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