Re: [R-sig-phylo] Iterating though multiple FASTA files via rbind.DNAbin
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$filepath, pattern = ".fas")
> tmp <- matrix()
> for (i in 1:length(file.names)) {
> seqs <- read.dna(file = file.names[i], format = "fasta")
> seqs <- rbind.DNAbin(tmp, seqs)
> }
>
> When run however, I get an error saying that the files do not have the same
> number of columns (i.e., alignments are all not of the same length).
>
> How can I avoid this error. I feel that it's a basic fix, but one that is
> not immediately obvious to me.
>
> Thanks!
>
> [[alternative HTML version deleted]]
>
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--
*Gustavo Silva de Miranda*
Peter Buck Postdoctoral Fellow - GGI |
ResearchGate
|
ORCID | Publons
(PT)
*Editor:* Check List
Re: [R-sig-phylo] Iterating though multiple FASTA files via rbind.DNAbin
Hi Jarrett,
read.FASTA() always returns a list. So you may do something (quite general)
like:
fls <- dir(pattern = "\\.fas$|\\.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]]
>
> ___
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
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Re: [R-sig-phylo] Iterating though multiple FASTA files via rbind.DNAbin
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 on behalf of Liam J.
Revell
Sent: Thursday, March 12, 2020 10:26 AM
To: Jarrett Phillips ; 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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