How can I use read.fasta to load a lot of sequences that are stored in a folder and then run a program for all of this files in R. (loops)

Question

[imda]

I need your help. I have one folder that stores a lot of fasta alignment files. I want to use a program in R and run it for all the files that are stored in my folder. So, I do not know how to loop my script

Here I set my working directory

w.d <- '/share/Part1/icruz/data/orthofinder_all/all_solanaceas_protein_cds_correction/cafe_headers/Results_Apr15/cds_extractions/Rmultiplefiles'

setwd(w.d)

cds.fa <- read.fasta( '/share/Part1/icruz/data/orthofinder_all/all_solanaceas_protein_cds_correction/cafe_headers/Results_Apr15/cds_extractions/all_cds_solanaceae.fasta', seqtype="DNA", strip.desc=T, as.string=T ) 

# Here is the problem because I do not know how to read all the fasta files instead of set manually one by one

msa.aa <- read.fasta( '/home/icruz/data/orthofinder_all/all_solanaceas_protein_cds_correction/cafe_headers/Results_Apr15/cds_extractions/Rmultiplefiles/*.fa', seqtype="AA", strip.desc=T, as.string=T ) 

#Also I need to modify the headers in all my fasta files
names(msa.aa) 
msa.san <- msa.aa
names(msa.san) <- sub("^.*_", "", names(msa.aa))
names(msa.san)

#THIS IS THE PROGRAM THAT I NEED TO LOOP once I have load all my fasta files
cds.msa <- alignCDSSetWithAlignedAAsAsGuide(cds.fa, msa.san)

[cpad0112]

first part reading multiple fasta files (at once) after setting working directory (where the fasta files are kept):

> fl=list.files(pattern = ".fa")
> library(seqinr)
> for (i in 1:length(fl)) assign(fl[i], read.fasta(fl[i],seqtype="DNA", strip.desc=T, as.string=T ))
> ls()
 [1] "fl"        "i"         "test1.fa"  "test10.fa" "test2.fa"  "test3.fa"  "test4.fa"  "test5.fa" 
 [9] "test6.fa"  "test7.fa"  "test8.fa"  "test9.fa"

script saves each fasta file in individual data frames for each fasta file.