ImportFastaAlignment <-
function(File,fixSpaceinHeaders=TRUE){
#import a fasta alignment and output a list containing a vector of names (rows)
#and a matrix of sequence nber by site
require(seqinr)
aln.fasta<- read.fasta(File) #list
Nseqs <- length(aln.fasta) #total nber of sequences
if(fixSpaceinHeaders){#to clean the headers for space; replace by underscore
for(i in 1:Nseqs){
attr(aln.fasta[[1]],"Annot") <- gsub(" ","_",x=attr(aln.fasta[[1]],"Annot"),)
}
}
Seq <- sapply(aln.fasta,FUN=function(A) {as.vector(A)}) #"matrix"
Seqs <- t(Seq)
Seqs.names <- rownames(Seqs)
Seqs.seqonly <- Seqs; rownames(Seqs.seqonly) <- 1:nrow(Seqs)
List <- list(Seqs.names=Seqs.names,
Seqs.only=Seqs.seqonly)
return(List)
}
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