#' findReplaceNames
#' @description This script will find and replace expressions in sequence names of fasta files.
#' @author Edward Myers and Marcelo Gehara
#' @param path.to.fasta character string. path to the directory of fasta files.
#' @param input.id.name character string. Text indicating a wildcard to find the loci to process.
#' @param expr.to.replace charactees to exclude from samples names
#' @param replacement
#' @return processed sequence alignmnents to the to the output directory.
#' @details Ex. if the names starts as DBS_355_uce-8046a, it will end up as DBS_355a (note the regex in 'gsub')
#' @export
findReplaceNames<-function(path.to.fasta,
input.id.name,
expr.to.replace = "(_uce-\\d+)",
replacement = "")
{
x<-list.files(pattern=input.id.name)
for(i in 1:length(x)){
fas <- read.dna(x[i],format="fasta")
nam <- row.names(fas)
gsub(expr.to.replace, replacement, nam, perl = TRUE) -> nam
rownames(fas) <- nam
write.dna(fas,x[i],format="fasta")
}
}
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