R/writefasta.R

In celiason/genomeR: Tools for the analysis and assembly of genomic data in R

#' Save as single-line fasta
#' 
#' @export
#' 
writefasta <- function(x, outpath=NULL, ext=".fa") {
	if (!is.null(names(unlist(x)))) {
		for (i in seq_along(x)) {
			cat(paste0(names(x[[i]]), "\n", x[[i]]), sep="\n", file=paste0(outpath, "/", names(x)[i], ext))
		}
	} else {
		stop("Need names")
	}
}

# Write single fasta file
# x=seqs
# length(seqs[[1]])
# write.fasta <- function(x, outpath=NULL, ext=".fa") {
# 	if (!is.null(names(unlist(x)))) {
# 		for (i in seq_along(x)) {
# 			cat(paste0(names(x[[i]]), "\n", x[[i]]), sep="\n", file=paste0(outpath, "/", names(x)[i], ext))
# 		}
# 	}
# }


#' Abbreviate scientific names
#' 
#' @param x character of scientific names
#' 
#' @value output genome species abbreviates (e.g., "homSap" for Homo sapiens)
#' 
#' @export
#' 
sppAbbrev <- function(x) {
	tmp <- str_split(x, " |_")
	paste0(tolower(substring(sapply(tmp, "[[", 1), 1, 3)),
		   toupper(substring(sapply(tmp, "[[", 2), 1, 1)),
		   substring(sapply(tmp, "[[", 2), 2, 3))
}