R/read_fasta.R

In biogram: N-Gram Analysis of Biological Sequences

#' Read FASTA files
#'
#' A lightweight tool to read nucleic or amino-acid sequences from a file 
#' in FASTA format.
#' 
#' @param file the name of the file which the data are to be read from.
#' @return a list of sequences.
#' @export
#' @seealso 
#' \code{\link[seqinr]{read.fasta}}: heavier function for processing FASTA files.
#' @examples 
#' \dontrun{
#'   read_fasta("https://www.uniprot.org/uniprot/P28307.fasta")
#'   }

read_fasta <- function(file) {
  all_lines <- readLines(file)
  prot_id <- cumsum(grepl("^>", all_lines))
  all_prots <- split(all_lines, prot_id)

  seq_list <- lapply(all_prots, function(ith_seq)
    unlist(strsplit(ith_seq[-1], split = "")))
  
  names(seq_list) <- sub(">", "", sapply(all_prots, function(ith_seq) ith_seq[1]), fixed = TRUE)
  
  seq_list
}


#' Write FASTA files
#'
#' A lightweight tool to read nucleic or amino-acid sequences from a file 
#' in FASTA format.
#' 
#' @param seq a list of sequences.
#' @param file the name of the output file.
#' @param nchar the number of characters per line.
#' @export
#' @seealso 
#' \code{\link[seqinr]{write.fasta}}: heavier function for writing FASTA files.
write_fasta <- function(seq, file, nchar = 80) {
  char_vec <- unlist(lapply(1L:length(seq), function(ith_id) 
    c(paste0(">", names(seq[ith_id])), 
      lapply(split(seq[[ith_id]], floor(seq_along(seq[[ith_id]])/nchar)), paste0, collapse = ""))))
  writeLines(text = char_vec, con = file)
}