R/fasta_output.R

In knausb/vcfR: Manipulate and Visualize VCF Data

#'
#'
#' @title Create fasta format output
#' @rdname fasta_output
#' @aliases write.fasta
#' 
#' @description Generate fasta format output
#' 
#' @param x object of class chromR
#' @param file name for output file
# @param gt_split character which delimits alleles in genotype
#' @param rowlength number of characters each row should not exceed
#' @param tolower convert all characters to lowercase (T/F)
#' @param verbose should verbose output be generated (T/F)
#' @param APPEND should data be appended to an existing file (T/F)
#' @param depr logical (T/F), this function has been deprecated, set to FALSE to override.
#' 
#' 
#' @details 
#' The function \strong{write_fasta} takes an object of class chromR and writes it to a fasta.gz (gzipped text) format file.
#' The sequence in the seq slot of the chromR object is used to fill in the invariant sites.
#' The parameter 'tolower', when set to TRUE, converts all the characters in teh sequence to lower case.
#' This is important because some software, such as ape::DNAbin, requires sequences to be in lower case.
#' 
#' 
#' @export
#' 
write.fasta <- function(x, file = "", rowlength=80, tolower=TRUE, verbose=TRUE, APPEND = FALSE, depr = TRUE){
#write.fasta <- function(x, file = "", gt_split = "|", rowlength=80, tolower=TRUE, verbose=TRUE, APPEND = FALSE){
  
  if( depr ){
    myMsg <- "The function write.fasta was deprecated in vcfR version 1.6.0. If you use this function and would like to advocate for its persistence, please contact the maintainer of vcfR. The maintainer can be contacted at maintainer('vcfR')"
    stop(myMsg)
  }
  
#  if(class(x) != "chromR"){
  if( !inherits(x, "chromR") ){
    stop("Expected object of class chromR")
  }
  if(APPEND == FALSE){
    if(file.exists(file)){
      file.remove(file)
    }
  }
#  haps <- extract_haps(x, gt_split = gt_split)
  haps <- .extract_haps(x)
  if(tolower == TRUE){
    haps <- apply(haps, MARGIN=2, tolower)
  }
  
  for(i in 1:ncol(haps)){
    seq <- as.character(x@seq)[1,]
#    seq[x@vcf.fix$POS] <- haps[,i]
    seq[x@var.info$POS] <- haps[,i]
#    invisible(.Call('vcfR_write_fasta', PACKAGE = 'vcfR', seq, colnames(haps)[i], file, rowlength, as.integer(verbose)))
    invisible(.write_fasta(seq, colnames(haps)[i], file, rowlength, as.integer(verbose)))
  }
  
  #invisible(.Call('vcfR_write_fasta', PACKAGE = 'vcfR', seq, seqname, filename, rowlength, verbose))  
}