R/fastaFunctions.r

In seqTools: Analysis of nucleotide, sequence and quality content on fastq files.

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##                                                                           ##
##  Project   :   seqTools                                                   ##
##  Created   :   26.August.2013                                             ##
##  Author    :   W. Kaisers                                                 ##
##  File      :   fastaFunctions.r                                           ##
##  Content   :   Functions which work on fastq and fastq and write output   ##
##                files: writeFai,  countFastaKmers                          ##
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writeFai <- function(infiles, outfiles)
{
  if(!is.character(infiles))
    stop("infiles must be character.")
  if(!is.character(outfiles))
    stop("outfiles must be character.")
  if(length(infiles) != length(outfiles))
    stop("infiles and outfiles must have equal length.")
  if(any( !file.exists(infiles) ) )
    stop("Some infile(s) do not exist!\n")
  
  .Call("write_fai", infiles, outfiles, PACKAGE = "seqTools")
  message("[write_fai] done.\n")
  return(invisible())
}


countFastaKmers <- function(filenames, k = 4)
{
  if(!is.character(filenames))
    stop("filenames must be character.")
  if(!is.numeric(k))
    stop("k must be numeric.")
  k <- as.integer(k)
  if( (k < 0) || (k > max_k) )  
    stop("k must be in range 0,  ... , ", max_k, ".")
  
  res <- .Call("count_fasta_Kmers", filenames, k, PACKAGE = "seqTools")
  return(res)
}

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## END OF FILE
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