R/importFA.R

In GenomicTools.fileHandler: File Handlers for Genomic Data Analysis

#' Importing a Fasta File.
#' 
#' This function imports a standard fasta file
#' 
#' This function imports a standard fasta file. Hereby, it does not matter if the identifier and sequence are alternating or not,
#' as the rows starting with '>' are used as identifer.
#' 
#' The example file was downloaded from here and was then further truncated respective transformed to fasta format:
#' 
#' ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/sequence_read/
#' 
#' @param file Specifies the filename/path
#' 
#' @return An object of class \code{fa} containing the sequences. The names correspond to the sequence names given in the fasta file.
#' 
#' @author Daniel Fischer
#' 
#' @seealso print.fa, summary.fa
#' 
#' @examples 
#' 
#'  # Define here the location on HDD for the example file
#'    fpath <- system.file("extdata","example.fasta", package="GenomicTools.fileHandler")
#'  # Import the example fasta file  
#'    fastaFile <- importFA(file=fpath)
#'  
#' @export

# This function reads in a fasta file and prepares the vector from it
  importFA <- function(file){
    res <- readLines(file)
  # Check if the Fasta file is alternating, one line label, the next line sequence
    greplRes <- grepl(">",res)
    sumAlternating <- sum(greplRes==c(TRUE,FALSE))
    if(sumAlternating!=length(res)){
      idRows <- which(greplRes)
      numberOfSequences <- length(idRows)

      # NOTE: Quick and dirty for now with a loop, fix that to be faster later!!!
      seq <- rep("", numberOfSequences)
      for(i in 1:(numberOfSequences-1)){
        seq[i] <- paste(res[(idRows[i]+1):(idRows[i+1]-1)], collapse="")
      }
      
      seq[numberOfSequences] <- paste(res[(idRows[i]+1):(length(res))], collapse="")
      names(seq) <- res[idRows]
      
      } else {
    # Sequences are alternating, hence we can use this to import the files
      seq <- res[seq(2,length(res),2)]
      names(seq) <- res[seq(1,length(res)-1,2)]
    }
    class(seq) <- "fa"
    seq
}