R/trimFastq.r

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

## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
##                                                                           ##
##  Project   :   seqTools                                                   ##
##  Created   :   26.August.2013                                             ##
##  Author    :   W. Kaisers                                                 ##
##  File      :   trimFastq.r                                                ##
##  Content   :   Functions which work on fastq and fastq and write output   ##
##                files: trimFastq, writeFai                                 ##
##                                                                           ##
## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
## trimFastq: Trimming and discarding reads based on quality values
## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

trimFastq<-function(infile, outfile = "keep.fq.gz", discard = "disc.fq.gz", qualDiscard = 0, qualMask = 0,
                    fixTrimLeft = 0, fixTrimRight = 0, qualTrimLeft = 0, qualTrimRight = 0, qualMaskValue = 78, minSeqLen = 0)
{
  if(!is.character(infile))
    stop("'infile' must be a string.")
  if(length(infile) != 1)
    stop("'infile' must have length 1.")
  if(!file.exists(infile))
    stop("File 'infile' not found.")
  
  if(!is.character(outfile))
    stop("'outfile' must be character.")
  if(!is.character(outfile))
    stop("'discard' (file) must be character.")
  
  if(!is.character(discard))
    stop("'discard' must be character.")
  if(!is.character(discard))
    stop("'discard' (file) must be character.")
  
  if(!is.numeric(qualDiscard))
    stop("'qualDiscard' must be numeric.")
  if(length(qualDiscard)!=1)
    stop("'qualDiscard' must have length 1.")
  qualDiscard<-as.integer(qualDiscard)
  if( (qualDiscard < 0) || (qualDiscard > 93))
    stop("'qualDiscard' out of range.")
  
  if(!is.numeric(qualMask))
    stop("'qualMask' must be numeric.")
  if(length(qualMask) != 1)
    stop("'qualMask' must have length 1.")
  qualMask<-as.integer(qualMask)
  if( (qualMask < 0) || (qualMask > 93) )
    stop("'qualMask' out of range.")
  
  if(!is.numeric(fixTrimLeft))
    stop("'fixTrimLeft' must be numeric.")
  if(length(fixTrimLeft) != 1)
    stop("'fixTrimLeft' must have length 1.")
  if( (fixTrimLeft < 0) || (fixTrimLeft > 100) )
    stop("'fixTrimLeft' out of range.")
  
  if(!is.numeric(fixTrimRight))
    stop("'fixTrimRight' must be numeric.")
  if(length(fixTrimRight) != 1)
    stop("'fixTrimRight' must have length 1.")
  if( (fixTrimRight < 0) || (fixTrimRight > 100) )
    stop("'fixTrimRight' out of range.")
  
  if(!is.numeric(qualTrimLeft))
    stop("'qualTrimLeft' must be numeric.")
  if(length(qualTrimLeft)!= 1)
    stop("'qualTrimLeft' must have length 1.")
  qualTrimLeft<-as.integer(qualTrimLeft)
  if( (qualTrimLeft < 0) || (qualTrimLeft > 93) )
    stop("'qualTrimLeft' out of range.")
  
  if(!is.numeric(qualTrimRight))
    stop("'qualTrimRight' must be numeric.")
  if(length(qualTrimRight) != 1)
    stop("'qualTrimRight' must have length 1.")
  qualTrimRight<-as.integer(qualTrimRight)
  if( (qualTrimRight < 0) || (qualTrimRight > 93) )
    stop("'qualTrimRight' out of range.")
  
  if(!is.numeric(qualMaskValue))
    stop("'qualMaskValue' must be numeric.")
  if(length(qualMaskValue) != 1)
    stop("'qualMaskValue' must have length 1.")
  if( (qualMaskValue < 0) || (qualMaskValue > 93) )
    stop("'qualMaskValue' out of range.")
  
  if(!is.numeric(minSeqLen))
    stop("'minSeqLen' must be numeric.")
  if(length(minSeqLen) != 1)
    stop("'minSeqLen' must have length 1.")
  if( (minSeqLen < 0) || (minSeqLen > 200) )
    stop("'minSeqLen' out of range.")
  
  val<-as.integer(c(
    fixTrimLeft,
    fixTrimRight,
    qualTrimLeft,
    qualTrimRight,
    qualDiscard,
    qualMask,
    qualMaskValue,
    minSeqLen
  ))
  res<-.Call("trim_fastq", infile, val, c(outfile,discard))
  
  bm<-Sys.localeconv()[7]
  message("[trimFastq] ", format(res[1], width = 11, big.mark = bm), "written to outfile.")
  message("[trimFastq] ", format(res[2], width = 11, big.mark = bm), "written to discard.")
  return(invisible(res))
}

## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
## END OF FILE
## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##