Browse code

Prepare for reimport

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqTools@128654 bc3139a8-67e5-0310-9ffc-ced21a209358

Wolfgang Kaisers authored on 13/04/2017 15:55:12
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-
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-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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-##                                                                           ##
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-##  Project   :   seqTools                                                   ##
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-##  Created   :   26.August.2013                                             ##
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-##  Author    :   W. Kaisers                                                 ##
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-##  File      :   trimFastq.r                                                ##
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-##  Content   :   Functions which work on fastq and fastq and write output   ##
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-##                files: trimFastq, writeFai                                 ##
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-##                                                                           ##
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-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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-
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-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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-## trimFastq: Trimming and discarding reads based on quality values
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-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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-
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-trimFastq<-function(infile, outfile="keep.fq.gz", discard="disc.fq.gz", 
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-        qualDiscard=0, qualMask=0, fixTrimLeft=0, fixTrimRight=0,
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-        qualTrimLeft=0, qualTrimRight=0, qualMaskValue=78, minSeqLen=0)
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-{
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-    if(!is.character(infile))
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-        stop("'infile' must be a string.")
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-    
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-    if(length(infile) != 1)
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-        stop("'infile' must have length 1.")
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-    
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-    if(!file.exists(infile))
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-        stop("File 'infile' not found.")
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-    
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-    if(!is.character(outfile))
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-        stop("'outfile' must be character.")
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-    
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-    if(!is.character(outfile))
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-        stop("'discard' (file) must be character.")
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-    
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-    if(!is.character(discard))
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-        stop("'discard' must be character.")
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-    
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-    if(!is.character(discard))
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-        stop("'discard' (file) must be character.")
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-    
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-    if(!is.numeric(qualDiscard))
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-        stop("'qualDiscard' must be numeric.")
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-    
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-    if(length(qualDiscard)!=1)
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-        stop("'qualDiscard' must have length 1.")
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-    
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-    qualDiscard<-as.integer(qualDiscard)
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-    if( (qualDiscard < 0) || (qualDiscard > 93))
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-        stop("'qualDiscard' out of range.")
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-    
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-    if(!is.numeric(qualMask))
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-        stop("'qualMask' must be numeric.")
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-    
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-    if(length(qualMask) != 1)
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-        stop("'qualMask' must have length 1.")
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-    
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-    qualMask<-as.integer(qualMask)
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-    if( (qualMask < 0) || (qualMask > 93) )
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-        stop("'qualMask' out of range.")
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-    
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-    if(!is.numeric(fixTrimLeft))
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-        stop("'fixTrimLeft' must be numeric.")
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-    
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-    if(length(fixTrimLeft) != 1)
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-        stop("'fixTrimLeft' must have length 1.")
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-    
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-    if( (fixTrimLeft < 0) || (fixTrimLeft > 100) )
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-        stop("'fixTrimLeft' out of range.")
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-    
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-    if(!is.numeric(fixTrimRight))
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-        stop("'fixTrimRight' must be numeric.")
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-    
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-    if(length(fixTrimRight) != 1)
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-        stop("'fixTrimRight' must have length 1.")
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-    
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-    if( (fixTrimRight < 0) || (fixTrimRight > 100) )
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-        stop("'fixTrimRight' out of range.")
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-    
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-    if(!is.numeric(qualTrimLeft))
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-        stop("'qualTrimLeft' must be numeric.")
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-    
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-    if(length(qualTrimLeft)!= 1)
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-        stop("'qualTrimLeft' must have length 1.")
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-    qualTrimLeft<-as.integer(qualTrimLeft)
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-    
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-    if( (qualTrimLeft < 0) || (qualTrimLeft > 93) )
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-        stop("'qualTrimLeft' out of range.")
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-    
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-    if(!is.numeric(qualTrimRight))
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-        stop("'qualTrimRight' must be numeric.")
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-    
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-    if(length(qualTrimRight) != 1)
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-        stop("'qualTrimRight' must have length 1.")
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-    qualTrimRight<-as.integer(qualTrimRight)
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-    
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-    if( (qualTrimRight < 0) || (qualTrimRight > 93) )
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-        stop("'qualTrimRight' out of range.")
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-    
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-    if(!is.numeric(qualMaskValue))
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-        stop("'qualMaskValue' must be numeric.")
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-    
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-    if(length(qualMaskValue) != 1)
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-        stop("'qualMaskValue' must have length 1.")
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-    
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-    if( (qualMaskValue < 0) || (qualMaskValue > 93) )
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-        stop("'qualMaskValue' out of range.")
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-    
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-    if(!is.numeric(minSeqLen))
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-        stop("'minSeqLen' must be numeric.")
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-    
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-    if(length(minSeqLen) != 1)
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-        stop("'minSeqLen' must have length 1.")
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-    
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-    if( (minSeqLen < 0) || (minSeqLen > 200) )
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-        stop("'minSeqLen' out of range.")
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-    
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-    val<-as.integer(c(
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-        fixTrimLeft,
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-        fixTrimRight,
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-        qualTrimLeft,
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-        qualTrimRight,
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-        qualDiscard,
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-        qualMask,
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-        qualMaskValue,
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-        minSeqLen
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-    ))
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-    res<-.Call("trim_fastq", infile, val, c(outfile,discard))
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-    
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-    bm <- Sys.localeconv()[7]
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-    message("[trimFastq] ", format(res[1], width=11, big.mark=bm),
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-                                            " records written to outfile.")
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-    message("[trimFastq] ", format(res[2], width=11, big.mark=bm),
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-                                            " records written to discard.")
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-    return(invisible(res))
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-}
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-
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-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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-## END OF FILE
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-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##