R/singleRCodeFile.R
In SimonSchafferer/CLIHelperPackage: A packages that manages easy access to cmdLine applications within R (related to RNA-Seq)
#--split CLIApplication
#'@title CLIApplication Virtual Class
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' }
#' @name CLIApplication-class
#' @export
setClass("CLIApplication", representation(inFilePath = "character",
inFileNames = "character",
cliParams = "character",
outFilePath = "character",
outputFlag = "character",
"VIRTUAL"))
#' @title Generates the commands and possibly resulting files/folders
#' @param CLIApplication
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setGeneric("generateCommandResult", function( object ) {
value = standardGeneric("generateCommandResult")
if( !is(value, "CmdGenResult") )
stop("Return Value must be CmdGenResult!")
value
})
#' @title Accessor getInFilePath
#' @export
#' @docType methods
#' @return inFilePath
setGeneric("getInFilePath", function(object) standardGeneric("getInFilePath"))
setMethod("getInFilePath",signature(object="CLIApplication"),function(object) {
slot(object, "inFilePath")
})
#' @title Accessor getInFileNames
#' @export
#' @docType methods
#' @return inFileNames
setGeneric("getInFileNames", function(object) standardGeneric("getInFileNames"))
setMethod("getInFileNames",signature(object="CLIApplication"),function(object) {
slot(object, "inFileNames")
})
#' @title Accessor getCliParams
#' @export
#' @docType methods
#' @return cliParams
setGeneric("getCliParams", function(object) standardGeneric("getCliParams"))
setMethod("getCliParams",signature(object="CLIApplication"),function(object) {
slot(object, "cliParams")
})
#' @title Accessor getOutFilePath
#' @export
#' @docType methods
#' @return outFilePath
setGeneric("getOutFilePath", function(object) standardGeneric("getOutFilePath"))
setMethod("getOutFilePath",signature(object="CLIApplication"),function(object) {
slot(object, "outFilePath")
})
#' @title Accessor getOutputFlag
#' @export
#' @docType methods
#' @return outputFlag
setGeneric("getOutputFlag", function(object) standardGeneric("getOutputFlag"))
setMethod("getOutputFlag",signature(object="CLIApplication"),function(object) {
slot(object, "outputFlag")
})
#--split OutResultReference
#'@title OutResultReference Virtual Class
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{outResultName \code{"character"}}
#' }
#' @name OutResultReference-class
#' @export
setClass("OutResultReference", representation(outResultName = "character", "VIRTUAL"))
#' @title Accessor getOutResultName
#' @export
#' @docType methods
#' @return outResultName
setGeneric("getOutResultName", function(object){standardGeneric("getOutResultName")})
setMethod("getOutResultName",signature(object="OutResultReference"),function(object) {
slot(object, "outResultName")
})
#--split FilesOutput
#@include OutResultReference
#'@title FilesOutput
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' }
#' @name FilesOutput-class
#' @export
setClass("FilesOutput", contains = "OutResultReference")
#--split FoldersOutput
#@include OutResultReference
#'@title FoldersOutput
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' }
#' @name FoldersOutput-class
#' @export
setClass("FoldersOutput", contains = "OutResultReference")
#' @title Constructor method for FoldersOutput
#' @param outResultName
#' @export
#' @docType methods
#' @return \code{"FoldersOutput"}
FoldersOutput = function(outResultName){
return( new("FoldersOutput", outResultName=outResultName) )
}
#' @title Constructor method for FilesOutput
#' @param outResultName
#' @export
#' @docType methods
#' @return \code{"FilesOutput"}
FilesOutput = function(outResultName){
return( new("FilesOutput", outResultName=outResultName) )
}
#' @title Constructor (factory) for OutResultReference
#' @param outResultName
#' @export
#' @docType methods
#' @return \code{OutResultReference} implementation
OutResultReference = function(outResultName){
if( file.exists(outResultName) ){
if( length(list.files(outResultName)) == 0 ){
return( FilesOutput(outResultName) )
} else{
return( FoldersOutput(outResultName) )
}
} else{
stop("Not a file or folder!")
}
}
#--split CmdGenResult
#'@title CmdGenResult
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{CLIApplication \code{"CLIApplication"}}
#' \item{\code{slot2}:}{OutResultReference \code{"OutResultReference"}}
#' \item{\code{slot3}:}{commands \code{"character"}}
#' }
#' @name CmdGenResult-class
#' @export
setClass( "CmdGenResult", representation( CLIApplication="CLIApplication",
OutResultReference="OutResultReference",
commands="character" ) )
setValidity ("CmdGenResult",
function ( object ){
retval = NULL
if ( is.null(retval)){
return(TRUE)
}
else{
return(retval)
}
})
#' @title Accessor CLIApplication
#' @export
#' @docType methods
#' @return CLIApplication
setGeneric("getCLIApplication", function(object) standardGeneric("getCLIApplication"))
setMethod("getCLIApplication",signature(object="CmdGenResult"),function(object) {
slot(object, "CLIApplication")
})
#' @title Accessor getOutResultReference
#' @export
#' @docType methods
#' @return OutResultReference
setGeneric("getOutResultReference", function(object) standardGeneric("getOutResultReference"))
setMethod("getOutResultReference",signature(object="CmdGenResult"),function(object) {
slot(object, "OutResultReference")
})
#' @title Accessor getCommands
#' @export
#' @docType methods
#' @return commands
setGeneric("getCommands", function(object) standardGeneric("getCommands"))
setMethod("getCommands",signature(object="CmdGenResult"),function(object) {
slot(object, "commands")
})
#' @title Accessor getCommandLog
#' @export
#' @docType methods
#' @return commands formatted
setGeneric("getCommandLog", function(object) standardGeneric("getCommandLog"))
setMethod("getCommandLog",signature(object="CmdGenResult"),function(object) {
paste0(paste0( getCommands(object),collapse="\n"), "\n")
})
#' @title Constructor method for CmdGenResult
#' @param CLIApplication
#' @param OutResultReference
#' @param commands
#' @export
#' @docType methods
#' @return \code{"CmdGenResult"}
CmdGenResult = function(CLIApplication,OutResultReference,commands ){
return( new("CmdGenResult",CLIApplication=CLIApplication,OutResultReference=OutResultReference,commands=commands) )
}
#' @title Executes the commands of a executeCommandResult object
#' @param \code{"CmdGenResult"}
#' @export
#' @docType methods
setGeneric("executeCommandResult", function(object, ...) {
standardGeneric("executeCommandResult") })
#' @title Executes the commands of a executeCommandResult object
#' @param \code{"CmdGenResult"}
#' @param \code{"testing"} boolean testing if true - command is not executed
#' @export
#' @docType methods
setMethod("executeCommandResult",signature(object="CmdGenResult"), function(object, testing=FALSE, useTee=TRUE) {
# message( paste0("Executing command:\n", getCommandLog(object)) )
logs = lapply( getCommands(object), function(x){
#setting the directory to the InputFilePath
currWD = getwd()
message( paste0("Executing command:\n", x) )
log = tryCatch({
if(!testing){
if(!useTee){
setwd(getInFilePath(getCLIApplication(object = object)))
cmdRes = system(x,intern = TRUE, ignore.stdout = FALSE, ignore.stderr = FALSE)
return(cmdRes)
} else{
setwd(getInFilePath(getCLIApplication(object = object)))
logFile = tempfile()
system(paste0(x," 2>&1 | tee ",logFile),intern = TRUE, ignore.stdout = FALSE, ignore.stderr = FALSE)
return( readLines(logFile) )
}
} else{
message("Testing ... command is not executed!")
return(x)
}
}, warning = function(w){
warning(w)
}, error = function(e){
paste0("Error when executing code ", e)
}, finally = {
setwd( currWD )
})
return(log)
})
return( CmdGenResultExec(cmdGenResult=object, execLog=logs))
})
#--split CmdGenResultExec
#'@title CmdGenResultExec
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{cmdGenResult \code{"CmdGenResult"}}
#' \item{\code{slot2}:}{execLog \code{"execLog"}}
#' }
#' @name CmdGenResultExec-class
#' @export
setClass( "CmdGenResultExec", representation(cmdGenResult="CmdGenResult", execLog="list" ) )
#' @title Constructor method for CmdGenResultExec
#' @param CmdGenResult
#' @param execLog
#' @export
#' @docType methods
#' @return \code{"CmdGenResultExec"}
CmdGenResultExec = function(cmdGenResult, execLog){
return( new("CmdGenResultExec",cmdGenResult=cmdGenResult,execLog=execLog) )
}
#' @title Accessor getCmdGenResult
#' @export
#' @docType methods
#' @return getCmdGenResult
setGeneric("getCmdGenResult", function(object) standardGeneric("getCmdGenResult"))
setMethod("getCmdGenResult",signature(object="CmdGenResultExec"),function(object) {
slot(object, "cmdGenResult")
})
#' @title Accessor getExecLog
#' @export
#' @docType methods
#' @return execLog
setGeneric("getExecLog", function(object) standardGeneric("getExecLog"))
setMethod("getExecLog",signature(object="CmdGenResultExec"),function(object) {
slot(object, "execLog")
})
#' @title Accessor getExecLogFormatted
#' @export
#' @docType methods
#' @return execLog formatted
setGeneric("getExecLogFormatted", function(object) standardGeneric("getExecLogFormatted"))
setMethod("getExecLogFormatted",signature(object="CmdGenResultExec"),function(object) {
tmp = lapply( getExecLog(object), function(x){
paste0(x,collapse="\n")
} )
return( paste0(unlist(tmp) ,collapse="\n\n") )
})
#--split Cutadapt_CLI
#@include CLIApplication
#'@title Cutadapt_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' }
#' @name Cutadapt_CLI-class
#' @export
setClass("Cutadapt_CLI", contains = "CLIApplication")
#' @title Constructor method for Cutadapt_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
setGeneric("Cutadapt_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath){standardGeneric("Cutadapt_CLI")})
setMethod("Cutadapt_CLI", signature(inFilePath="character", inFileNames="missing", cliParams="character",
outputFlag="character", outFilePath="character"), function(inFilePath, cliParams, outputFlag, outFilePath){
inFileNames = list.files(path = inFilePath, pattern = ".*\\.fastq$")
return(new("Cutadapt_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams, outputFlag=outputFlag,outFilePath=outFilePath))
})
setMethod("Cutadapt_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character"), function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath ){
return(new("Cutadapt_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams, outputFlag=outputFlag,outFilePath=outFilePath))
})
#' @title Generates the commands and possibly resulting files/folders of Cutadapt
#'
#' @param Cutadapt_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="Cutadapt_CLI"),function(object) {
allFiles = getInFileNames(object)
cmd1 = paste0("cd ",getInFilePath(object))
allFilesOut = paste0( sub("\\.fastq$","",allFiles) ,getOutputFlag(object), ".fastq")
# dir.create(getOutFilePath(object))
cmd2 = paste0("mkdir ", getOutFilePath(object))
cmd3 = paste0("cutadapt ", paste0(getCliParams(object),collapse=" "), " -o ", file.path(getOutFilePath(object), allFilesOut), " ", allFiles)
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(allFilesOut), commands = c(cmd1, cmd2, cmd3))
return(res)
})
#--split HTSeqCount_CLI
#@include CLIApplication
#'@title HTSeqCount_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{gffFile \code{"character"}}
#' }
#' @name HTSeqCount_CLI-class
#' @export
setClass("HTSeqCount_CLI", contains = "CLIApplication", representation(gffFile="character"))
#' @title Accessor HTSeqCount_CLI
#' @export
#' @docType methods
#' @return gffFile
setGeneric("getGffFile", function(object){standardGeneric("getGffFile")})
setMethod("getGffFile",signature(object="HTSeqCount_CLI"),function(object) {
slot(object, "gffFile")
})
#' @title Constructor method for HTSeqCount_CLI
#' @export
#' @docType methods
setGeneric("HTSeqCount_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, gffFile){standardGeneric("HTSeqCount_CLI")})
setMethod("HTSeqCount_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", gffFile="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, gffFile ){
return(
new("HTSeqCount_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, gffFile=gffFile)
)
})
#' @title Generates the commands and possibly resulting files/folders of HTSeqCount_CLI
#'
#' @param HTSeqCount_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="HTSeqCount_CLI"),function(object) {
# Usage: htseq-count [options] alignment_file gff_file
inFN = getInFileNames(object)
cmd1 = paste0("cd ",getInFilePath(object))
outFN = paste0( sub( "\\..*$","",inFN), getOutputFlag(object) )
cmd2 = paste0( "htseq-count ", paste0(getCliParams(object),collapse=" "), " ", inFN, " ", getGffFile(object), " > ", file.path(getOutFilePath(object),outFN) )
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2))
return(res)
})
#--split IntersectBed_CLI
#@include CLIApplication
#'@title IntersectBed_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{outFileName \code{"character"}}
#' }
#' @name IntersectBed_CLI-class
#' @export
setClass("IntersectBed_CLI", contains = "CLIApplication", representation(outFileName="character"))
#' @title Constructor method for IntersectBed_CLI
#' @param inFilePath only one filename allowed!
#' @export
#' @docType methods
setGeneric("IntersectBed_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, outFileName){standardGeneric("IntersectBed_CLI")})
setMethod("IntersectBed_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", outFileName="character"), function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath,
outFileName ){
return(new("IntersectBed_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams, outputFlag=outputFlag,
outFilePath=outFilePath, outFileName=outFileName))
})
#' @title Accessor getOutFileName
#' @export
#' @docType methods
#' @return outFileName
setGeneric("getOutFileName", function(object){standardGeneric("getOutFileName")})
setMethod("getOutFileName",signature(object="IntersectBed_CLI"),function(object) {
slot(object, "outFileName")
})
#' @title Generates the commands and possibly resulting files of linux sort command IntersectBed_CLI
#'
#' @param IntersectBed_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="IntersectBed_CLI"),function(object) {
if( length(getInFileNames(object)) > 2 ){
message("First File will be taken as a and all others as b")
} else if( length(getInFileNames(object)) < 2 ){
stop("Please provide at least two files as input!")
}
inFN_a = getInFileNames(object)[1]
inFN_b = getInFileNames(object)[-1]
if( length(getInFilePath(object)) == 1 ){
message("All files have to be present in the inFilePath directory!")
inFN_a_path = getInFilePath(object)
inFN_b_path = getInFilePath(object)
} else if( length(getInFilePath(object)) != length(getInFileNames(object)) ){
stop("Please provide the same number of paths to the input files as input file names")
} else{
inFN_a_path = getInFilePath(object)[1]
inFN_b_path = getInFilePath(object)[-1]
}
cmd1 = paste0("cd ",getInFilePath(object))
inFNtrimmed = sub("\\..+$","",inFN_a)
inFilending = sub( inFNtrimmed, "", inFN_a )
cmd2 = paste0( "mkdir ", getOutFilePath(object) )
outFN = paste0( getOutFileName(object), getOutputFlag(object), inFilending)
cmd3 = paste0( "intersectBed ", getCliParams(object), " -a ", file.path(inFN_a_path, inFN_a), " -b ",
paste0( file.path(inFN_b_path, inFN_b), collapse=" "), " > ", file.path(getOutFilePath(object), outFN) )
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2, cmd3))
return(res)
})
#--split MergeBedFile_CLI
#@include CLIApplication
#'@title MergeBedFile_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' }
#' @name MergeBedFile_CLI-class
#' @export
setClass("MergeBedFile_CLI", contains = "CLIApplication")
#' @title Constructor method for MergeBedFile_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
setGeneric("MergeBedFile_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath){standardGeneric("MergeBedFile_CLI")})
setMethod("MergeBedFile_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character"), function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath ){
return(new("MergeBedFile_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams, outputFlag=outputFlag,outFilePath=outFilePath))
})
setMethod("MergeBedFile_CLI", signature(inFilePath="character", inFileNames="character", cliParams="missing",
outputFlag="character", outFilePath="character"), function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath ){
cliParams = "-s -c 4,5,6 -o mean,mean,distinct"
return(new("MergeBedFile_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams, outputFlag=outputFlag,outFilePath=outFilePath))
})
#' @title Generates the commands and possibly resulting files/folders of Cutadapt
#'
#' @param MergeBedFile_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="MergeBedFile_CLI"),function(object) {
if( length(getInFileNames(object)) > 1 ){
warning("More than one input file given, using the first one!")
}
inFN = getInFileNames(object)[1]
cmd1 = paste0("cd ",getInFilePath(object))
inFNtrimmed = sub("\\..+$","",inFN)
inFilending = sub( inFNtrimmed, "", inFN )
outFN = paste0( inFNtrimmed, getOutputFlag(object), inFilending)
cmd2 = paste0( "sort -k1,1 -k2,2n ", file.path(getInFilePath(object), getInFileNames(object) ), " | ",
"mergeBed ", " -i stdin ", getCliParams(object), " | sort -k1,1 -k2,2n > ", file.path(getOutFilePath(object), outFN) )
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2))
return(res)
})
#--split MultiBamCov_CLI
#@include CLIApplication
#'@title MultiBamCov_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{annotationFileMB \code{"character"}}
#' \item{\code{slot7}:}{annotationType \code{"character"}}
#' }
#' @name MultiBamCov_CLI-class
#' @export
setClass("MultiBamCov_CLI", contains = "CLIApplication", representation(annotationFileMB="character", annotationType = "character"))
#' @title Accessor annotationFileMB
#' @export
#' @docType methods
#' @return annotationFileMB
setGeneric("getAnnotationFileMB", function(object){standardGeneric("getAnnotationFileMB")})
setMethod("getAnnotationFileMB",signature(object="MultiBamCov_CLI"),function(object) {
slot(object, "annotationFileMB")
})
#' @title Accessor annotationType
#' @export
#' @docType methods
#' @return annotationType
setGeneric("getAnnotationType", function(object){standardGeneric("getAnnotationType")})
setMethod("getAnnotationType",signature(object="MultiBamCov_CLI"),function(object) {
slot(object, "annotationType")
})
#' @title Constructor method for MultiBamCov_CLI
#' @export
#' @docType methods
setGeneric("MultiBamCov_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, annotationFileMB, annotationType){standardGeneric("MultiBamCov_CLI")})
setMethod("MultiBamCov_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", annotationFileMB="character", annotationType="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, annotationFileMB,annotationType ){
return(
new("MultiBamCov_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, annotationFileMB=annotationFileMB,annotationType=annotationType)
)
})
setMethod("MultiBamCov_CLI", signature(inFilePath="character", inFileNames="missing", cliParams="character",
outputFlag="character", outFilePath="character", annotationFileMB="character", annotationType="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, annotationFileMB,annotationType ){
inFileNames = list.files(path = inFilePath, pattern = ".*\\.sam$")
return(
new("MultiBamCov_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, annotationFileMB=annotationFileMB,annotationType=annotationType)
)
})
#' @title Generates the commands and possibly resulting files/folders of MultiBamCov_CLI
#'
#' @param MultiBamCov_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="MultiBamCov_CLI"),function(object) {
# Usage: bedtools multicov [OPTIONS] -bams aln.1.bam aln.2.bam ... aln.n.bam -bed <bed/gff/vcf>
inFNs = getInFileNames(object)
cmd1 = paste0("cd ",getInFilePath(object))
# outFN = paste0( gsub(".*/","",sub( "\\..*$","",inFNs[1])), getOutputFlag(object) )
outFN = paste0( getOutputFlag(object) )
cmd2 = paste0( "bedtools multicov ", paste0(getCliParams(object),collapse=" "), " -bams ", paste0(inFNs, collapse=" "), " -",
getAnnotationType(object)," ", getAnnotationFileMB(object), " > ", file.path(getOutFilePath(object),outFN) )
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2))
return(res)
})
#--split Genomecov_CLI
# Needs to be placed after IntersectBed_CLI
#@include CLIApplication
#'@title Genomecov_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}} In this class the flag may be bedgraph (not used but specifies filetype)
#' \item{\code{slot6}:}{outFileName \code{"character"}}
#' \item{\code{slot7}:}{inFileBam \code{"logical"}}
#' }
#' @name Genomecov_CLI-class
#' @export
setClass("Genomecov_CLI", contains = "CLIApplication", representation(outFileName="character", inFileBam="logical"))
#' @title Constructor method for Genomecov_CLI
#' @param inFilePath only one filename allowed!
#' @export
#' @docType methods
setGeneric("Genomecov_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, outFileName, inFileBam){standardGeneric("Genomecov_CLI")})
setMethod("Genomecov_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", outFileName="character",
inFileBam="logical"), function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath,
outFileName,inFileBam ){
return(new("Genomecov_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams, outputFlag=outputFlag,
outFilePath=outFilePath, outFileName=outFileName, inFileBam=inFileBam))
})
#' @title Accessor getOutFileName
#' @export
#' @docType methods
#' @return outFileName
setMethod("getOutFileName",signature(object="Genomecov_CLI"),function(object) {
slot(object, "outFileName")
})
#' @title Accessor getInFileBam
#' @export
#' @docType methods
#' @return inFileBam
setGeneric("getInFileBam", function(object){standardGeneric("getInFileBam")})
setMethod("getInFileBam",signature(object="Genomecov_CLI"),function(object) {
slot(object, "inFileBam")
})
#' @title Generates the commands and possibly resulting files of linux sort command Genomecov_CLI
#'
#' @param Genomecov_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="Genomecov_CLI"),function(object) {
if( length(getInFileNames(object)) > 1 ){
warning("Only one file allowed, the first one will be chosen!")
}
inFN = getInFileNames(object)[1]
outFN = getOutFileName(object)
inFN_path = getInFilePath(object)
cmd1 = paste0("cd ",getInFilePath(object))
cmd2 = paste0( "bedtools genomecov ", getCliParams(object), ifelse( getInFileBam(object), " -ibam ", " -i " ) ,file.path(inFN_path, inFN), " > ",
file.path(getOutFilePath(object), outFN) )
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2))
return(res)
})
#--split Samtools_CLI
#@include CLIApplication
#'@title Samtools_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{samtoolsApplication \code{"character"}}
#' \item{\code{slot6}:}{outputFormat \code{"character"}}
#' }
#' @name Samtools_CLI-class
#' @export
setClass("Samtools_CLI", contains = "CLIApplication", representation(samtoolsApplication="character", outputFormat = "character") )
# @title Validity method for Samtools_CLI
# @export
# @name validitySamtools_CLI
# @rdname validitySamtools_CLI
# @docType methods
setValidity ("Samtools_CLI",
function ( object ){
retval = NULL
if( length(getInFileNames(object)) > 1 ){ retval = "Only one input file is allowed!" }
if ( is.null(retval)){
return(TRUE)
}
else{
return(retval)
}
})
#' @title Accessor getSamtoolsApplication
#' @export
#' @docType methods
#' @return samtoolsApplication
setGeneric("getSamtoolsApplication", function(object){standardGeneric("getSamtoolsApplication")})
setMethod("getSamtoolsApplication", signature(object="Samtools_CLI"), function(object){
slot(object, "samtoolsApplication")
})
#' @title Accessor getOutputFormat
#' @export
#' @docType methods
#' @return outputFormat
setGeneric("getOutputFormat", function(object){standardGeneric("getOutputFormat")})
setMethod("getOutputFormat", signature(object="Samtools_CLI"), function(object){
slot(object, "outputFormat")
})
#' @title Constructor method for Samtools_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
setGeneric("Samtools_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, samtoolsApplication, outputFormat){standardGeneric("Samtools_CLI")})
setMethod("Samtools_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", samtoolsApplication="character", outputFormat="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, samtoolsApplication, outputFormat){
return(
new("Samtools_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, samtoolsApplication=samtoolsApplication, outputFormat=outputFormat)
)
})
#' @title Generates the commands and possibly resulting files/folders of Samtools
#'
#' @param Samtools_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="Samtools_CLI"),function(object) {
cmd1 = paste0("cd ",getInFilePath(object))
#select different samtools applications by name
stapp = getSamtoolsApplication(object)
inFN = getInFileNames(object)
outfmt = getOutputFormat(object)
outFN = ""
cmd2 = ""
switch(stapp,
view = {
#samtools view -o aligned_sn.sam aligned_sn.bam
outFN = paste0( sub("\\..*$","",inFN),getOutputFlag(object),".",outfmt)
params = getCliParams(object)
params = params[ which( params != "-o" ) ]
cmd2 = paste0("samtools view ",paste0(params,collapse=" ")," -o ",outFN," ", inFN)
},
sort = {
#samtools sort -n aligned.bam aligned_sn
outFNprefix = paste0( sub("\\..*$","",inFN),getOutputFlag(object) )
outFN = paste0(outFNprefix, ".", outfmt)
cmd2 = paste0("samtools sort ",paste0(getCliParams(object),collapse=" ")," ", inFN," -o ", outFN )
},
index = {
#samtools index aligned_s.bam
cmd2 = paste0("samtools index ",paste0(getCliParams(object),collapse=" ")," ",inFN)
outFN = sub( "bam","bai", inFN)
},
{
stop("Samtools application not recognized (supported: view, sort, index)")
})
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2))
return(res)
})
#--split BamToBed_CLI
#'@title BamToBed_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{outputFormat \code{"character"}}
#' }
#' @name BamToBed_CLI-class
#' @export
setClass("BamToBed_CLI", contains = "CLIApplication", representation(outputFormat="character"))
#' @title Constructor method for BamToBed_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
setGeneric("BamToBed_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, outputFormat){standardGeneric("BamToBed_CLI")})
setMethod("BamToBed_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", outputFormat="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, outputFormat ){
return(new("BamToBed_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams, outputFlag=outputFlag,
outFilePath=outFilePath, outputFormat=outputFormat))
})
#' @title Accessor getOutputFormat
#' @export
#' @docType methods
#' @return outputFormat
setMethod("getOutputFormat", signature(object="BamToBed_CLI"), function(object){
slot(object, "outputFormat")
})
#' @title Generates the commands and possibly resulting files/folders of BamToBed_CLI
#'
#' @param BamToBed_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="BamToBed_CLI"),function(object) {
if( length(getInFileNames(object)) > 1 ){
warning("More than one input file given, using the first one!")
}
inFN = getInFileNames(object)[1]
cmd1 = paste0("cd ",getInFilePath(object))
inFNtrimmed = sub("\\..+$","",inFN)
outFN = paste0( inFNtrimmed, getOutputFlag(object),".", getOutputFormat(object))
cmd2 = paste0( "bamToBed ", getCliParams(object)," -i ", file.path(getInFilePath(object), getInFileNames(object) ),
" > ", file.path(getOutFilePath(object), outFN) )
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2))
return(res)
})
#--split SortFile_CLI
#@include CLIApplication
#'@title SortFile_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' }
#' @name SortFile_CLI-class
#' @export
setClass("SortFile_CLI", contains = "CLIApplication")
#' @title Constructor method for SortFile_CLI
#' @param inFilePath only one filename allowed!
#' @export
#' @docType methods
setGeneric("SortFile_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath){standardGeneric("SortFile_CLI")})
setMethod("SortFile_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character"), function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath ){
return(new("SortFile_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams, outputFlag=outputFlag,outFilePath=outFilePath))
})
setMethod("SortFile_CLI", signature(inFilePath="character", inFileNames="character", cliParams="missing",
outputFlag="character", outFilePath="character"), function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath ){
cliParams = "-k1,1 -k2,2n"
return(new("SortFile_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams, outputFlag=outputFlag,outFilePath=outFilePath))
})
#' @title Generates the commands and possibly resulting files of linux sort command SortFile_CLI
#'
#' @param SortFile_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="SortFile_CLI"),function(object) {
if( length(getInFileNames(object)) > 1 ){
warning("More than one input file given, using the first one!")
}
inFN = getInFileNames(object)[1]
cmd1 = paste0("cd ",getInFilePath(object))
inFNtrimmed = sub("\\..+$","",inFN)
inFilending = sub( inFNtrimmed, "", inFN )
outFN = paste0( inFNtrimmed, getOutputFlag(object), inFilending)
cmd2 = paste0( "sort ", getCliParams(object), " ", file.path(getInFilePath(object), getInFileNames(object) ), " > ", file.path(getOutFilePath(object), outFN) )
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2))
return(res)
})
#--split Bowtie2_CLI
#################################################
# General generic function definitions that are implemented in several subclasses!
#################################################
#@include CLIApplication
#'@title Bowtie2_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{bowtieIndexFilePath \code{"character"}}
#' \item{\code{slot7}:}{matepairFileNames \code{"character"}}
#' }
#' @name Bowtie2_CLI-class
#' @export
setClass("Bowtie2_CLI", contains = "CLIApplication", representation(bowtieIndexFilePath="character", matepairFileNames="character") )
#' @title Accessor getBowtieIndexFilePath
#' @export
#' @docType methods
#' @return bowtieIndexFilePath
setGeneric("getBowtieIndexFilePath", function(object) standardGeneric("getBowtieIndexFilePath"))
setMethod("getBowtieIndexFilePath",signature(object="Bowtie2_CLI"),function(object) {
slot(object, "bowtieIndexFilePath")
})
#' @title Accessor getMatepairFileNames
#' @export
#' @docType methods
#' @return matepairFileNames
setGeneric("getMatepairFileNames", function(object){standardGeneric("getMatepairFileNames")})
setMethod("getMatepairFileNames",signature(object="Bowtie2_CLI"),function(object) {
slot(object, "matepairFileNames")
})
#' @title Constructor method for Bowtie2_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
setGeneric("Bowtie2_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath, matepairFileNames){standardGeneric("Bowtie2_CLI")})
setMethod("Bowtie2_CLI", signature(inFilePath="character", inFileNames="missing", cliParams="character",
outputFlag="character", outFilePath="character", bowtieIndexFilePath="character", matepairFileNames="missing"),
function(inFilePath, cliParams, outputFlag, outFilePath, bowtieIndexFilePath,matepairFileNames){
inFileNames = list.files(path = inFilePath, pattern = ".*\\.fastq$")
return(
new("Bowtie2_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath,matepairFileNames="")
)
})
setMethod("Bowtie2_CLI", signature(inFilePath="character", inFileNames="missing", cliParams="character",
outputFlag="character", outFilePath="character", bowtieIndexFilePath="character", matepairFileNames="character"),
function(inFilePath, cliParams, outputFlag, outFilePath, bowtieIndexFilePath,matepairFileNames){
inFileNames = list.files(path = inFilePath, pattern = ".*\\.fastq$")
return(
new("Bowtie2_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath,matepairFileNames=matepairFileNames)
)
})
setMethod("Bowtie2_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", bowtieIndexFilePath="character", matepairFileNames="missing"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath,matepairFileNames ){
return(
new("Bowtie2_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath, matepairFileNames="")
)
})
setMethod("Bowtie2_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", bowtieIndexFilePath="character", matepairFileNames="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath,matepairFileNames ){
return(
new("Bowtie2_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath, matepairFileNames=matepairFileNames)
)
})
#' @title Generates the commands and possibly resulting files/folders of Bowtie2
#'
#' @param Bowtie2_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="Bowtie2_CLI"),function(object) {
#USAGE: bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]
allFiles = getInFileNames(object)
cmd1 = paste0("cd ",getInFilePath(object))
allFilesOut = paste0( sub("\\.fastq$","",allFiles), getOutputFlag(object), ".fastq")
# dir.create(getOutFilePath(object))
cmd2 = paste0("mkdir ", getOutFilePath(object)) #if only executed in terminal!
if( getMatepairFileNames(object)[1] == "" ){
cmd3 = paste0("bowtie2 ", paste0(getCliParams(object),collapse=" "), " -x ", getBowtieIndexFilePath(object), " -U ", allFiles, " -S ",
file.path(getOutFilePath(object), allFilesOut) )
} else{
cmd3 = paste0("bowtie2 ", paste0(getCliParams(object),collapse=" "), " -x ", getBowtieIndexFilePath(object), " -1 ", allFiles,
" -2 ",getMatepairFileNames(object), " -S ", file.path(getOutFilePath(object), allFilesOut) )
}
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(allFilesOut), commands = c(cmd1, cmd2, cmd3))
return(res)
})
#--split Bowtie2TophatIon_CLI
#@include Bowtie2_CLI
#'@title Bowtie2TophatIon_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{bowtieIndexFilePath \code{"character"}}
#' \item{\code{slot7}:}{matepairFileNames \code{"character"}}
#' \item{\code{slot8}:}{outFileNames \code{"character"}}
#' \item{\code{slot9}:}{pathToPicardTools \code{"character"}}
#' \item{\code{slot9}:}{addNHTag \code{"character"}}
#' }
#' @name Bowtie2TophatIon_CLI-class
#' @export
setClass("Bowtie2TophatIon_CLI", contains = "Bowtie2_CLI", representation(outFileNames="character", pathToPicardTools="character", addNHTag="logical"),
prototype(outFileNames = "unmapped"))
# @title Validity method for Bowtie2TophatIon_CLI
# @name validityBowtie2TophatIon_CLI
# @rdname validityBowtie2TophatIon_CLI
# @export
# @docType methods
setValidity ("Bowtie2TophatIon_CLI",
function ( object ){
retval = NULL
if(length(getInFilePath(object)) > 1){ retval = "Multiple In File Paths (Tophat output directories are not allowed!)" }
if ( is.null(retval)){
return(TRUE)
}
else{
return(retval)
}
})
#' @title Constructor method for Bowtie2TophatIon_CLI
#' @export
#' @docType methods
setGeneric("Bowtie2TophatIon_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath,matepairFileNames,
outFileNames, pathToPicardTools, addNHTag){standardGeneric("Bowtie2TophatIon_CLI")})
setMethod("Bowtie2TophatIon_CLI", signature(inFilePath="character", inFileNames="missing", cliParams="missing",
outputFlag="character", outFilePath="missing", bowtieIndexFilePath="character", matepairFileNames="missing",
outFileNames="missing", pathToPicardTools="missing", addNHTag="logical"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath,matepairFileNames,outFileNames, pathToPicardTools, addNHTag){
warning("Options are locked and input file name is set to unmapped, outfile is set to bam mate pairs are not supported!")
if(missing(outFileNames)){outFileNames = "aligned"}
if(missing(pathToPicardTools)){pathToPicardTools = "/usr/local/applications/picard-tools-1.77/"}
if(missing(outFilePath)){outFilePath = inFilePath; warning("outFilePath is set to inFilePath")}
return(
new("Bowtie2TophatIon_CLI", inFilePath=inFilePath, inFileNames="unmapped", cliParams=c("--local","--very-sensitive-local","-p 8","--mm"),
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath, matepairFileNames="",
outFileNames = outFileNames, pathToPicardTools=pathToPicardTools, addNHTag = addNHTag)
)
})
setMethod("Bowtie2TophatIon_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", bowtieIndexFilePath="character", matepairFileNames="character",
outFileNames="character", pathToPicardTools="character", addNHTag="logical"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath,matepairFileNames,outFileNames, pathToPicardTools, addNHTag){
return(
new("Bowtie2TophatIon_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath, matepairFileNames=matepairFileNames,
outFileNames = outFileNames, pathToPicardTools=pathToPicardTools, addNHTag = addNHTag)
)
})
#' @title Accessor getOutFileNames
#' @export
#' @docType methods
#' @return outFileNames
setGeneric("getOutFileNames", function(object){standardGeneric("getOutFileNames")})
setMethod("getOutFileNames",signature(object="Bowtie2_CLI"),function(object) {
slot(object, "outFileNames")
})
#' @title Accessor getAddNHTag
#' @export
#' @docType methods
#' @return addNHTag
setGeneric("getAddNHTag", function(object){standardGeneric("getAddNHTag")})
setMethod("getAddNHTag",signature(object="Bowtie2_CLI"),function(object) {
slot(object, "addNHTag")
})
#' @title Accessor getPathToPicardTools
#' @export
#' @docType methods
#' @return pathToPicardTools
setGeneric("getPathToPicardTools", function(object){standardGeneric("getPathToPicardTools")})
setMethod("getPathToPicardTools",signature(object="Bowtie2_CLI"),function(object) {
slot(object, "pathToPicardTools")
})
#' @title Generates the commands and possibly resulting files/folders of Bowtie2 in combination with Tophat output for ion Torrent
#'
#' @param Bowtie2TophatIon_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="Bowtie2TophatIon_CLI"),function(object) {
#USAGE: bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]
#When Tophout2 results are created, bam2fastq is callled, then bowtie 2 is called, results are merged by picard tools MergeSamFiles
allFiles = getInFileNames(object)
inFP = getInFilePath(object)
cmd1 = paste0("cd ",inFP)
outFile = paste0( getOutFileNames(object), getOutputFlag(object), ".bam")
cmd2 = paste0("bam2fastq -o unmapped.fastq unmapped.bam")
cmd3 = paste0("bowtie2 ", paste0(getCliParams(object),collapse=" "), " -x ", getBowtieIndexFilePath(object), " -U ", "unmapped.fastq",
" | samtools view -uhS -F4 - | samtools sort - unmapped_remap")
if( getAddNHTag(object) ){
cmd3 = c(cmd3, paste0("samtools sort -n unmapped_remap.bam unmapped_remap_sn") )
cmd3 = c(cmd3, paste0( "python -c \"import bbcflib.mapseq; bbcflib.mapseq.add_nh_flag('",file.path( inFP,"unmapped_remap_sn.bam"),
"', '",file.path( inFP,"unmapped_remap.bam"),"')\"" ) )
}
cmd4 = paste0("java -jar ", file.path( getPathToPicardTools(object), "MergeSamFiles.jar"),
" USE_THREADING=true MSD=true AS=true I=accepted_hits.bam I=unmapped_remap.bam O=",file.path(getOutFilePath(object), outFile) )
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFile), commands = c(cmd1, cmd2, cmd3, cmd4))
return(res)
} )
#--split Tophat2_CLI
#@include CLIApplication
#'@title Tophat2_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{bowtieIndexFilePath \code{"character"}}
#' }
#' @name Tophat2_CLI-class
#' @export
setClass("Tophat2_CLI", contains = "CLIApplication", representation(bowtieIndexFilePath="character") )
#' @title Accessor getBowtieIndexFilePath Tophat2
#' @export
#' @docType methods
#' @return bowtieIndexFilePath
setMethod("getBowtieIndexFilePath",signature(object="Tophat2_CLI"),function(object) {
slot(object, "bowtieIndexFilePath")
})
#' @title Constructor method for Tophat2_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
setGeneric("Tophat2_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath,bowtieIndexFilePath){standardGeneric("Tophat2_CLI")})
setMethod("Tophat2_CLI", signature( inFilePath="character", inFileNames="missing", cliParams="character",
outputFlag="character", outFilePath="character",
bowtieIndexFilePath="character"),
function(inFilePath, cliParams, outputFlag, outFilePath, bowtieIndexFilePath){
inFileNames = list.files(path = inFilePath, pattern = ".*\\.fastq$")
return(
new("Tophat2_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath)
)
})
setMethod("Tophat2_CLI", signature( inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character",
bowtieIndexFilePath="character"),
function(inFilePath,inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath){
return(
new("Tophat2_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath)
)
})
#' @title Generates the commands and possibly resulting files/folders of Tophat2
#'
#' @param Tophat2_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="Tophat2_CLI"),function(object) {
# USAGE:
# tophat [options] <bowtie_index> <reads1[,reads2,...]> [reads1[,reads2,...]] \
# [quals1,[quals2,...]] [quals1[,quals2,...]]
#preparing input files
inFP = getInFilePath(object)
inFN = getInFileNames(object)
#preparing output files
sampleOutDir = paste0( paste0( sub("\\.fastq$","",inFN),getOutputFlag(object)) )
#generating the tophat base directory
outfilepath = getOutFilePath(object)
# dir.create(outfilepath)
# setwd(outfilepath)
cmd1 = paste("mkdir", outfilepath) #if only executed in terminal!
cmd2 = paste("cd ", outfilepath)
#generating the tophat command
cmd3 = paste0( "tophat2 ", paste0(getCliParams(object), collapse=" "),
" --output-dir ", file.path(file.path(getOutFilePath(object), sampleOutDir)), " ", getBowtieIndexFilePath(object), " ", file.path(inFP,inFN) )
#IN FILENAME UND BOWTIE INDEX PATH FEHLEN!
# tophat2 --num-threads 12 --keep-fasta-order --output-dir /home/simon/PHDStudies/RNA-Seq/IonProton/MSA_LusserWenning/SampleAnalysis/tophat-out_sampleAnalysis --GTF /home/simon/dbsOfflineUse/GTF_repos/Mus_musculus.GRCm38.78_mod.gtf /home/simon/dbsOfflineUse/MusMusculus/Mouse_mm10_fasta/bowtie2/mm10 /home/simon/PHDStudies/RNA-Seq/IonProton/MSA_LusserWenning/SampleAnalysis/sampleFastq_larger20.fastq
res = CmdGenResult(CLIApplication = object, OutResultReference = FoldersOutput(sampleOutDir), commands = c(cmd1, cmd2, cmd3))
return(res)
})
#--split Bowtie_CLI
#################################################
# General generic function definitions that are implemented in several subclasses!
# MUST BE PLACED AFTER Bowtie2TophatIon_CLI class!
#################################################
#@include Samtools_CLI,Bowtie2Tophation_CLI
#'@title Bowtie_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{bowtieIndexFilePath \code{"character"}}
#' \item{\code{slot7}:}{matepairFileNames \code{"character"}}
#' \item{\code{slot8}:}{addNHTag \code{"logical"}}
#' \item{\code{slot9}:}{outputPipeString \code{"character"}}
#' \item{\code{slot10}:}{outputFormat \code{"character"}}
#' }
#' @name Bowtie_CLI-class
#' @export
setClass("Bowtie_CLI", contains = "CLIApplication", representation(bowtieIndexFilePath="character", matepairFileNames="character",
addNHTag="logical", outputPipeString="character", outputFormat = "character") )
#' @title Accessor getBowtieIndexFilePath
#' @export
#' @docType methods
#' @return bowtieIndexFilePath
setMethod("getBowtieIndexFilePath",signature(object="Bowtie_CLI"),function(object) {
slot(object, "bowtieIndexFilePath")
})
#' @title Accessor getMatepairFileNames
#' @export
#' @docType methods
#' @return matepairFileNames
setMethod("getMatepairFileNames",signature(object="Bowtie_CLI"),function(object) {
slot(object, "matepairFileNames")
})
#' @title Accessor getAddNHTag
#' @export
#' @docType methods
#' @return addNHTag
setMethod("getAddNHTag",signature(object="Bowtie_CLI"),function(object) {
slot(object, "addNHTag")
})
#' @title Accessor getOutputPipeString
#' @export
#' @docType methods
#' @return outputPipeString
setGeneric("getOutputPipeString", function(object){standardGeneric("getOutputPipeString")})
setMethod("getOutputPipeString",signature(object="Bowtie_CLI"),function(object) {
slot(object, "outputPipeString")
})
#' @title Accessor getOutputFormat
#' @export
#' @docType methods
#' @return outputFormat
setMethod("getOutputFormat", signature(object="Bowtie_CLI"), function(object){
slot(object, "outputFormat")
})
#' @title Constructor method for Bowtie_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
setGeneric("Bowtie_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath, matepairFileNames,
addNHTag, outputPipeString, outputFormat){standardGeneric("Bowtie_CLI")})
setMethod("Bowtie_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", bowtieIndexFilePath="character",
matepairFileNames="missing", addNHTag="logical", outputPipeString="character", outputFormat="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath,matepairFileNames, addNHTag, outputPipeString, outputFormat ){
return(
new("Bowtie_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath, matepairFileNames="",
addNHTag=addNHTag, outputPipeString=outputPipeString, outputFormat=outputFormat)
)
})
setMethod("Bowtie_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", bowtieIndexFilePath="character",
matepairFileNames="character", addNHTag="logical", outputPipeString="character", outputFormat="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath,matepairFileNames, addNHTag, outputPipeString, outputFormat ){
return(
new("Bowtie_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath,
matepairFileNames=matepairFileNames, addNHTag=addNHTag, outputPipeString=outputPipeString, outputFormat=outputFormat)
)
})
#' @title Generates the commands and possibly resulting files/folders of Bowtie2
#'
#' @param Bowtie_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="Bowtie_CLI"),function(object) {
#USAGE: bowtie [options]* <ebwt> {-1 <m1> -2 <m2> | --12 <r> | <s>} [<hit>]
#bowtie -qSya -n 1 -p 3 --chunkmbs 1024 --best -l 28 -m 100 --phred64-quals --strata /home/simon/dbsOfflineUse/apartdbs/mouse_mm9/genome test_trimmed.fastq | samtools view -uhS -F4 - | samtools sort - /tmp/mapped
#This command -l 18 nt seed, -n 1 in seed 1 mismatch (seed generated from left), -m maximum 100 alignments reported (not randomly chosen if more -> would be -M 100)
#the maximum 100 alignments are chosen from the best stratum of the aligner, -p n number of processor cores, outputPipeString is optional here
inFN = getInFileNames(object)
cmd1 = paste0("cd ",getInFilePath(object))
#trim the file extension to create the outputFileName
inFNtrimmed = sub("\\..+$","",inFN)
outFN = paste0( inFNtrimmed, getOutputFlag(object),".", getOutputFormat(object))
outFNtrimmed = paste0( inFNtrimmed, getOutputFlag(object))
# create the output directory
cmd2 = paste0("mkdir ", getOutFilePath(object)) #if only executed in terminal!
cmd2 = c(cmd2,paste0("cd ",getOutFilePath(object)))
#Executing bowtie
inFileNames = paste0( file.path(getInFilePath(object),inFN), collapse=",")
if( getMatepairFileNames(object)[1] == "" ){
cmd3 = paste0("bowtie ", paste0(getCliParams(object),collapse=" "), " ", getBowtieIndexFilePath(object), " ", inFileNames, " ",
" ", getOutputPipeString(object), " ", file.path(getOutFilePath(object), outFNtrimmed) )
} else{
cmd3 = paste0("bowtie ", paste0(getCliParams(object),collapse=" "), " ", getBowtieIndexFilePath(object), " -1 ", inFileNames,
" -2 ",paste0( getMatepairFileNames(object), collapse=","), " ", getOutputPipeString(object), " ", file.path(getOutFilePath(object), outFNtrimmed) )
}
if( getAddNHTag(object) ){
sortedFN = paste0(file.path(getOutFilePath(object), outFNtrimmed),"_sn")
cmd3 = c(cmd3, paste0("samtools sort -n ",file.path(getOutFilePath(object), outFN), " ", sortedFN ) )
cmd3 = c(cmd3, paste0( "python -c \"import bbcflib.mapseq; bbcflib.mapseq.add_nh_flag('",paste0(sortedFN,".",getOutputFormat(object)),"', '",file.path(getOutFilePath(object), outFN),"')\"" ) )
cmd3 = c(cmd3, paste0("rm ", paste0(sortedFN,".",getOutputFormat(object)) ) )#Another sorting so that the sorted file contains the flag too
}
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2, cmd3))
return(res)
})
#--split MultiIntersectBed_CLI
#@include CLIApplication
#'@title MultiIntersectBed_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{sortInFiles \code{"logical"}}
#' \item{\code{slot7}:}{requireStrandness \code{"logical"}}
#' \item{\code{slot8}:}{strandColumn \code{"numeric"}}
#' \item{\code{slot9}:}{filterConditions \code{"character"}}
#' }
#' @name MultiIntersectBed_CLI-class
#' @export
setClass("MultiIntersectBed_CLI", contains = "CLIApplication", representation(sortInFiles="logical", requireStrandness="logical",
strandColumn="numeric", filterConditions="character"))
#' @title Constructor method for MultiIntersectBed_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
setGeneric("MultiIntersectBed_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, sortInFiles,requireStrandness, strandColumn,filterConditions){standardGeneric("MultiIntersectBed_CLI")})
setMethod("MultiIntersectBed_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character",sortInFiles="logical",requireStrandness="logical",
strandColumn="numeric", filterConditions="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath,sortInFiles,requireStrandness, strandColumn, filterConditions ){
return(new("MultiIntersectBed_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, sortInFiles=sortInFiles,
requireStrandness=requireStrandness, strandColumn=strandColumn, filterConditions=filterConditions))
})
setMethod("MultiIntersectBed_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character",sortInFiles="logical",requireStrandness="logical",
strandColumn="missing", filterConditions="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath,sortInFiles,requireStrandness, strandColumn, filterConditions ){
strandColumn = 0
return(new("MultiIntersectBed_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, sortInFiles=sortInFiles,
requireStrandness=requireStrandness, strandColumn=strandColumn, filterConditions=filterConditions))
})
#' @title Accessor getSortInFiles
#' @export
#' @docType methods
#' @return sortInFiles
setGeneric("getSortInFiles", function(object) standardGeneric("getSortInFiles"))
setMethod("getSortInFiles",signature(object="MultiIntersectBed_CLI"),function(object) {
slot(object, "sortInFiles")
})
#' @title Accessor getRequireStrandness
#' @export
#' @docType methods
#' @return requireStrandness
setGeneric("getRequireStrandness", function(object) standardGeneric("getRequireStrandness"))
setMethod("getRequireStrandness",signature(object="MultiIntersectBed_CLI"),function(object) {
slot(object, "requireStrandness")
})
#' @title Accessor getStrandColumn
#' @export
#' @docType methods
#' @return strandColumn
setGeneric("getStrandColumn", function(object) standardGeneric("getStrandColumn"))
setMethod("getStrandColumn",signature(object="MultiIntersectBed_CLI"),function(object) {
slot(object, "strandColumn")
})
#' @title Accessor getFilterConditions
#' @export
#' @docType methods
#' @return filterConditions
setGeneric("getFilterConditions", function(object) standardGeneric("getFilterConditions"))
setMethod("getFilterConditions",signature(object="MultiIntersectBed_CLI"),function(object) {
slot(object, "filterConditions")
})
#' @title Generates the commands and possibly resulting files/folders of Cutadapt
#'
#' @param MultiIntersectBed_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="MultiIntersectBed_CLI"),function(object) {
#bedtools multiinter [OPTIONS] -i FILE1 FILE2 .. FILEn
if( length(getInFilePath(object)) > 1 & length(getInFilePath(object)) != length(getInFileNames(object)) ){
warning("Either one file path is given, containnig all files, or the file path vector must match the filename vector in length!")
}
inFN = getInFileNames(object)
inFNtrimmed = sub("\\..+$","",inFN)
inFilending = sub( inFNtrimmed[1], "", inFN[1] )
outFN = paste0( getOutputFlag(object), inFilending)
if( getSortInFiles(object) ){
message(" ... sorting inputFiles ... ")
cmd1 = mapply( function(fp,fn) {
tmpFileName = "testTmp321"
cmdCurr = paste0("\nsort -k1,1 -k2,2n ",file.path(fp,fn), " > ", file.path(fp,tmpFileName) )
cmdCurr = c(cmdCurr, paste0("cat ", file.path(fp,tmpFileName), " > ", file.path(fp,fn) ))
cmdCurr = c(cmdCurr, paste0("rm ", file.path(fp,tmpFileName) ) )
return( cmdCurr )
}, getInFilePath(object), getInFileNames(object) )
} else{
cmd1 = ""
}
if(getRequireStrandness(object)){
if( length(getStrandColumn(object)) == 0 | getStrandColumn(object) < 1 ){
stop("Column where the strand is defined in the Bed file has to be specified and needs to be greater than 0 when strandness is required!!")
}
tmpFileName = "testTmp321"
message(" ... splitting input Files by strand ... ")
cmd1 = c( cmd1, mapply( function(fp,fn) {
cmdCurr = paste0("cat ", file.path(fp,fn), " | ", "awk \'{if($",getStrandColumn(object)," == \"-\") print }\' > " , file.path(fp,paste0("minus_",fn)) )
cmdCurr = c( cmdCurr, paste0("cat ", file.path(fp,fn), " | ", "awk \'{if($",getStrandColumn(object)," == \"+\") print }\' > " , file.path(fp,paste0("plus_",fn)) ) )
return( cmdCurr )
}, getInFilePath(object), getInFileNames(object) ) )
cmd2 = paste0( "bedtools multiinter ",getCliParams(object), " -i ", paste0( file.path(getInFilePath(object), paste0("plus_",getInFileNames(object)) ),collapse=" "), " > ",
file.path(getOutFilePath(object), paste0("plus_",outFN) ) )
cmd2 = c(cmd2, paste0( "bedtools multiinter ",getCliParams(object), " -i ", paste0( file.path(getInFilePath(object), paste0("minus_",getInFileNames(object)) ),collapse=" "), " > ",
file.path(getOutFilePath(object), paste0("minus_",outFN) ) ) )
#Adding the minus sign to the multiinter file
cmd2 = c(cmd2, paste0( "awk -Ft \'BEGIN {OFS=\"\\t\"}{print $0, \"-\"}\' ", file.path(getOutFilePath(object), paste0("minus_",outFN) ), " > ", file.path(getOutFilePath(object),tmpFileName) ) )
cmd2 = c(cmd2, paste0("cat ", file.path(getOutFilePath(object),tmpFileName), " > ", file.path(getOutFilePath(object),paste0("minus_",outFN)) ))
cmd2 = c(cmd2, paste0("rm ", file.path(getOutFilePath(object),tmpFileName) ) )
cmd2 = c(cmd2, paste0( "awk -Ft \'BEGIN {OFS=\"\\t\"}{print $0, \"+\"}\' ", file.path(getOutFilePath(object), paste0("plus_",outFN) ), " > ", file.path(getOutFilePath(object),tmpFileName) ) )
cmd2 = c(cmd2, paste0("cat ", file.path(getOutFilePath(object),tmpFileName), " > ", file.path(getOutFilePath(object),paste0("plus_",outFN)) ))
cmd2 = c(cmd2, paste0("rm ", file.path(getOutFilePath(object),tmpFileName) ) )
cmd2 = c(cmd2, paste0( "cat ", file.path(getOutFilePath(object), paste0("plus_",outFN)), " ",
file.path(getOutFilePath(object), paste0("minus_",outFN)),
" | awk \'/./\' > ", file.path(getOutFilePath(object), outFN) ) ) #also removing blank lines from the file
#sorting again
cmd2 = c(cmd2, paste0("\nsort -k1,1 -k2,2n ",file.path(getOutFilePath(object), outFN), " > ", file.path(getOutFilePath(object),tmpFileName) ))
cmd2 = c(cmd2, paste0("cat ", file.path(getOutFilePath(object),tmpFileName), " > ", file.path(getOutFilePath(object),outFN) ))
cmd2 = c(cmd2, paste0("rm ", file.path(getOutFilePath(object),tmpFileName) ) )
} else{
cmd2 = paste0( "bedtools multiinter ",getCliParams(object), " -i ", paste0( file.path(getInFilePath(object), getInFileNames(object) ),collapse=" "), " > ",
file.path(getOutFilePath(object),outFN ) )
}
if( length(getFilterConditions(object)) > 1 ){
generateFilterCmd = function(conditions, inputFileName, inputFilePath){
#starting at column 6 in multiIntersectBed file
conditions_u = unique(conditions)
idx_conditions = lapply( conditions_u, function(x){which(conditions == x)})
conditionStr = paste0( sapply( idx_conditions, function(x){
if( length(x) > 1){
paste0( paste0( "$",x, " > 0", sep=" && " ), collapse="")
} else{
paste0( "$",x, " > 0")
}
} ), collapse=" || ")
cmd1 = paste0( "\ncat ", file.path(inputFilePath,inputFileName), " > ", file.path(inputFilePath,paste0("UnFiltered_",inputFileName )))
cmd2 = paste0( "\ncat ", file.path(inputFilePath, paste0("UnFiltered_", inputFileName)),
" | awk \'{if( ", conditionStr,") print}\' > ",
file.path(inputFilePath,inputFileName), "\n" )
return(c(cmd1,cmd2))
}
cmd3 = generateFilterCmd(getFilterConditions(object),outFN, getOutFilePath(object))
} else{
cmd3 = ""
}
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2, cmd3))
return(res)
})
#--split MultiIntersectBed_perl_CLI
#@include IntersectBed_CLI
#'@title MultiIntersectBed_perl_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{groupVect \code{"numeric"}}
#' \item{\code{slot7}:}{withinGroupTH \code{"numeric"}}
#' \item{\code{slot8}:}{outFileName \code{"character"}}
#' \item{\code{slot9}:}{perlPath \code{"character"}}
#' }
#' @name MultiIntersectBed_perl_CLI-class
#' @export
setClass("MultiIntersectBed_perl_CLI", contains = "CLIApplication", representation(groupVect="numeric", withinGroupTH="numeric", outFileName="character", perlPath="character"))
#' @title Constructor method for MultiIntersectBed_perl_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
# setGeneric("MultiIntersectBed_perl_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, groupVect,withinGroupTH,outFileName){standardGeneric("MultiIntersectBed_perl_CLI")})
setGeneric("MultiIntersectBed_perl_CLI", function(inFilePath, inFileNames, outputFlag, outFilePath, outFileName, ...){standardGeneric("MultiIntersectBed_perl_CLI")})
setMethod("MultiIntersectBed_perl_CLI", signature(inFilePath="character", inFileNames="character",
outputFlag="character", outFilePath="character",outFileName="character"),
function(inFilePath, inFileNames, outputFlag, outFilePath, outFileName, cliParams="",withinGroupTH=0, groupVect=numeric(),perlPath=""){
return(new("MultiIntersectBed_perl_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, groupVect=groupVect,withinGroupTH=withinGroupTH, outFileName=outFileName, perlPath=perlPath ))
})
#
# setMethod("MultiIntersectBed_perl_CLI", signature(inFilePath="character", inFileNames="character", cliParams="missing",
# outputFlag="character", outFilePath="character",groupVect="numeric",withinGroupTH="numeric",outFileName="character"),
# function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, groupVect, withinGroupTH, outFileName ){
# cliParams=""
# return(new("MultiIntersectBed_perl_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams="",
# outputFlag=outputFlag, outFilePath=outFilePath, groupVect=groupVect,withinGroupTH=withinGroupTH, outFileName=outFileName ))
# })
# setMethod("MultiIntersectBed_perl_CLI", signature(inFilePath="character", inFileNames="character", cliParams="missing",
# outputFlag="character", outFilePath="character",groupVect="numeric",withinGroupTH="missing",outFileName="character"),
# function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, groupVect, withinGroupTH, outFileName ){
# cliParams=""
# withinGroupTH = 0
# return(new("MultiIntersectBed_perl_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams="",
# outputFlag=outputFlag, outFilePath=outFilePath, groupVect=groupVect,withinGroupTH=withinGroupTH, outFileName=outFileName ))
# })
# setMethod("MultiIntersectBed_perl_CLI", signature(inFilePath="character", inFileNames="character", cliParams="missing",
# outputFlag="character", outFilePath="character",groupVect="missing",withinGroupTH="numeric",outFileName="character"),
# function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, groupVect,withinGroupTH, outFileName ){
# groupVect = numeric()
# cliParams=""
# return(new("MultiIntersectBed_perl_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
# outputFlag=outputFlag, outFilePath=outFilePath, groupVect=groupVect, withinGroupTH=withinGroupTH, outFileName=outFileName ))
# })
# setMethod("MultiIntersectBed_perl_CLI", signature(inFilePath="character", inFileNames="character", cliParams="missing",
# outputFlag="character", outFilePath="character",groupVect="missing",withinGroupTH="missing",outFileName="character"),
# function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, groupVect,withinGroupTH, outFileName ){
# groupVect = numeric()
# cliParams=""
# withinGroupTH = 0
# return(new("MultiIntersectBed_perl_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
# outputFlag=outputFlag, outFilePath=outFilePath, groupVect=groupVect, withinGroupTH=withinGroupTH, outFileName=outFileName ))
# })
#' @title Accessor getGroupVect
#' @export
#' @docType methods
#' @return groupVect
setGeneric("getGroupVect", function(object){standardGeneric("getGroupVect")})
setMethod("getGroupVect",signature(object="MultiIntersectBed_perl_CLI"),function(object) {
slot(object, "groupVect")
})
#' @title Accessor getPerlPath
#' @export
#' @docType methods
#' @return perlPath
setGeneric("getPerlPath", function(object){standardGeneric("getPerlPath")})
setMethod("getPerlPath",signature(object="MultiIntersectBed_perl_CLI"),function(object) {
slot(object, "perlPath")
})
#' @title Accessor getWithinGroupTH
#' @export
#' @docType methods
#' @return withinGroupTH
setGeneric("getWithinGroupTH", function(object){standardGeneric("getWithinGroupTH")})
setMethod("getWithinGroupTH",signature(object="MultiIntersectBed_perl_CLI"),function(object) {
slot(object, "withinGroupTH")
})
#' @title Accessor getOutFileName
#' @export
#' @docType methods
#' @return outFileName
setMethod("getOutFileName",signature(object="MultiIntersectBed_perl_CLI"),function(object) {
slot(object, "outFileName")
})
#' @title Generates the commands and file for MultiIntersectBed
#'
#' @param MultiIntersectBed_perl_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="MultiIntersectBed_perl_CLI"),function(object) {
#bedtools multiinter [OPTIONS] -i FILE1 FILE2 .. FILEn
if( length(getInFilePath(object)) > 1 & length(getInFilePath(object)) != length(getInFileNames(object)) ){
warning("Either one file path is given, containnig all files, or the file path vector must match the filename vector in length!")
}
if( length(getGroupVect(object)) > 1 & length(getGroupVect(object)) != length(getInFileNames(object)) ){
warning("Either one file path is given, containnig all files, or the group vector must match the filename vector in length!")
}
inFN = getInFileNames(object)
inFNtrimmed = sub("\\..+$","",inFN)
inFilending = sub( inFNtrimmed[1], "", inFN[1] )
outFN = paste0( getOutFileName(object), inFilending)
cmd1 = paste0("cd ", getOutFilePath(object))
perlApp = ifelse(getPerlPath(object) == "", "perl", file.path(getPerlPath(object), "perl"))
if(length(getGroupVect(object)) == 0){
cmd2 = paste0( perlApp," ",system.file("data/multiIntersectBed_helper.pl",package="CLIHelperPackage"),
" -o ", file.path(getOutFilePath(object),outFN ),
" -w ", getWithinGroupTH(object),
" -i ", paste0( file.path(getInFilePath(object), getInFileNames(object) ),collapse=" ") )
} else{
cmd2 = paste0( perlApp," ",system.file("data/multiIntersectBed_helper.pl",package="CLIHelperPackage"),
" -o ", file.path(getOutFilePath(object),outFN ),
" -w ", getWithinGroupTH(object),
" -g ", paste0(getGroupVect(object),collapse=" "),
" -i ", paste0( file.path(getInFilePath(object), getInFileNames(object) ),collapse=" ") )
}
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2))
return(res)
})
#--split RNAStar_CLI
#@include CLIApplication
#'@title RNAStar_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{genomeIndexFilePath \code{"character"}}
#' \item{\code{slot7}:}{filterSam \code{"logical"}}
#' \item{\code{slot8}:}{outputFormat \code{"character"}}
#' }
#' @name RNAStar_CLI-class
#' @export
setClass("RNAStar_CLI", contains = "CLIApplication", representation(genomeIndexFilePath="character", filterSam="logical", outputFormat="character") )
#' @title Accessor genomeIndexFilePath
#' @export
#' @docType methods
#' @return genomeIndexFilePath
setGeneric("getGenomeIndexFilePath", function(object) standardGeneric("getGenomeIndexFilePath"))
setMethod("getGenomeIndexFilePath",signature(object="RNAStar_CLI"),function(object) {
slot(object, "genomeIndexFilePath")
})
#' @title Accessor getOutputFormat already defined in Samtools
#' @export
#' @docType methods
#' @return outputFormat
setMethod("getOutputFormat",signature(object="RNAStar_CLI"),function(object) {
slot(object, "outputFormat")
})
#' @title Accessor filterSam
#' @export
#' @docType methods
#' @return getFilterSam
setGeneric("getFilterSam", function(object) standardGeneric("getFilterSam"))
setMethod("getFilterSam",signature(object="RNAStar_CLI"),function(object) {
slot(object, "filterSam")
})
#' @title Constructor method for RNAStar_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
setGeneric("RNAStar_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath,genomeIndexFilePath,filterSam, outputFormat){standardGeneric("RNAStar_CLI")})
setMethod("RNAStar_CLI", signature( inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character",
genomeIndexFilePath="character", filterSam="logical", outputFormat="character"),
function(inFilePath,inFileNames, cliParams, outputFlag, outFilePath, genomeIndexFilePath,filterSam, outputFormat){
return(
new("RNAStar_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, genomeIndexFilePath=genomeIndexFilePath,filterSam=filterSam, outputFormat=outputFormat)
)
})
#' @title Generates the commands and possibly resulting files/folders of Tophat2
#'
#' @param RNAStar_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="RNAStar_CLI"),function(object) {
# USAGE:
# STAR --genomeDir <Directory with the Genome Index> --runThreadN <# cpus> --readFilesIn <FASTQ file> --outFileNamePrefix <OutputPrefix>
if(length(getInFileNames(object)) > 1){
stop("Only one fasta file per call, if more calls please use option --genomeLoad LoadAndKeep which will keep the index file in the memory")
}
#preparing input files
inFP = getInFilePath(object)
inFN = getInFileNames(object)
#preparing output files
sampleOutDir = paste0( paste0( sub("\\.fastq$","",inFN),getOutputFlag(object)) )
#generating the tophat base directory
outfilepath = getOutFilePath(object)
if( getOutputFormat(object) == "bam" ){
outFileName = paste0(getOutputFlag(object), "Aligned.out.bam")
} else{
outFileName = paste0(getOutputFlag(object), "Aligned.out.sam")
outFileName_filt = paste0(getOutputFlag(object), "Aligned.out.filtered.sam")
}
# dir.create(outfilepath)
# setwd(outfilepath)
cmd1 = paste("mkdir", outfilepath) #if only executed in terminal!
cmd2 = paste("cd ", outfilepath)
#generating the tophat command
cmd3 = paste0( "STAR --genomeDir ",getGenomeIndexFilePath(object)," --readFilesIn ",file.path(inFP,inFN),
" --outFileNamePrefix ",getOutputFlag(object), " ", paste0(getCliParams(object), collapse=" ") )
#" --runThreadN 6 --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1 --clip3pAdapterSeq ATCACCGACTGCCCATAGAGAGGCTGAGAC --clip3pAdapterMMp 0.1 --outFilterMultimapNmax 100"
#(>=16b matched to the genome, number of mismatches <= 5% of mapped length, i.e. 0MM for 16-19b, 1MM for 20-39b etc, splicing switched off). will also trim by IonProton 3pAdapter obtained from Martina. If more than 100 matches in the genome - filter out reads!
#After running, filtering: awk script will filter out all alignments that are trimmed by more than 1 base from the 5' end!
cmd4 = ""
if(getFilterSam(object) & getOutputFormat(object) != "bam"){
cmd4 = paste("cd ", outfilepath)
cmd5 = paste0( "awk '{S=0; split($6,C,/[0-9]*/); n=split($6,L,/[NMSID]/);
if (and($2,0x10)>0 && C[n]==\"S\") {S=L[n-1]} else if (and($2,0x10)==0 && C[2]==\"S\") {S=L[1]}; if (S<=1) print }' ",outFileName," > ",outFileName_filt )
cmd6 = paste0( "rm ",outFileName )#removing the unfiltered file
cmd7 = paste0( "mv ", outFileName_filt, " ", outFileName) #renaming the file
cmd3 = c(cmd3, cmd4, cmd5, cmd6, cmd7)
}
if( getOutputFormat(object) != "bam" ){
outBamFN = paste0(sub(".sam$","",outFileName ),".bam")
#Writing sam to bam file
cmd4 = paste0( "samtools view -Sb ",outFileName," > ",outBamFN)
cmd4 = c(cmd4, paste0("rm ",outFileName) )
} else{
outBamFN = outFileName
}
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outBamFN) , commands = c(cmd1, cmd2, cmd3, cmd4))
return(res)
})
SimonSchafferer/CLIHelperPackage documentation built on May 9, 2019, 1:32 p.m.
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#--split CLIApplication
#'@title CLIApplication Virtual Class
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' }
#' @name CLIApplication-class
#' @export
setClass("CLIApplication", representation(inFilePath = "character",
inFileNames = "character",
cliParams = "character",
outFilePath = "character",
outputFlag = "character",
"VIRTUAL"))
#' @title Generates the commands and possibly resulting files/folders
#' @param CLIApplication
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setGeneric("generateCommandResult", function( object ) {
value = standardGeneric("generateCommandResult")
if( !is(value, "CmdGenResult") )
stop("Return Value must be CmdGenResult!")
value
})
#' @title Accessor getInFilePath
#' @export
#' @docType methods
#' @return inFilePath
setGeneric("getInFilePath", function(object) standardGeneric("getInFilePath"))
setMethod("getInFilePath",signature(object="CLIApplication"),function(object) {
slot(object, "inFilePath")
})
#' @title Accessor getInFileNames
#' @export
#' @docType methods
#' @return inFileNames
setGeneric("getInFileNames", function(object) standardGeneric("getInFileNames"))
setMethod("getInFileNames",signature(object="CLIApplication"),function(object) {
slot(object, "inFileNames")
})
#' @title Accessor getCliParams
#' @export
#' @docType methods
#' @return cliParams
setGeneric("getCliParams", function(object) standardGeneric("getCliParams"))
setMethod("getCliParams",signature(object="CLIApplication"),function(object) {
slot(object, "cliParams")
})
#' @title Accessor getOutFilePath
#' @export
#' @docType methods
#' @return outFilePath
setGeneric("getOutFilePath", function(object) standardGeneric("getOutFilePath"))
setMethod("getOutFilePath",signature(object="CLIApplication"),function(object) {
slot(object, "outFilePath")
})
#' @title Accessor getOutputFlag
#' @export
#' @docType methods
#' @return outputFlag
setGeneric("getOutputFlag", function(object) standardGeneric("getOutputFlag"))
setMethod("getOutputFlag",signature(object="CLIApplication"),function(object) {
slot(object, "outputFlag")
})
#--split OutResultReference
#'@title OutResultReference Virtual Class
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{outResultName \code{"character"}}
#' }
#' @name OutResultReference-class
#' @export
setClass("OutResultReference", representation(outResultName = "character", "VIRTUAL"))
#' @title Accessor getOutResultName
#' @export
#' @docType methods
#' @return outResultName
setGeneric("getOutResultName", function(object){standardGeneric("getOutResultName")})
setMethod("getOutResultName",signature(object="OutResultReference"),function(object) {
slot(object, "outResultName")
})
#--split FilesOutput
#@include OutResultReference
#'@title FilesOutput
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' }
#' @name FilesOutput-class
#' @export
setClass("FilesOutput", contains = "OutResultReference")
#--split FoldersOutput
#@include OutResultReference
#'@title FoldersOutput
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' }
#' @name FoldersOutput-class
#' @export
setClass("FoldersOutput", contains = "OutResultReference")
#' @title Constructor method for FoldersOutput
#' @param outResultName
#' @export
#' @docType methods
#' @return \code{"FoldersOutput"}
FoldersOutput = function(outResultName){
return( new("FoldersOutput", outResultName=outResultName) )
}
#' @title Constructor method for FilesOutput
#' @param outResultName
#' @export
#' @docType methods
#' @return \code{"FilesOutput"}
FilesOutput = function(outResultName){
return( new("FilesOutput", outResultName=outResultName) )
}
#' @title Constructor (factory) for OutResultReference
#' @param outResultName
#' @export
#' @docType methods
#' @return \code{OutResultReference} implementation
OutResultReference = function(outResultName){
if( file.exists(outResultName) ){
if( length(list.files(outResultName)) == 0 ){
return( FilesOutput(outResultName) )
} else{
return( FoldersOutput(outResultName) )
}
} else{
stop("Not a file or folder!")
}
}
#--split CmdGenResult
#'@title CmdGenResult
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{CLIApplication \code{"CLIApplication"}}
#' \item{\code{slot2}:}{OutResultReference \code{"OutResultReference"}}
#' \item{\code{slot3}:}{commands \code{"character"}}
#' }
#' @name CmdGenResult-class
#' @export
setClass( "CmdGenResult", representation( CLIApplication="CLIApplication",
OutResultReference="OutResultReference",
commands="character" ) )
setValidity ("CmdGenResult",
function ( object ){
retval = NULL
if ( is.null(retval)){
return(TRUE)
}
else{
return(retval)
}
})
#' @title Accessor CLIApplication
#' @export
#' @docType methods
#' @return CLIApplication
setGeneric("getCLIApplication", function(object) standardGeneric("getCLIApplication"))
setMethod("getCLIApplication",signature(object="CmdGenResult"),function(object) {
slot(object, "CLIApplication")
})
#' @title Accessor getOutResultReference
#' @export
#' @docType methods
#' @return OutResultReference
setGeneric("getOutResultReference", function(object) standardGeneric("getOutResultReference"))
setMethod("getOutResultReference",signature(object="CmdGenResult"),function(object) {
slot(object, "OutResultReference")
})
#' @title Accessor getCommands
#' @export
#' @docType methods
#' @return commands
setGeneric("getCommands", function(object) standardGeneric("getCommands"))
setMethod("getCommands",signature(object="CmdGenResult"),function(object) {
slot(object, "commands")
})
#' @title Accessor getCommandLog
#' @export
#' @docType methods
#' @return commands formatted
setGeneric("getCommandLog", function(object) standardGeneric("getCommandLog"))
setMethod("getCommandLog",signature(object="CmdGenResult"),function(object) {
paste0(paste0( getCommands(object),collapse="\n"), "\n")
})
#' @title Constructor method for CmdGenResult
#' @param CLIApplication
#' @param OutResultReference
#' @param commands
#' @export
#' @docType methods
#' @return \code{"CmdGenResult"}
CmdGenResult = function(CLIApplication,OutResultReference,commands ){
return( new("CmdGenResult",CLIApplication=CLIApplication,OutResultReference=OutResultReference,commands=commands) )
}
#' @title Executes the commands of a executeCommandResult object
#' @param \code{"CmdGenResult"}
#' @export
#' @docType methods
setGeneric("executeCommandResult", function(object, ...) {
standardGeneric("executeCommandResult") })
#' @title Executes the commands of a executeCommandResult object
#' @param \code{"CmdGenResult"}
#' @param \code{"testing"} boolean testing if true - command is not executed
#' @export
#' @docType methods
setMethod("executeCommandResult",signature(object="CmdGenResult"), function(object, testing=FALSE, useTee=TRUE) {
# message( paste0("Executing command:\n", getCommandLog(object)) )
logs = lapply( getCommands(object), function(x){
#setting the directory to the InputFilePath
currWD = getwd()
message( paste0("Executing command:\n", x) )
log = tryCatch({
if(!testing){
if(!useTee){
setwd(getInFilePath(getCLIApplication(object = object)))
cmdRes = system(x,intern = TRUE, ignore.stdout = FALSE, ignore.stderr = FALSE)
return(cmdRes)
} else{
setwd(getInFilePath(getCLIApplication(object = object)))
logFile = tempfile()
system(paste0(x," 2>&1 | tee ",logFile),intern = TRUE, ignore.stdout = FALSE, ignore.stderr = FALSE)
return( readLines(logFile) )
}
} else{
message("Testing ... command is not executed!")
return(x)
}
}, warning = function(w){
warning(w)
}, error = function(e){
paste0("Error when executing code ", e)
}, finally = {
setwd( currWD )
})
return(log)
})
return( CmdGenResultExec(cmdGenResult=object, execLog=logs))
})
#--split CmdGenResultExec
#'@title CmdGenResultExec
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{cmdGenResult \code{"CmdGenResult"}}
#' \item{\code{slot2}:}{execLog \code{"execLog"}}
#' }
#' @name CmdGenResultExec-class
#' @export
setClass( "CmdGenResultExec", representation(cmdGenResult="CmdGenResult", execLog="list" ) )
#' @title Constructor method for CmdGenResultExec
#' @param CmdGenResult
#' @param execLog
#' @export
#' @docType methods
#' @return \code{"CmdGenResultExec"}
CmdGenResultExec = function(cmdGenResult, execLog){
return( new("CmdGenResultExec",cmdGenResult=cmdGenResult,execLog=execLog) )
}
#' @title Accessor getCmdGenResult
#' @export
#' @docType methods
#' @return getCmdGenResult
setGeneric("getCmdGenResult", function(object) standardGeneric("getCmdGenResult"))
setMethod("getCmdGenResult",signature(object="CmdGenResultExec"),function(object) {
slot(object, "cmdGenResult")
})
#' @title Accessor getExecLog
#' @export
#' @docType methods
#' @return execLog
setGeneric("getExecLog", function(object) standardGeneric("getExecLog"))
setMethod("getExecLog",signature(object="CmdGenResultExec"),function(object) {
slot(object, "execLog")
})
#' @title Accessor getExecLogFormatted
#' @export
#' @docType methods
#' @return execLog formatted
setGeneric("getExecLogFormatted", function(object) standardGeneric("getExecLogFormatted"))
setMethod("getExecLogFormatted",signature(object="CmdGenResultExec"),function(object) {
tmp = lapply( getExecLog(object), function(x){
paste0(x,collapse="\n")
} )
return( paste0(unlist(tmp) ,collapse="\n\n") )
})
#--split Cutadapt_CLI
#@include CLIApplication
#'@title Cutadapt_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' }
#' @name Cutadapt_CLI-class
#' @export
setClass("Cutadapt_CLI", contains = "CLIApplication")
#' @title Constructor method for Cutadapt_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
setGeneric("Cutadapt_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath){standardGeneric("Cutadapt_CLI")})
setMethod("Cutadapt_CLI", signature(inFilePath="character", inFileNames="missing", cliParams="character",
outputFlag="character", outFilePath="character"), function(inFilePath, cliParams, outputFlag, outFilePath){
inFileNames = list.files(path = inFilePath, pattern = ".*\\.fastq$")
return(new("Cutadapt_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams, outputFlag=outputFlag,outFilePath=outFilePath))
})
setMethod("Cutadapt_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character"), function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath ){
return(new("Cutadapt_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams, outputFlag=outputFlag,outFilePath=outFilePath))
})
#' @title Generates the commands and possibly resulting files/folders of Cutadapt
#'
#' @param Cutadapt_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="Cutadapt_CLI"),function(object) {
allFiles = getInFileNames(object)
cmd1 = paste0("cd ",getInFilePath(object))
allFilesOut = paste0( sub("\\.fastq$","",allFiles) ,getOutputFlag(object), ".fastq")
# dir.create(getOutFilePath(object))
cmd2 = paste0("mkdir ", getOutFilePath(object))
cmd3 = paste0("cutadapt ", paste0(getCliParams(object),collapse=" "), " -o ", file.path(getOutFilePath(object), allFilesOut), " ", allFiles)
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(allFilesOut), commands = c(cmd1, cmd2, cmd3))
return(res)
})
#--split HTSeqCount_CLI
#@include CLIApplication
#'@title HTSeqCount_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{gffFile \code{"character"}}
#' }
#' @name HTSeqCount_CLI-class
#' @export
setClass("HTSeqCount_CLI", contains = "CLIApplication", representation(gffFile="character"))
#' @title Accessor HTSeqCount_CLI
#' @export
#' @docType methods
#' @return gffFile
setGeneric("getGffFile", function(object){standardGeneric("getGffFile")})
setMethod("getGffFile",signature(object="HTSeqCount_CLI"),function(object) {
slot(object, "gffFile")
})
#' @title Constructor method for HTSeqCount_CLI
#' @export
#' @docType methods
setGeneric("HTSeqCount_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, gffFile){standardGeneric("HTSeqCount_CLI")})
setMethod("HTSeqCount_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", gffFile="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, gffFile ){
return(
new("HTSeqCount_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, gffFile=gffFile)
)
})
#' @title Generates the commands and possibly resulting files/folders of HTSeqCount_CLI
#'
#' @param HTSeqCount_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="HTSeqCount_CLI"),function(object) {
# Usage: htseq-count [options] alignment_file gff_file
inFN = getInFileNames(object)
cmd1 = paste0("cd ",getInFilePath(object))
outFN = paste0( sub( "\\..*$","",inFN), getOutputFlag(object) )
cmd2 = paste0( "htseq-count ", paste0(getCliParams(object),collapse=" "), " ", inFN, " ", getGffFile(object), " > ", file.path(getOutFilePath(object),outFN) )
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2))
return(res)
})
#--split IntersectBed_CLI
#@include CLIApplication
#'@title IntersectBed_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{outFileName \code{"character"}}
#' }
#' @name IntersectBed_CLI-class
#' @export
setClass("IntersectBed_CLI", contains = "CLIApplication", representation(outFileName="character"))
#' @title Constructor method for IntersectBed_CLI
#' @param inFilePath only one filename allowed!
#' @export
#' @docType methods
setGeneric("IntersectBed_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, outFileName){standardGeneric("IntersectBed_CLI")})
setMethod("IntersectBed_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", outFileName="character"), function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath,
outFileName ){
return(new("IntersectBed_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams, outputFlag=outputFlag,
outFilePath=outFilePath, outFileName=outFileName))
})
#' @title Accessor getOutFileName
#' @export
#' @docType methods
#' @return outFileName
setGeneric("getOutFileName", function(object){standardGeneric("getOutFileName")})
setMethod("getOutFileName",signature(object="IntersectBed_CLI"),function(object) {
slot(object, "outFileName")
})
#' @title Generates the commands and possibly resulting files of linux sort command IntersectBed_CLI
#'
#' @param IntersectBed_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="IntersectBed_CLI"),function(object) {
if( length(getInFileNames(object)) > 2 ){
message("First File will be taken as a and all others as b")
} else if( length(getInFileNames(object)) < 2 ){
stop("Please provide at least two files as input!")
}
inFN_a = getInFileNames(object)[1]
inFN_b = getInFileNames(object)[-1]
if( length(getInFilePath(object)) == 1 ){
message("All files have to be present in the inFilePath directory!")
inFN_a_path = getInFilePath(object)
inFN_b_path = getInFilePath(object)
} else if( length(getInFilePath(object)) != length(getInFileNames(object)) ){
stop("Please provide the same number of paths to the input files as input file names")
} else{
inFN_a_path = getInFilePath(object)[1]
inFN_b_path = getInFilePath(object)[-1]
}
cmd1 = paste0("cd ",getInFilePath(object))
inFNtrimmed = sub("\\..+$","",inFN_a)
inFilending = sub( inFNtrimmed, "", inFN_a )
cmd2 = paste0( "mkdir ", getOutFilePath(object) )
outFN = paste0( getOutFileName(object), getOutputFlag(object), inFilending)
cmd3 = paste0( "intersectBed ", getCliParams(object), " -a ", file.path(inFN_a_path, inFN_a), " -b ",
paste0( file.path(inFN_b_path, inFN_b), collapse=" "), " > ", file.path(getOutFilePath(object), outFN) )
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2, cmd3))
return(res)
})
#--split MergeBedFile_CLI
#@include CLIApplication
#'@title MergeBedFile_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' }
#' @name MergeBedFile_CLI-class
#' @export
setClass("MergeBedFile_CLI", contains = "CLIApplication")
#' @title Constructor method for MergeBedFile_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
setGeneric("MergeBedFile_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath){standardGeneric("MergeBedFile_CLI")})
setMethod("MergeBedFile_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character"), function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath ){
return(new("MergeBedFile_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams, outputFlag=outputFlag,outFilePath=outFilePath))
})
setMethod("MergeBedFile_CLI", signature(inFilePath="character", inFileNames="character", cliParams="missing",
outputFlag="character", outFilePath="character"), function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath ){
cliParams = "-s -c 4,5,6 -o mean,mean,distinct"
return(new("MergeBedFile_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams, outputFlag=outputFlag,outFilePath=outFilePath))
})
#' @title Generates the commands and possibly resulting files/folders of Cutadapt
#'
#' @param MergeBedFile_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="MergeBedFile_CLI"),function(object) {
if( length(getInFileNames(object)) > 1 ){
warning("More than one input file given, using the first one!")
}
inFN = getInFileNames(object)[1]
cmd1 = paste0("cd ",getInFilePath(object))
inFNtrimmed = sub("\\..+$","",inFN)
inFilending = sub( inFNtrimmed, "", inFN )
outFN = paste0( inFNtrimmed, getOutputFlag(object), inFilending)
cmd2 = paste0( "sort -k1,1 -k2,2n ", file.path(getInFilePath(object), getInFileNames(object) ), " | ",
"mergeBed ", " -i stdin ", getCliParams(object), " | sort -k1,1 -k2,2n > ", file.path(getOutFilePath(object), outFN) )
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2))
return(res)
})
#--split MultiBamCov_CLI
#@include CLIApplication
#'@title MultiBamCov_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{annotationFileMB \code{"character"}}
#' \item{\code{slot7}:}{annotationType \code{"character"}}
#' }
#' @name MultiBamCov_CLI-class
#' @export
setClass("MultiBamCov_CLI", contains = "CLIApplication", representation(annotationFileMB="character", annotationType = "character"))
#' @title Accessor annotationFileMB
#' @export
#' @docType methods
#' @return annotationFileMB
setGeneric("getAnnotationFileMB", function(object){standardGeneric("getAnnotationFileMB")})
setMethod("getAnnotationFileMB",signature(object="MultiBamCov_CLI"),function(object) {
slot(object, "annotationFileMB")
})
#' @title Accessor annotationType
#' @export
#' @docType methods
#' @return annotationType
setGeneric("getAnnotationType", function(object){standardGeneric("getAnnotationType")})
setMethod("getAnnotationType",signature(object="MultiBamCov_CLI"),function(object) {
slot(object, "annotationType")
})
#' @title Constructor method for MultiBamCov_CLI
#' @export
#' @docType methods
setGeneric("MultiBamCov_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, annotationFileMB, annotationType){standardGeneric("MultiBamCov_CLI")})
setMethod("MultiBamCov_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", annotationFileMB="character", annotationType="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, annotationFileMB,annotationType ){
return(
new("MultiBamCov_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, annotationFileMB=annotationFileMB,annotationType=annotationType)
)
})
setMethod("MultiBamCov_CLI", signature(inFilePath="character", inFileNames="missing", cliParams="character",
outputFlag="character", outFilePath="character", annotationFileMB="character", annotationType="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, annotationFileMB,annotationType ){
inFileNames = list.files(path = inFilePath, pattern = ".*\\.sam$")
return(
new("MultiBamCov_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, annotationFileMB=annotationFileMB,annotationType=annotationType)
)
})
#' @title Generates the commands and possibly resulting files/folders of MultiBamCov_CLI
#'
#' @param MultiBamCov_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="MultiBamCov_CLI"),function(object) {
# Usage: bedtools multicov [OPTIONS] -bams aln.1.bam aln.2.bam ... aln.n.bam -bed <bed/gff/vcf>
inFNs = getInFileNames(object)
cmd1 = paste0("cd ",getInFilePath(object))
# outFN = paste0( gsub(".*/","",sub( "\\..*$","",inFNs[1])), getOutputFlag(object) )
outFN = paste0( getOutputFlag(object) )
cmd2 = paste0( "bedtools multicov ", paste0(getCliParams(object),collapse=" "), " -bams ", paste0(inFNs, collapse=" "), " -",
getAnnotationType(object)," ", getAnnotationFileMB(object), " > ", file.path(getOutFilePath(object),outFN) )
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2))
return(res)
})
#--split Genomecov_CLI
# Needs to be placed after IntersectBed_CLI
#@include CLIApplication
#'@title Genomecov_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}} In this class the flag may be bedgraph (not used but specifies filetype)
#' \item{\code{slot6}:}{outFileName \code{"character"}}
#' \item{\code{slot7}:}{inFileBam \code{"logical"}}
#' }
#' @name Genomecov_CLI-class
#' @export
setClass("Genomecov_CLI", contains = "CLIApplication", representation(outFileName="character", inFileBam="logical"))
#' @title Constructor method for Genomecov_CLI
#' @param inFilePath only one filename allowed!
#' @export
#' @docType methods
setGeneric("Genomecov_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, outFileName, inFileBam){standardGeneric("Genomecov_CLI")})
setMethod("Genomecov_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", outFileName="character",
inFileBam="logical"), function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath,
outFileName,inFileBam ){
return(new("Genomecov_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams, outputFlag=outputFlag,
outFilePath=outFilePath, outFileName=outFileName, inFileBam=inFileBam))
})
#' @title Accessor getOutFileName
#' @export
#' @docType methods
#' @return outFileName
setMethod("getOutFileName",signature(object="Genomecov_CLI"),function(object) {
slot(object, "outFileName")
})
#' @title Accessor getInFileBam
#' @export
#' @docType methods
#' @return inFileBam
setGeneric("getInFileBam", function(object){standardGeneric("getInFileBam")})
setMethod("getInFileBam",signature(object="Genomecov_CLI"),function(object) {
slot(object, "inFileBam")
})
#' @title Generates the commands and possibly resulting files of linux sort command Genomecov_CLI
#'
#' @param Genomecov_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="Genomecov_CLI"),function(object) {
if( length(getInFileNames(object)) > 1 ){
warning("Only one file allowed, the first one will be chosen!")
}
inFN = getInFileNames(object)[1]
outFN = getOutFileName(object)
inFN_path = getInFilePath(object)
cmd1 = paste0("cd ",getInFilePath(object))
cmd2 = paste0( "bedtools genomecov ", getCliParams(object), ifelse( getInFileBam(object), " -ibam ", " -i " ) ,file.path(inFN_path, inFN), " > ",
file.path(getOutFilePath(object), outFN) )
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2))
return(res)
})
#--split Samtools_CLI
#@include CLIApplication
#'@title Samtools_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{samtoolsApplication \code{"character"}}
#' \item{\code{slot6}:}{outputFormat \code{"character"}}
#' }
#' @name Samtools_CLI-class
#' @export
setClass("Samtools_CLI", contains = "CLIApplication", representation(samtoolsApplication="character", outputFormat = "character") )
# @title Validity method for Samtools_CLI
# @export
# @name validitySamtools_CLI
# @rdname validitySamtools_CLI
# @docType methods
setValidity ("Samtools_CLI",
function ( object ){
retval = NULL
if( length(getInFileNames(object)) > 1 ){ retval = "Only one input file is allowed!" }
if ( is.null(retval)){
return(TRUE)
}
else{
return(retval)
}
})
#' @title Accessor getSamtoolsApplication
#' @export
#' @docType methods
#' @return samtoolsApplication
setGeneric("getSamtoolsApplication", function(object){standardGeneric("getSamtoolsApplication")})
setMethod("getSamtoolsApplication", signature(object="Samtools_CLI"), function(object){
slot(object, "samtoolsApplication")
})
#' @title Accessor getOutputFormat
#' @export
#' @docType methods
#' @return outputFormat
setGeneric("getOutputFormat", function(object){standardGeneric("getOutputFormat")})
setMethod("getOutputFormat", signature(object="Samtools_CLI"), function(object){
slot(object, "outputFormat")
})
#' @title Constructor method for Samtools_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
setGeneric("Samtools_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, samtoolsApplication, outputFormat){standardGeneric("Samtools_CLI")})
setMethod("Samtools_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", samtoolsApplication="character", outputFormat="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, samtoolsApplication, outputFormat){
return(
new("Samtools_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, samtoolsApplication=samtoolsApplication, outputFormat=outputFormat)
)
})
#' @title Generates the commands and possibly resulting files/folders of Samtools
#'
#' @param Samtools_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="Samtools_CLI"),function(object) {
cmd1 = paste0("cd ",getInFilePath(object))
#select different samtools applications by name
stapp = getSamtoolsApplication(object)
inFN = getInFileNames(object)
outfmt = getOutputFormat(object)
outFN = ""
cmd2 = ""
switch(stapp,
view = {
#samtools view -o aligned_sn.sam aligned_sn.bam
outFN = paste0( sub("\\..*$","",inFN),getOutputFlag(object),".",outfmt)
params = getCliParams(object)
params = params[ which( params != "-o" ) ]
cmd2 = paste0("samtools view ",paste0(params,collapse=" ")," -o ",outFN," ", inFN)
},
sort = {
#samtools sort -n aligned.bam aligned_sn
outFNprefix = paste0( sub("\\..*$","",inFN),getOutputFlag(object) )
outFN = paste0(outFNprefix, ".", outfmt)
cmd2 = paste0("samtools sort ",paste0(getCliParams(object),collapse=" ")," ", inFN," -o ", outFN )
},
index = {
#samtools index aligned_s.bam
cmd2 = paste0("samtools index ",paste0(getCliParams(object),collapse=" ")," ",inFN)
outFN = sub( "bam","bai", inFN)
},
{
stop("Samtools application not recognized (supported: view, sort, index)")
})
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2))
return(res)
})
#--split BamToBed_CLI
#'@title BamToBed_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{outputFormat \code{"character"}}
#' }
#' @name BamToBed_CLI-class
#' @export
setClass("BamToBed_CLI", contains = "CLIApplication", representation(outputFormat="character"))
#' @title Constructor method for BamToBed_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
setGeneric("BamToBed_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, outputFormat){standardGeneric("BamToBed_CLI")})
setMethod("BamToBed_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", outputFormat="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, outputFormat ){
return(new("BamToBed_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams, outputFlag=outputFlag,
outFilePath=outFilePath, outputFormat=outputFormat))
})
#' @title Accessor getOutputFormat
#' @export
#' @docType methods
#' @return outputFormat
setMethod("getOutputFormat", signature(object="BamToBed_CLI"), function(object){
slot(object, "outputFormat")
})
#' @title Generates the commands and possibly resulting files/folders of BamToBed_CLI
#'
#' @param BamToBed_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="BamToBed_CLI"),function(object) {
if( length(getInFileNames(object)) > 1 ){
warning("More than one input file given, using the first one!")
}
inFN = getInFileNames(object)[1]
cmd1 = paste0("cd ",getInFilePath(object))
inFNtrimmed = sub("\\..+$","",inFN)
outFN = paste0( inFNtrimmed, getOutputFlag(object),".", getOutputFormat(object))
cmd2 = paste0( "bamToBed ", getCliParams(object)," -i ", file.path(getInFilePath(object), getInFileNames(object) ),
" > ", file.path(getOutFilePath(object), outFN) )
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2))
return(res)
})
#--split SortFile_CLI
#@include CLIApplication
#'@title SortFile_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' }
#' @name SortFile_CLI-class
#' @export
setClass("SortFile_CLI", contains = "CLIApplication")
#' @title Constructor method for SortFile_CLI
#' @param inFilePath only one filename allowed!
#' @export
#' @docType methods
setGeneric("SortFile_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath){standardGeneric("SortFile_CLI")})
setMethod("SortFile_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character"), function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath ){
return(new("SortFile_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams, outputFlag=outputFlag,outFilePath=outFilePath))
})
setMethod("SortFile_CLI", signature(inFilePath="character", inFileNames="character", cliParams="missing",
outputFlag="character", outFilePath="character"), function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath ){
cliParams = "-k1,1 -k2,2n"
return(new("SortFile_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams, outputFlag=outputFlag,outFilePath=outFilePath))
})
#' @title Generates the commands and possibly resulting files of linux sort command SortFile_CLI
#'
#' @param SortFile_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="SortFile_CLI"),function(object) {
if( length(getInFileNames(object)) > 1 ){
warning("More than one input file given, using the first one!")
}
inFN = getInFileNames(object)[1]
cmd1 = paste0("cd ",getInFilePath(object))
inFNtrimmed = sub("\\..+$","",inFN)
inFilending = sub( inFNtrimmed, "", inFN )
outFN = paste0( inFNtrimmed, getOutputFlag(object), inFilending)
cmd2 = paste0( "sort ", getCliParams(object), " ", file.path(getInFilePath(object), getInFileNames(object) ), " > ", file.path(getOutFilePath(object), outFN) )
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2))
return(res)
})
#--split Bowtie2_CLI
#################################################
# General generic function definitions that are implemented in several subclasses!
#################################################
#@include CLIApplication
#'@title Bowtie2_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{bowtieIndexFilePath \code{"character"}}
#' \item{\code{slot7}:}{matepairFileNames \code{"character"}}
#' }
#' @name Bowtie2_CLI-class
#' @export
setClass("Bowtie2_CLI", contains = "CLIApplication", representation(bowtieIndexFilePath="character", matepairFileNames="character") )
#' @title Accessor getBowtieIndexFilePath
#' @export
#' @docType methods
#' @return bowtieIndexFilePath
setGeneric("getBowtieIndexFilePath", function(object) standardGeneric("getBowtieIndexFilePath"))
setMethod("getBowtieIndexFilePath",signature(object="Bowtie2_CLI"),function(object) {
slot(object, "bowtieIndexFilePath")
})
#' @title Accessor getMatepairFileNames
#' @export
#' @docType methods
#' @return matepairFileNames
setGeneric("getMatepairFileNames", function(object){standardGeneric("getMatepairFileNames")})
setMethod("getMatepairFileNames",signature(object="Bowtie2_CLI"),function(object) {
slot(object, "matepairFileNames")
})
#' @title Constructor method for Bowtie2_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
setGeneric("Bowtie2_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath, matepairFileNames){standardGeneric("Bowtie2_CLI")})
setMethod("Bowtie2_CLI", signature(inFilePath="character", inFileNames="missing", cliParams="character",
outputFlag="character", outFilePath="character", bowtieIndexFilePath="character", matepairFileNames="missing"),
function(inFilePath, cliParams, outputFlag, outFilePath, bowtieIndexFilePath,matepairFileNames){
inFileNames = list.files(path = inFilePath, pattern = ".*\\.fastq$")
return(
new("Bowtie2_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath,matepairFileNames="")
)
})
setMethod("Bowtie2_CLI", signature(inFilePath="character", inFileNames="missing", cliParams="character",
outputFlag="character", outFilePath="character", bowtieIndexFilePath="character", matepairFileNames="character"),
function(inFilePath, cliParams, outputFlag, outFilePath, bowtieIndexFilePath,matepairFileNames){
inFileNames = list.files(path = inFilePath, pattern = ".*\\.fastq$")
return(
new("Bowtie2_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath,matepairFileNames=matepairFileNames)
)
})
setMethod("Bowtie2_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", bowtieIndexFilePath="character", matepairFileNames="missing"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath,matepairFileNames ){
return(
new("Bowtie2_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath, matepairFileNames="")
)
})
setMethod("Bowtie2_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", bowtieIndexFilePath="character", matepairFileNames="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath,matepairFileNames ){
return(
new("Bowtie2_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath, matepairFileNames=matepairFileNames)
)
})
#' @title Generates the commands and possibly resulting files/folders of Bowtie2
#'
#' @param Bowtie2_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="Bowtie2_CLI"),function(object) {
#USAGE: bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]
allFiles = getInFileNames(object)
cmd1 = paste0("cd ",getInFilePath(object))
allFilesOut = paste0( sub("\\.fastq$","",allFiles), getOutputFlag(object), ".fastq")
# dir.create(getOutFilePath(object))
cmd2 = paste0("mkdir ", getOutFilePath(object)) #if only executed in terminal!
if( getMatepairFileNames(object)[1] == "" ){
cmd3 = paste0("bowtie2 ", paste0(getCliParams(object),collapse=" "), " -x ", getBowtieIndexFilePath(object), " -U ", allFiles, " -S ",
file.path(getOutFilePath(object), allFilesOut) )
} else{
cmd3 = paste0("bowtie2 ", paste0(getCliParams(object),collapse=" "), " -x ", getBowtieIndexFilePath(object), " -1 ", allFiles,
" -2 ",getMatepairFileNames(object), " -S ", file.path(getOutFilePath(object), allFilesOut) )
}
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(allFilesOut), commands = c(cmd1, cmd2, cmd3))
return(res)
})
#--split Bowtie2TophatIon_CLI
#@include Bowtie2_CLI
#'@title Bowtie2TophatIon_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{bowtieIndexFilePath \code{"character"}}
#' \item{\code{slot7}:}{matepairFileNames \code{"character"}}
#' \item{\code{slot8}:}{outFileNames \code{"character"}}
#' \item{\code{slot9}:}{pathToPicardTools \code{"character"}}
#' \item{\code{slot9}:}{addNHTag \code{"character"}}
#' }
#' @name Bowtie2TophatIon_CLI-class
#' @export
setClass("Bowtie2TophatIon_CLI", contains = "Bowtie2_CLI", representation(outFileNames="character", pathToPicardTools="character", addNHTag="logical"),
prototype(outFileNames = "unmapped"))
# @title Validity method for Bowtie2TophatIon_CLI
# @name validityBowtie2TophatIon_CLI
# @rdname validityBowtie2TophatIon_CLI
# @export
# @docType methods
setValidity ("Bowtie2TophatIon_CLI",
function ( object ){
retval = NULL
if(length(getInFilePath(object)) > 1){ retval = "Multiple In File Paths (Tophat output directories are not allowed!)" }
if ( is.null(retval)){
return(TRUE)
}
else{
return(retval)
}
})
#' @title Constructor method for Bowtie2TophatIon_CLI
#' @export
#' @docType methods
setGeneric("Bowtie2TophatIon_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath,matepairFileNames,
outFileNames, pathToPicardTools, addNHTag){standardGeneric("Bowtie2TophatIon_CLI")})
setMethod("Bowtie2TophatIon_CLI", signature(inFilePath="character", inFileNames="missing", cliParams="missing",
outputFlag="character", outFilePath="missing", bowtieIndexFilePath="character", matepairFileNames="missing",
outFileNames="missing", pathToPicardTools="missing", addNHTag="logical"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath,matepairFileNames,outFileNames, pathToPicardTools, addNHTag){
warning("Options are locked and input file name is set to unmapped, outfile is set to bam mate pairs are not supported!")
if(missing(outFileNames)){outFileNames = "aligned"}
if(missing(pathToPicardTools)){pathToPicardTools = "/usr/local/applications/picard-tools-1.77/"}
if(missing(outFilePath)){outFilePath = inFilePath; warning("outFilePath is set to inFilePath")}
return(
new("Bowtie2TophatIon_CLI", inFilePath=inFilePath, inFileNames="unmapped", cliParams=c("--local","--very-sensitive-local","-p 8","--mm"),
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath, matepairFileNames="",
outFileNames = outFileNames, pathToPicardTools=pathToPicardTools, addNHTag = addNHTag)
)
})
setMethod("Bowtie2TophatIon_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", bowtieIndexFilePath="character", matepairFileNames="character",
outFileNames="character", pathToPicardTools="character", addNHTag="logical"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath,matepairFileNames,outFileNames, pathToPicardTools, addNHTag){
return(
new("Bowtie2TophatIon_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath, matepairFileNames=matepairFileNames,
outFileNames = outFileNames, pathToPicardTools=pathToPicardTools, addNHTag = addNHTag)
)
})
#' @title Accessor getOutFileNames
#' @export
#' @docType methods
#' @return outFileNames
setGeneric("getOutFileNames", function(object){standardGeneric("getOutFileNames")})
setMethod("getOutFileNames",signature(object="Bowtie2_CLI"),function(object) {
slot(object, "outFileNames")
})
#' @title Accessor getAddNHTag
#' @export
#' @docType methods
#' @return addNHTag
setGeneric("getAddNHTag", function(object){standardGeneric("getAddNHTag")})
setMethod("getAddNHTag",signature(object="Bowtie2_CLI"),function(object) {
slot(object, "addNHTag")
})
#' @title Accessor getPathToPicardTools
#' @export
#' @docType methods
#' @return pathToPicardTools
setGeneric("getPathToPicardTools", function(object){standardGeneric("getPathToPicardTools")})
setMethod("getPathToPicardTools",signature(object="Bowtie2_CLI"),function(object) {
slot(object, "pathToPicardTools")
})
#' @title Generates the commands and possibly resulting files/folders of Bowtie2 in combination with Tophat output for ion Torrent
#'
#' @param Bowtie2TophatIon_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="Bowtie2TophatIon_CLI"),function(object) {
#USAGE: bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]
#When Tophout2 results are created, bam2fastq is callled, then bowtie 2 is called, results are merged by picard tools MergeSamFiles
allFiles = getInFileNames(object)
inFP = getInFilePath(object)
cmd1 = paste0("cd ",inFP)
outFile = paste0( getOutFileNames(object), getOutputFlag(object), ".bam")
cmd2 = paste0("bam2fastq -o unmapped.fastq unmapped.bam")
cmd3 = paste0("bowtie2 ", paste0(getCliParams(object),collapse=" "), " -x ", getBowtieIndexFilePath(object), " -U ", "unmapped.fastq",
" | samtools view -uhS -F4 - | samtools sort - unmapped_remap")
if( getAddNHTag(object) ){
cmd3 = c(cmd3, paste0("samtools sort -n unmapped_remap.bam unmapped_remap_sn") )
cmd3 = c(cmd3, paste0( "python -c \"import bbcflib.mapseq; bbcflib.mapseq.add_nh_flag('",file.path( inFP,"unmapped_remap_sn.bam"),
"', '",file.path( inFP,"unmapped_remap.bam"),"')\"" ) )
}
cmd4 = paste0("java -jar ", file.path( getPathToPicardTools(object), "MergeSamFiles.jar"),
" USE_THREADING=true MSD=true AS=true I=accepted_hits.bam I=unmapped_remap.bam O=",file.path(getOutFilePath(object), outFile) )
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFile), commands = c(cmd1, cmd2, cmd3, cmd4))
return(res)
} )
#--split Tophat2_CLI
#@include CLIApplication
#'@title Tophat2_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{bowtieIndexFilePath \code{"character"}}
#' }
#' @name Tophat2_CLI-class
#' @export
setClass("Tophat2_CLI", contains = "CLIApplication", representation(bowtieIndexFilePath="character") )
#' @title Accessor getBowtieIndexFilePath Tophat2
#' @export
#' @docType methods
#' @return bowtieIndexFilePath
setMethod("getBowtieIndexFilePath",signature(object="Tophat2_CLI"),function(object) {
slot(object, "bowtieIndexFilePath")
})
#' @title Constructor method for Tophat2_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
setGeneric("Tophat2_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath,bowtieIndexFilePath){standardGeneric("Tophat2_CLI")})
setMethod("Tophat2_CLI", signature( inFilePath="character", inFileNames="missing", cliParams="character",
outputFlag="character", outFilePath="character",
bowtieIndexFilePath="character"),
function(inFilePath, cliParams, outputFlag, outFilePath, bowtieIndexFilePath){
inFileNames = list.files(path = inFilePath, pattern = ".*\\.fastq$")
return(
new("Tophat2_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath)
)
})
setMethod("Tophat2_CLI", signature( inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character",
bowtieIndexFilePath="character"),
function(inFilePath,inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath){
return(
new("Tophat2_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath)
)
})
#' @title Generates the commands and possibly resulting files/folders of Tophat2
#'
#' @param Tophat2_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="Tophat2_CLI"),function(object) {
# USAGE:
# tophat [options] <bowtie_index> <reads1[,reads2,...]> [reads1[,reads2,...]] \
# [quals1,[quals2,...]] [quals1[,quals2,...]]
#preparing input files
inFP = getInFilePath(object)
inFN = getInFileNames(object)
#preparing output files
sampleOutDir = paste0( paste0( sub("\\.fastq$","",inFN),getOutputFlag(object)) )
#generating the tophat base directory
outfilepath = getOutFilePath(object)
# dir.create(outfilepath)
# setwd(outfilepath)
cmd1 = paste("mkdir", outfilepath) #if only executed in terminal!
cmd2 = paste("cd ", outfilepath)
#generating the tophat command
cmd3 = paste0( "tophat2 ", paste0(getCliParams(object), collapse=" "),
" --output-dir ", file.path(file.path(getOutFilePath(object), sampleOutDir)), " ", getBowtieIndexFilePath(object), " ", file.path(inFP,inFN) )
#IN FILENAME UND BOWTIE INDEX PATH FEHLEN!
# tophat2 --num-threads 12 --keep-fasta-order --output-dir /home/simon/PHDStudies/RNA-Seq/IonProton/MSA_LusserWenning/SampleAnalysis/tophat-out_sampleAnalysis --GTF /home/simon/dbsOfflineUse/GTF_repos/Mus_musculus.GRCm38.78_mod.gtf /home/simon/dbsOfflineUse/MusMusculus/Mouse_mm10_fasta/bowtie2/mm10 /home/simon/PHDStudies/RNA-Seq/IonProton/MSA_LusserWenning/SampleAnalysis/sampleFastq_larger20.fastq
res = CmdGenResult(CLIApplication = object, OutResultReference = FoldersOutput(sampleOutDir), commands = c(cmd1, cmd2, cmd3))
return(res)
})
#--split Bowtie_CLI
#################################################
# General generic function definitions that are implemented in several subclasses!
# MUST BE PLACED AFTER Bowtie2TophatIon_CLI class!
#################################################
#@include Samtools_CLI,Bowtie2Tophation_CLI
#'@title Bowtie_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{bowtieIndexFilePath \code{"character"}}
#' \item{\code{slot7}:}{matepairFileNames \code{"character"}}
#' \item{\code{slot8}:}{addNHTag \code{"logical"}}
#' \item{\code{slot9}:}{outputPipeString \code{"character"}}
#' \item{\code{slot10}:}{outputFormat \code{"character"}}
#' }
#' @name Bowtie_CLI-class
#' @export
setClass("Bowtie_CLI", contains = "CLIApplication", representation(bowtieIndexFilePath="character", matepairFileNames="character",
addNHTag="logical", outputPipeString="character", outputFormat = "character") )
#' @title Accessor getBowtieIndexFilePath
#' @export
#' @docType methods
#' @return bowtieIndexFilePath
setMethod("getBowtieIndexFilePath",signature(object="Bowtie_CLI"),function(object) {
slot(object, "bowtieIndexFilePath")
})
#' @title Accessor getMatepairFileNames
#' @export
#' @docType methods
#' @return matepairFileNames
setMethod("getMatepairFileNames",signature(object="Bowtie_CLI"),function(object) {
slot(object, "matepairFileNames")
})
#' @title Accessor getAddNHTag
#' @export
#' @docType methods
#' @return addNHTag
setMethod("getAddNHTag",signature(object="Bowtie_CLI"),function(object) {
slot(object, "addNHTag")
})
#' @title Accessor getOutputPipeString
#' @export
#' @docType methods
#' @return outputPipeString
setGeneric("getOutputPipeString", function(object){standardGeneric("getOutputPipeString")})
setMethod("getOutputPipeString",signature(object="Bowtie_CLI"),function(object) {
slot(object, "outputPipeString")
})
#' @title Accessor getOutputFormat
#' @export
#' @docType methods
#' @return outputFormat
setMethod("getOutputFormat", signature(object="Bowtie_CLI"), function(object){
slot(object, "outputFormat")
})
#' @title Constructor method for Bowtie_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
setGeneric("Bowtie_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath, matepairFileNames,
addNHTag, outputPipeString, outputFormat){standardGeneric("Bowtie_CLI")})
setMethod("Bowtie_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", bowtieIndexFilePath="character",
matepairFileNames="missing", addNHTag="logical", outputPipeString="character", outputFormat="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath,matepairFileNames, addNHTag, outputPipeString, outputFormat ){
return(
new("Bowtie_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath, matepairFileNames="",
addNHTag=addNHTag, outputPipeString=outputPipeString, outputFormat=outputFormat)
)
})
setMethod("Bowtie_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character", bowtieIndexFilePath="character",
matepairFileNames="character", addNHTag="logical", outputPipeString="character", outputFormat="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, bowtieIndexFilePath,matepairFileNames, addNHTag, outputPipeString, outputFormat ){
return(
new("Bowtie_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, bowtieIndexFilePath=bowtieIndexFilePath,
matepairFileNames=matepairFileNames, addNHTag=addNHTag, outputPipeString=outputPipeString, outputFormat=outputFormat)
)
})
#' @title Generates the commands and possibly resulting files/folders of Bowtie2
#'
#' @param Bowtie_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="Bowtie_CLI"),function(object) {
#USAGE: bowtie [options]* <ebwt> {-1 <m1> -2 <m2> | --12 <r> | <s>} [<hit>]
#bowtie -qSya -n 1 -p 3 --chunkmbs 1024 --best -l 28 -m 100 --phred64-quals --strata /home/simon/dbsOfflineUse/apartdbs/mouse_mm9/genome test_trimmed.fastq | samtools view -uhS -F4 - | samtools sort - /tmp/mapped
#This command -l 18 nt seed, -n 1 in seed 1 mismatch (seed generated from left), -m maximum 100 alignments reported (not randomly chosen if more -> would be -M 100)
#the maximum 100 alignments are chosen from the best stratum of the aligner, -p n number of processor cores, outputPipeString is optional here
inFN = getInFileNames(object)
cmd1 = paste0("cd ",getInFilePath(object))
#trim the file extension to create the outputFileName
inFNtrimmed = sub("\\..+$","",inFN)
outFN = paste0( inFNtrimmed, getOutputFlag(object),".", getOutputFormat(object))
outFNtrimmed = paste0( inFNtrimmed, getOutputFlag(object))
# create the output directory
cmd2 = paste0("mkdir ", getOutFilePath(object)) #if only executed in terminal!
cmd2 = c(cmd2,paste0("cd ",getOutFilePath(object)))
#Executing bowtie
inFileNames = paste0( file.path(getInFilePath(object),inFN), collapse=",")
if( getMatepairFileNames(object)[1] == "" ){
cmd3 = paste0("bowtie ", paste0(getCliParams(object),collapse=" "), " ", getBowtieIndexFilePath(object), " ", inFileNames, " ",
" ", getOutputPipeString(object), " ", file.path(getOutFilePath(object), outFNtrimmed) )
} else{
cmd3 = paste0("bowtie ", paste0(getCliParams(object),collapse=" "), " ", getBowtieIndexFilePath(object), " -1 ", inFileNames,
" -2 ",paste0( getMatepairFileNames(object), collapse=","), " ", getOutputPipeString(object), " ", file.path(getOutFilePath(object), outFNtrimmed) )
}
if( getAddNHTag(object) ){
sortedFN = paste0(file.path(getOutFilePath(object), outFNtrimmed),"_sn")
cmd3 = c(cmd3, paste0("samtools sort -n ",file.path(getOutFilePath(object), outFN), " ", sortedFN ) )
cmd3 = c(cmd3, paste0( "python -c \"import bbcflib.mapseq; bbcflib.mapseq.add_nh_flag('",paste0(sortedFN,".",getOutputFormat(object)),"', '",file.path(getOutFilePath(object), outFN),"')\"" ) )
cmd3 = c(cmd3, paste0("rm ", paste0(sortedFN,".",getOutputFormat(object)) ) )#Another sorting so that the sorted file contains the flag too
}
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2, cmd3))
return(res)
})
#--split MultiIntersectBed_CLI
#@include CLIApplication
#'@title MultiIntersectBed_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{sortInFiles \code{"logical"}}
#' \item{\code{slot7}:}{requireStrandness \code{"logical"}}
#' \item{\code{slot8}:}{strandColumn \code{"numeric"}}
#' \item{\code{slot9}:}{filterConditions \code{"character"}}
#' }
#' @name MultiIntersectBed_CLI-class
#' @export
setClass("MultiIntersectBed_CLI", contains = "CLIApplication", representation(sortInFiles="logical", requireStrandness="logical",
strandColumn="numeric", filterConditions="character"))
#' @title Constructor method for MultiIntersectBed_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
setGeneric("MultiIntersectBed_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, sortInFiles,requireStrandness, strandColumn,filterConditions){standardGeneric("MultiIntersectBed_CLI")})
setMethod("MultiIntersectBed_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character",sortInFiles="logical",requireStrandness="logical",
strandColumn="numeric", filterConditions="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath,sortInFiles,requireStrandness, strandColumn, filterConditions ){
return(new("MultiIntersectBed_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, sortInFiles=sortInFiles,
requireStrandness=requireStrandness, strandColumn=strandColumn, filterConditions=filterConditions))
})
setMethod("MultiIntersectBed_CLI", signature(inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character",sortInFiles="logical",requireStrandness="logical",
strandColumn="missing", filterConditions="character"),
function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath,sortInFiles,requireStrandness, strandColumn, filterConditions ){
strandColumn = 0
return(new("MultiIntersectBed_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, sortInFiles=sortInFiles,
requireStrandness=requireStrandness, strandColumn=strandColumn, filterConditions=filterConditions))
})
#' @title Accessor getSortInFiles
#' @export
#' @docType methods
#' @return sortInFiles
setGeneric("getSortInFiles", function(object) standardGeneric("getSortInFiles"))
setMethod("getSortInFiles",signature(object="MultiIntersectBed_CLI"),function(object) {
slot(object, "sortInFiles")
})
#' @title Accessor getRequireStrandness
#' @export
#' @docType methods
#' @return requireStrandness
setGeneric("getRequireStrandness", function(object) standardGeneric("getRequireStrandness"))
setMethod("getRequireStrandness",signature(object="MultiIntersectBed_CLI"),function(object) {
slot(object, "requireStrandness")
})
#' @title Accessor getStrandColumn
#' @export
#' @docType methods
#' @return strandColumn
setGeneric("getStrandColumn", function(object) standardGeneric("getStrandColumn"))
setMethod("getStrandColumn",signature(object="MultiIntersectBed_CLI"),function(object) {
slot(object, "strandColumn")
})
#' @title Accessor getFilterConditions
#' @export
#' @docType methods
#' @return filterConditions
setGeneric("getFilterConditions", function(object) standardGeneric("getFilterConditions"))
setMethod("getFilterConditions",signature(object="MultiIntersectBed_CLI"),function(object) {
slot(object, "filterConditions")
})
#' @title Generates the commands and possibly resulting files/folders of Cutadapt
#'
#' @param MultiIntersectBed_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="MultiIntersectBed_CLI"),function(object) {
#bedtools multiinter [OPTIONS] -i FILE1 FILE2 .. FILEn
if( length(getInFilePath(object)) > 1 & length(getInFilePath(object)) != length(getInFileNames(object)) ){
warning("Either one file path is given, containnig all files, or the file path vector must match the filename vector in length!")
}
inFN = getInFileNames(object)
inFNtrimmed = sub("\\..+$","",inFN)
inFilending = sub( inFNtrimmed[1], "", inFN[1] )
outFN = paste0( getOutputFlag(object), inFilending)
if( getSortInFiles(object) ){
message(" ... sorting inputFiles ... ")
cmd1 = mapply( function(fp,fn) {
tmpFileName = "testTmp321"
cmdCurr = paste0("\nsort -k1,1 -k2,2n ",file.path(fp,fn), " > ", file.path(fp,tmpFileName) )
cmdCurr = c(cmdCurr, paste0("cat ", file.path(fp,tmpFileName), " > ", file.path(fp,fn) ))
cmdCurr = c(cmdCurr, paste0("rm ", file.path(fp,tmpFileName) ) )
return( cmdCurr )
}, getInFilePath(object), getInFileNames(object) )
} else{
cmd1 = ""
}
if(getRequireStrandness(object)){
if( length(getStrandColumn(object)) == 0 | getStrandColumn(object) < 1 ){
stop("Column where the strand is defined in the Bed file has to be specified and needs to be greater than 0 when strandness is required!!")
}
tmpFileName = "testTmp321"
message(" ... splitting input Files by strand ... ")
cmd1 = c( cmd1, mapply( function(fp,fn) {
cmdCurr = paste0("cat ", file.path(fp,fn), " | ", "awk \'{if($",getStrandColumn(object)," == \"-\") print }\' > " , file.path(fp,paste0("minus_",fn)) )
cmdCurr = c( cmdCurr, paste0("cat ", file.path(fp,fn), " | ", "awk \'{if($",getStrandColumn(object)," == \"+\") print }\' > " , file.path(fp,paste0("plus_",fn)) ) )
return( cmdCurr )
}, getInFilePath(object), getInFileNames(object) ) )
cmd2 = paste0( "bedtools multiinter ",getCliParams(object), " -i ", paste0( file.path(getInFilePath(object), paste0("plus_",getInFileNames(object)) ),collapse=" "), " > ",
file.path(getOutFilePath(object), paste0("plus_",outFN) ) )
cmd2 = c(cmd2, paste0( "bedtools multiinter ",getCliParams(object), " -i ", paste0( file.path(getInFilePath(object), paste0("minus_",getInFileNames(object)) ),collapse=" "), " > ",
file.path(getOutFilePath(object), paste0("minus_",outFN) ) ) )
#Adding the minus sign to the multiinter file
cmd2 = c(cmd2, paste0( "awk -Ft \'BEGIN {OFS=\"\\t\"}{print $0, \"-\"}\' ", file.path(getOutFilePath(object), paste0("minus_",outFN) ), " > ", file.path(getOutFilePath(object),tmpFileName) ) )
cmd2 = c(cmd2, paste0("cat ", file.path(getOutFilePath(object),tmpFileName), " > ", file.path(getOutFilePath(object),paste0("minus_",outFN)) ))
cmd2 = c(cmd2, paste0("rm ", file.path(getOutFilePath(object),tmpFileName) ) )
cmd2 = c(cmd2, paste0( "awk -Ft \'BEGIN {OFS=\"\\t\"}{print $0, \"+\"}\' ", file.path(getOutFilePath(object), paste0("plus_",outFN) ), " > ", file.path(getOutFilePath(object),tmpFileName) ) )
cmd2 = c(cmd2, paste0("cat ", file.path(getOutFilePath(object),tmpFileName), " > ", file.path(getOutFilePath(object),paste0("plus_",outFN)) ))
cmd2 = c(cmd2, paste0("rm ", file.path(getOutFilePath(object),tmpFileName) ) )
cmd2 = c(cmd2, paste0( "cat ", file.path(getOutFilePath(object), paste0("plus_",outFN)), " ",
file.path(getOutFilePath(object), paste0("minus_",outFN)),
" | awk \'/./\' > ", file.path(getOutFilePath(object), outFN) ) ) #also removing blank lines from the file
#sorting again
cmd2 = c(cmd2, paste0("\nsort -k1,1 -k2,2n ",file.path(getOutFilePath(object), outFN), " > ", file.path(getOutFilePath(object),tmpFileName) ))
cmd2 = c(cmd2, paste0("cat ", file.path(getOutFilePath(object),tmpFileName), " > ", file.path(getOutFilePath(object),outFN) ))
cmd2 = c(cmd2, paste0("rm ", file.path(getOutFilePath(object),tmpFileName) ) )
} else{
cmd2 = paste0( "bedtools multiinter ",getCliParams(object), " -i ", paste0( file.path(getInFilePath(object), getInFileNames(object) ),collapse=" "), " > ",
file.path(getOutFilePath(object),outFN ) )
}
if( length(getFilterConditions(object)) > 1 ){
generateFilterCmd = function(conditions, inputFileName, inputFilePath){
#starting at column 6 in multiIntersectBed file
conditions_u = unique(conditions)
idx_conditions = lapply( conditions_u, function(x){which(conditions == x)})
conditionStr = paste0( sapply( idx_conditions, function(x){
if( length(x) > 1){
paste0( paste0( "$",x, " > 0", sep=" && " ), collapse="")
} else{
paste0( "$",x, " > 0")
}
} ), collapse=" || ")
cmd1 = paste0( "\ncat ", file.path(inputFilePath,inputFileName), " > ", file.path(inputFilePath,paste0("UnFiltered_",inputFileName )))
cmd2 = paste0( "\ncat ", file.path(inputFilePath, paste0("UnFiltered_", inputFileName)),
" | awk \'{if( ", conditionStr,") print}\' > ",
file.path(inputFilePath,inputFileName), "\n" )
return(c(cmd1,cmd2))
}
cmd3 = generateFilterCmd(getFilterConditions(object),outFN, getOutFilePath(object))
} else{
cmd3 = ""
}
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2, cmd3))
return(res)
})
#--split MultiIntersectBed_perl_CLI
#@include IntersectBed_CLI
#'@title MultiIntersectBed_perl_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{groupVect \code{"numeric"}}
#' \item{\code{slot7}:}{withinGroupTH \code{"numeric"}}
#' \item{\code{slot8}:}{outFileName \code{"character"}}
#' \item{\code{slot9}:}{perlPath \code{"character"}}
#' }
#' @name MultiIntersectBed_perl_CLI-class
#' @export
setClass("MultiIntersectBed_perl_CLI", contains = "CLIApplication", representation(groupVect="numeric", withinGroupTH="numeric", outFileName="character", perlPath="character"))
#' @title Constructor method for MultiIntersectBed_perl_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
# setGeneric("MultiIntersectBed_perl_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, groupVect,withinGroupTH,outFileName){standardGeneric("MultiIntersectBed_perl_CLI")})
setGeneric("MultiIntersectBed_perl_CLI", function(inFilePath, inFileNames, outputFlag, outFilePath, outFileName, ...){standardGeneric("MultiIntersectBed_perl_CLI")})
setMethod("MultiIntersectBed_perl_CLI", signature(inFilePath="character", inFileNames="character",
outputFlag="character", outFilePath="character",outFileName="character"),
function(inFilePath, inFileNames, outputFlag, outFilePath, outFileName, cliParams="",withinGroupTH=0, groupVect=numeric(),perlPath=""){
return(new("MultiIntersectBed_perl_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, groupVect=groupVect,withinGroupTH=withinGroupTH, outFileName=outFileName, perlPath=perlPath ))
})
#
# setMethod("MultiIntersectBed_perl_CLI", signature(inFilePath="character", inFileNames="character", cliParams="missing",
# outputFlag="character", outFilePath="character",groupVect="numeric",withinGroupTH="numeric",outFileName="character"),
# function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, groupVect, withinGroupTH, outFileName ){
# cliParams=""
# return(new("MultiIntersectBed_perl_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams="",
# outputFlag=outputFlag, outFilePath=outFilePath, groupVect=groupVect,withinGroupTH=withinGroupTH, outFileName=outFileName ))
# })
# setMethod("MultiIntersectBed_perl_CLI", signature(inFilePath="character", inFileNames="character", cliParams="missing",
# outputFlag="character", outFilePath="character",groupVect="numeric",withinGroupTH="missing",outFileName="character"),
# function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, groupVect, withinGroupTH, outFileName ){
# cliParams=""
# withinGroupTH = 0
# return(new("MultiIntersectBed_perl_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams="",
# outputFlag=outputFlag, outFilePath=outFilePath, groupVect=groupVect,withinGroupTH=withinGroupTH, outFileName=outFileName ))
# })
# setMethod("MultiIntersectBed_perl_CLI", signature(inFilePath="character", inFileNames="character", cliParams="missing",
# outputFlag="character", outFilePath="character",groupVect="missing",withinGroupTH="numeric",outFileName="character"),
# function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, groupVect,withinGroupTH, outFileName ){
# groupVect = numeric()
# cliParams=""
# return(new("MultiIntersectBed_perl_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
# outputFlag=outputFlag, outFilePath=outFilePath, groupVect=groupVect, withinGroupTH=withinGroupTH, outFileName=outFileName ))
# })
# setMethod("MultiIntersectBed_perl_CLI", signature(inFilePath="character", inFileNames="character", cliParams="missing",
# outputFlag="character", outFilePath="character",groupVect="missing",withinGroupTH="missing",outFileName="character"),
# function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath, groupVect,withinGroupTH, outFileName ){
# groupVect = numeric()
# cliParams=""
# withinGroupTH = 0
# return(new("MultiIntersectBed_perl_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
# outputFlag=outputFlag, outFilePath=outFilePath, groupVect=groupVect, withinGroupTH=withinGroupTH, outFileName=outFileName ))
# })
#' @title Accessor getGroupVect
#' @export
#' @docType methods
#' @return groupVect
setGeneric("getGroupVect", function(object){standardGeneric("getGroupVect")})
setMethod("getGroupVect",signature(object="MultiIntersectBed_perl_CLI"),function(object) {
slot(object, "groupVect")
})
#' @title Accessor getPerlPath
#' @export
#' @docType methods
#' @return perlPath
setGeneric("getPerlPath", function(object){standardGeneric("getPerlPath")})
setMethod("getPerlPath",signature(object="MultiIntersectBed_perl_CLI"),function(object) {
slot(object, "perlPath")
})
#' @title Accessor getWithinGroupTH
#' @export
#' @docType methods
#' @return withinGroupTH
setGeneric("getWithinGroupTH", function(object){standardGeneric("getWithinGroupTH")})
setMethod("getWithinGroupTH",signature(object="MultiIntersectBed_perl_CLI"),function(object) {
slot(object, "withinGroupTH")
})
#' @title Accessor getOutFileName
#' @export
#' @docType methods
#' @return outFileName
setMethod("getOutFileName",signature(object="MultiIntersectBed_perl_CLI"),function(object) {
slot(object, "outFileName")
})
#' @title Generates the commands and file for MultiIntersectBed
#'
#' @param MultiIntersectBed_perl_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="MultiIntersectBed_perl_CLI"),function(object) {
#bedtools multiinter [OPTIONS] -i FILE1 FILE2 .. FILEn
if( length(getInFilePath(object)) > 1 & length(getInFilePath(object)) != length(getInFileNames(object)) ){
warning("Either one file path is given, containnig all files, or the file path vector must match the filename vector in length!")
}
if( length(getGroupVect(object)) > 1 & length(getGroupVect(object)) != length(getInFileNames(object)) ){
warning("Either one file path is given, containnig all files, or the group vector must match the filename vector in length!")
}
inFN = getInFileNames(object)
inFNtrimmed = sub("\\..+$","",inFN)
inFilending = sub( inFNtrimmed[1], "", inFN[1] )
outFN = paste0( getOutFileName(object), inFilending)
cmd1 = paste0("cd ", getOutFilePath(object))
perlApp = ifelse(getPerlPath(object) == "", "perl", file.path(getPerlPath(object), "perl"))
if(length(getGroupVect(object)) == 0){
cmd2 = paste0( perlApp," ",system.file("data/multiIntersectBed_helper.pl",package="CLIHelperPackage"),
" -o ", file.path(getOutFilePath(object),outFN ),
" -w ", getWithinGroupTH(object),
" -i ", paste0( file.path(getInFilePath(object), getInFileNames(object) ),collapse=" ") )
} else{
cmd2 = paste0( perlApp," ",system.file("data/multiIntersectBed_helper.pl",package="CLIHelperPackage"),
" -o ", file.path(getOutFilePath(object),outFN ),
" -w ", getWithinGroupTH(object),
" -g ", paste0(getGroupVect(object),collapse=" "),
" -i ", paste0( file.path(getInFilePath(object), getInFileNames(object) ),collapse=" ") )
}
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outFN), commands = c(cmd1, cmd2))
return(res)
})
#--split RNAStar_CLI
#@include CLIApplication
#'@title RNAStar_CLI
#'@section Slots:
#' \describe{
#' \item{\code{slot1}:}{inFilePath \code{"character"}}
#' \item{\code{slot2}:}{inFileNames \code{"character"}}
#' \item{\code{slot3}:}{cliParams \code{"character"}}
#' \item{\code{slot4}:}{outFilePath \code{"character"}}
#' \item{\code{slot5}:}{outputFlag \code{"character"}}
#' \item{\code{slot6}:}{genomeIndexFilePath \code{"character"}}
#' \item{\code{slot7}:}{filterSam \code{"logical"}}
#' \item{\code{slot8}:}{outputFormat \code{"character"}}
#' }
#' @name RNAStar_CLI-class
#' @export
setClass("RNAStar_CLI", contains = "CLIApplication", representation(genomeIndexFilePath="character", filterSam="logical", outputFormat="character") )
#' @title Accessor genomeIndexFilePath
#' @export
#' @docType methods
#' @return genomeIndexFilePath
setGeneric("getGenomeIndexFilePath", function(object) standardGeneric("getGenomeIndexFilePath"))
setMethod("getGenomeIndexFilePath",signature(object="RNAStar_CLI"),function(object) {
slot(object, "genomeIndexFilePath")
})
#' @title Accessor getOutputFormat already defined in Samtools
#' @export
#' @docType methods
#' @return outputFormat
setMethod("getOutputFormat",signature(object="RNAStar_CLI"),function(object) {
slot(object, "outputFormat")
})
#' @title Accessor filterSam
#' @export
#' @docType methods
#' @return getFilterSam
setGeneric("getFilterSam", function(object) standardGeneric("getFilterSam"))
setMethod("getFilterSam",signature(object="RNAStar_CLI"),function(object) {
slot(object, "filterSam")
})
#' @title Constructor method for RNAStar_CLI
#' @param inFilePath (inFileNames may also be specified otherwise they will be fetched by list.files)
#' @export
#' @docType methods
setGeneric("RNAStar_CLI", function(inFilePath, inFileNames, cliParams, outputFlag, outFilePath,genomeIndexFilePath,filterSam, outputFormat){standardGeneric("RNAStar_CLI")})
setMethod("RNAStar_CLI", signature( inFilePath="character", inFileNames="character", cliParams="character",
outputFlag="character", outFilePath="character",
genomeIndexFilePath="character", filterSam="logical", outputFormat="character"),
function(inFilePath,inFileNames, cliParams, outputFlag, outFilePath, genomeIndexFilePath,filterSam, outputFormat){
return(
new("RNAStar_CLI", inFilePath=inFilePath, inFileNames=inFileNames, cliParams=cliParams,
outputFlag=outputFlag, outFilePath=outFilePath, genomeIndexFilePath=genomeIndexFilePath,filterSam=filterSam, outputFormat=outputFormat)
)
})
#' @title Generates the commands and possibly resulting files/folders of Tophat2
#'
#' @param RNAStar_CLI
#' @return CmdGenResult
#' @rdname generateCommandResult-method
#' @export
setMethod("generateCommandResult",signature(object="RNAStar_CLI"),function(object) {
# USAGE:
# STAR --genomeDir <Directory with the Genome Index> --runThreadN <# cpus> --readFilesIn <FASTQ file> --outFileNamePrefix <OutputPrefix>
if(length(getInFileNames(object)) > 1){
stop("Only one fasta file per call, if more calls please use option --genomeLoad LoadAndKeep which will keep the index file in the memory")
}
#preparing input files
inFP = getInFilePath(object)
inFN = getInFileNames(object)
#preparing output files
sampleOutDir = paste0( paste0( sub("\\.fastq$","",inFN),getOutputFlag(object)) )
#generating the tophat base directory
outfilepath = getOutFilePath(object)
if( getOutputFormat(object) == "bam" ){
outFileName = paste0(getOutputFlag(object), "Aligned.out.bam")
} else{
outFileName = paste0(getOutputFlag(object), "Aligned.out.sam")
outFileName_filt = paste0(getOutputFlag(object), "Aligned.out.filtered.sam")
}
# dir.create(outfilepath)
# setwd(outfilepath)
cmd1 = paste("mkdir", outfilepath) #if only executed in terminal!
cmd2 = paste("cd ", outfilepath)
#generating the tophat command
cmd3 = paste0( "STAR --genomeDir ",getGenomeIndexFilePath(object)," --readFilesIn ",file.path(inFP,inFN),
" --outFileNamePrefix ",getOutputFlag(object), " ", paste0(getCliParams(object), collapse=" ") )
#" --runThreadN 6 --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1 --clip3pAdapterSeq ATCACCGACTGCCCATAGAGAGGCTGAGAC --clip3pAdapterMMp 0.1 --outFilterMultimapNmax 100"
#(>=16b matched to the genome, number of mismatches <= 5% of mapped length, i.e. 0MM for 16-19b, 1MM for 20-39b etc, splicing switched off). will also trim by IonProton 3pAdapter obtained from Martina. If more than 100 matches in the genome - filter out reads!
#After running, filtering: awk script will filter out all alignments that are trimmed by more than 1 base from the 5' end!
cmd4 = ""
if(getFilterSam(object) & getOutputFormat(object) != "bam"){
cmd4 = paste("cd ", outfilepath)
cmd5 = paste0( "awk '{S=0; split($6,C,/[0-9]*/); n=split($6,L,/[NMSID]/);
if (and($2,0x10)>0 && C[n]==\"S\") {S=L[n-1]} else if (and($2,0x10)==0 && C[2]==\"S\") {S=L[1]}; if (S<=1) print }' ",outFileName," > ",outFileName_filt )
cmd6 = paste0( "rm ",outFileName )#removing the unfiltered file
cmd7 = paste0( "mv ", outFileName_filt, " ", outFileName) #renaming the file
cmd3 = c(cmd3, cmd4, cmd5, cmd6, cmd7)
}
if( getOutputFormat(object) != "bam" ){
outBamFN = paste0(sub(".sam$","",outFileName ),".bam")
#Writing sam to bam file
cmd4 = paste0( "samtools view -Sb ",outFileName," > ",outBamFN)
cmd4 = c(cmd4, paste0("rm ",outFileName) )
} else{
outBamFN = outFileName
}
res = CmdGenResult(CLIApplication = object, OutResultReference = FilesOutput(outBamFN) , commands = c(cmd1, cmd2, cmd3, cmd4))
return(res)
})
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