annotate lib.r @ 0:ac5f2936575b draft

planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0

##
## This function launch IPO functions to get the best parameters for xcmsSet
## A sample among the whole dataset is used to save time
##
ipo4xcmsSet = function(directory, parametersOutput, listArguments, samplebyclass=4) {
    setwd(directory)

    files = list.files(".", recursive=T)  # "KO/ko15.CDF" "KO/ko16.CDF" "WT/wt15.CDF" "WT/wt16.CDF"
    files_classes = basename(dirname(files))    # "KO", "KO", "WT", "WT"

    mzmlfile = files
    if (samplebyclass > 0) {
        #random selection of N files for IPO in each class
        classes<-unique(basename(dirname(files)))
        mzmlfile = NULL
        for (class_i in classes){
            files_class_i = files[files_classes==class_i]
            if (samplebyclass > length(files_class_i)) {
                mzmlfile = c(mzmlfile, files_class_i)
            } else {
                mzmlfile = c(mzmlfile,sample(files_class_i,samplebyclass))
            }
        }
    }
    #@TODO: else, must we keep the RData to been use directly by group?

    cat("\t\tSamples used:\n")
    print(mzmlfile)

    peakpickingParameters = getDefaultXcmsSetStartingParams(listArguments[["method"]]) #get default parameters of IPO

    # filter listArguments to only get releavant parameters and complete with those that are not declared
    peakpickingParametersUser = c(listArguments[names(listArguments) %in% names(peakpickingParameters)], peakpickingParameters[!(names(peakpickingParameters) %in% names(listArguments))])
    peakpickingParametersUser$verbose.columns = TRUE

    #peakpickingParametersUser$profparam <- list(step=0.005) #not yet used by IPO have to think of it for futur improvement
    resultPeakpicking = optimizeXcmsSet(mzmlfile, peakpickingParametersUser, nSlaves=peakpickingParametersUser$nSlaves, subdir="../IPO_results") #some images generated by IPO

    # export
    resultPeakpicking_best_settings_parameters = resultPeakpicking$best_settings$parameters[!(names(resultPeakpicking$best_settings$parameters) %in% c("nSlaves","verbose.columns"))]
    write.table(t(as.data.frame(resultPeakpicking_best_settings_parameters)), file=parametersOutput,  sep="\t", row.names=T, col.names=F, quote=F)  #can be read by user

    return (resultPeakpicking$best_settings$xset)
}

##
## This function launch IPO functions to get the best parameters for group and retcor
##
ipo4retgroup = function(xset, directory, parametersOutput, listArguments, samplebyclass=4) {
    setwd(directory)

    files = list.files(".", recursive=T)  # "KO/ko15.CDF" "KO/ko16.CDF" "WT/wt15.CDF" "WT/wt16.CDF"
    files_classes = basename(dirname(files))    # "KO", "KO", "WT", "WT"

    retcorGroupParameters = getDefaultRetGroupStartingParams(listArguments[["retcorMethod"]]) #get default parameters of IPO
    print(retcorGroupParameters)
    # filter listArguments to only get releavant parameters and complete with those that are not declared
    retcorGroupParametersUser = c(listArguments[names(listArguments) %in% names(retcorGroupParameters)], retcorGroupParameters[!(names(retcorGroupParameters) %in% names(listArguments))])
    print("retcorGroupParametersUser")
    print(retcorGroupParametersUser)
    resultRetcorGroup = optimizeRetGroup(xset, retcorGroupParametersUser, nSlaves=listArguments[["nSlaves"]], subdir="../IPO_results") #some images generated by IPO

    # export
    resultRetcorGroup_best_settings_parameters = resultRetcorGroup$best_settings
    write.table(t(as.data.frame(resultRetcorGroup_best_settings_parameters)), file=parametersOutput,  sep="\t", row.names=T, col.names=F, quote=F)  #can be read by user
}




##
## This function check if xcms will found all the files
##
#@author Gildas Le Corguille [e-mail] ABiMS TEAM
checkFilesCompatibilityWithXcms <- function(directory) {
  cat("Checking files filenames compatibilities with xmcs...\n")
  # WHAT XCMS WILL FIND
  filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
  filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
  info <- file.info(directory)
  listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
  files <- c(directory[!info$isdir], listed)
  files_abs <- file.path(getwd(), files)
  exists <- file.exists(files_abs)
  files[exists] <- files_abs[exists]
  files[exists] <- sub("//","/",files[exists])

  # WHAT IS ON THE FILESYSTEM
  filesystem_filepaths=system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T)
  filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]

  # COMPARISON
  if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
    write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
    write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
    stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")

  }
}



##
## This function check if XML contains special caracters. It also checks integrity and completness.
##
#@author Misharl Monsoor [e-mail] ABiMS TEAM
checkXmlStructure <- function (directory) {
  cat("Checking XML structure...\n")

  cmd=paste("IFS=$'\n'; for xml in $(find",directory,"-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
  capture=system(cmd,intern=TRUE)

  if (length(capture)>0){
    #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
    write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
    write(capture, stderr())
    stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
  }

}