Mercurial > repos > lecorguille > ipo
diff lib.r @ 0:ac5f2936575b draft
planemo upload commit 131562ad89c33a2f87754936ce3c8fe6899484c0
author | lecorguille |
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date | Thu, 03 Aug 2017 06:00:00 -0400 |
parents | |
children | ae8de756dfcf |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib.r Thu Aug 03 06:00:00 2017 -0400 @@ -0,0 +1,120 @@ +## +## 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 lecorguille@sb-roscoff.fr 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 $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T) + filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)] + + # COMPARISON + if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) { + write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr()) + write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr()) + stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.") + + } +} + + + +## +## This function check if XML contains special caracters. It also checks integrity and completness. +## +#@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM +checkXmlStructure <- function (directory) { + cat("Checking XML structure...\n") + + cmd=paste("IFS=$'\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") + } + +}