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planemo upload commit 8dfb0b11442ccce78165b5d8f07555ccbd303cce
author lecorguille
date Thu, 30 Mar 2017 11:27:09 -0400
parents 9fa5856f6184
children 364756ea5f42
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1 ##
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2 ## This function launch IPO functions to get the best parameters for xcmsSet
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3 ## A sample among the whole dataset is used to save time
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4 ##
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5 ipo4xcmsSet = function(directory, parametersOutput, listArguments, samplebyclass=4) {
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6 setwd(directory)
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8 files = list.files(".", recursive=T) # "KO/ko15.CDF" "KO/ko16.CDF" "WT/wt15.CDF" "WT/wt16.CDF"
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9 files_classes = basename(dirname(files)) # "KO", "KO", "WT", "WT"
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11 mzmlfile = files
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12 if (samplebyclass > 0) {
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13 #random selection of N files for IPO in each class
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14 classes<-unique(basename(dirname(files)))
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15 mzmlfile = NULL
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16 for (class_i in classes){
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17 files_class_i = files[files_classes==class_i]
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18 if (samplebyclass > length(files_class_i)) {
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19 mzmlfile = c(mzmlfile, files_class_i)
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20 } else {
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21 mzmlfile = c(mzmlfile,sample(files_class_i,samplebyclass))
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22 }
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23 }
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24 }
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25 #@TODO: else, must we keep the RData to been use directly by group?
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27 cat("\t\tSamples used:\n")
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28 print(mzmlfile)
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30 peakpickingParameters = getDefaultXcmsSetStartingParams(listArguments[["method"]]) #get default parameters of IPO
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32 # filter listArguments to only get releavant parameters and complete with those that are not declared
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33 peakpickingParametersUser = c(listArguments[names(listArguments) %in% names(peakpickingParameters)], peakpickingParameters[!(names(peakpickingParameters) %in% names(listArguments))])
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34 peakpickingParametersUser$verbose.columns = TRUE
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36 #peakpickingParametersUser$profparam <- list(step=0.005) #not yet used by IPO have to think of it for futur improvement
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37 resultPeakpicking = optimizeXcmsSet(mzmlfile, peakpickingParametersUser, nSlaves=peakpickingParametersUser$nSlaves, subdir="../IPO_results") #some images generated by IPO
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39 # export
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40 resultPeakpicking_best_settings_parameters = resultPeakpicking$best_settings$parameters[!(names(resultPeakpicking$best_settings$parameters) %in% c("nSlaves","verbose.columns"))]
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41 write.table(t(as.data.frame(resultPeakpicking_best_settings_parameters)), file=parametersOutput, sep="\t", row.names=T, col.names=F, quote=F) #can be read by user
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42
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43 return (resultPeakpicking$best_settings$xset)
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44 }
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46 ##
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47 ## This function launch IPO functions to get the best parameters for group and retcor
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48 ##
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49 ipo4retgroup = function(xset, directory, parametersOutput, listArguments, samplebyclass=4) {
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50 setwd(directory)
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52 files = list.files(".", recursive=T) # "KO/ko15.CDF" "KO/ko16.CDF" "WT/wt15.CDF" "WT/wt16.CDF"
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53 files_classes = basename(dirname(files)) # "KO", "KO", "WT", "WT"
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55 retcorGroupParameters = getDefaultRetGroupStartingParams(listArguments[["retcorMethod"]]) #get default parameters of IPO
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56 print(retcorGroupParameters)
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57 # filter listArguments to only get releavant parameters and complete with those that are not declared
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58 retcorGroupParametersUser = c(listArguments[names(listArguments) %in% names(retcorGroupParameters)], retcorGroupParameters[!(names(retcorGroupParameters) %in% names(listArguments))])
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59 print("retcorGroupParametersUser")
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60 print(retcorGroupParametersUser)
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61 resultRetcorGroup = optimizeRetGroup(xset, retcorGroupParametersUser, nSlaves=listArguments[["nSlaves"]], subdir="../IPO_results") #some images generated by IPO
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62
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63 # export
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64 resultRetcorGroup_best_settings_parameters = resultRetcorGroup$best_settings
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65 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
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66 }
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71 ##
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72 ## This function check if xcms will found all the files
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73 ##
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74 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
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75 checkFilesCompatibilityWithXcms <- function(directory) {
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76 cat("Checking files filenames compatibilities with xmcs...\n")
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77 # WHAT XCMS WILL FIND
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78 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
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79 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
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80 info <- file.info(directory)
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81 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
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82 files <- c(directory[!info$isdir], listed)
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83 files_abs <- file.path(getwd(), files)
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84 exists <- file.exists(files_abs)
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85 files[exists] <- files_abs[exists]
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86 files[exists] <- sub("//","/",files[exists])
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87
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88 # WHAT IS ON THE FILESYSTEM
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89 filesystem_filepaths=system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T)
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90 filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
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91
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92 # COMPARISON
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93 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
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94 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
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95 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
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96 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
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97
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98 }
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99 }
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102
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103 ##
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104 ## This function check if XML contains special caracters. It also checks integrity and completness.
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105 ##
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106 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
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107 checkXmlStructure <- function (directory) {
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108 cat("Checking XML structure...\n")
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109
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110 cmd=paste("IFS=$'\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;")
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111 capture=system(cmd,intern=TRUE)
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112
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113 if (length(capture)>0){
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114 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
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115 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
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116 write(capture, stderr())
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117 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
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118 }
6
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119
3
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120 }