Mercurial > repos > tomnl > mspurity_createmsp

annotate createDatabase.R @ 6:2b13f1ae8041 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 14eafbdb65f491713d1314d77c454defd137c392
author tomnl
date Tue, 18 Jun 2019 11:03:56 -0400
parents 3de08f3c4fb6
children e6a78f89ee07
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1 library(msPurity)
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2 library(optparse)
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3 library(xcms)
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4 library(CAMERA)
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5 print(sessionInfo())
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6 print('CREATING DATABASE')
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10 xset_pa_filename_fix <- function(opt, pa, xset){
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12 if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
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13 # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
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14 # needs to be done due to Galaxy moving the files around and screwing up any links to files
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16 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
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17 filepaths <- filepaths[filepaths != ""]
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18 new_names <- basename(filepaths)
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20 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
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21 galaxy_names <- galaxy_names[galaxy_names != ""]
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23 nsave <- names(pa@fileList)
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24 old_filenames <- basename(pa@fileList)
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25 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
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26 names(pa@fileList) <- nsave
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28 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
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29 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
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30 }
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33 if(!all(basename(pa@fileList)==basename(xset@filepaths))){
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34 if(!all(names(pa@fileList)==basename(xset@filepaths))){
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35 print('FILELISTS DO NOT MATCH')
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36 message('FILELISTS DO NOT MATCH')
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37 quit(status = 1)
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38 }else{
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39 xset@filepaths <- unname(pa@fileList)
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40 }
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41 }
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43 print(xset@phenoData)
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44 print(xset@filepaths)
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46 return(list(pa, xset))
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47 }
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52 option_list <- list(
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53 make_option(c("-o", "--outDir"), type="character"),
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54 make_option("--pa", type="character"),
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55 make_option("--xset_xa", type="character"),
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56 make_option("--xcms_camera_option", type="character"),
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57 make_option("--eic", action="store_true"),
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58 make_option("--cores", default=4),
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59 make_option("--mzML_files", type="character"),
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60 make_option("--galaxy_names", type="character"),
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61 make_option("--grpPeaklist", type="character")
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62 )
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65 # store options
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66 opt<- parse_args(OptionParser(option_list=option_list))
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67 print(opt)
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69 loadRData <- function(rdata_path, name){
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70 #loads an RData file, and returns the named xset object if it is there
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71 load(rdata_path)
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72 return(get(ls()[ls() %in% name]))
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73 }
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74
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75 getxcmsSetObject <- function(xobject) {
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76 # XCMS 1.x
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77 if (class(xobject) == "xcmsSet")
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78 return (xobject)
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79 # XCMS 3.x
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80 if (class(xobject) == "XCMSnExp") {
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81 # Get the legacy xcmsSet object
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82 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
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83 sampclass(xset) <- xset@phenoData$sample_group
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84 return (xset)
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85 }
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86 }
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88
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89 print(paste('pa', opt$pa))
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90 print(opt$xset)
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92 print(opt$xcms_camera_option)
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93 # Requires
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94 pa <- loadRData(opt$pa, 'pa')
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97 print(pa@fileList)
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98
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99
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100
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101 if (opt$xcms_camera_option=='xcms'){
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102
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103 xset <- loadRData(opt$xset, c('xset','xdata'))
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104 xset <- getxcmsSetObject(xset)
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105 fix <- xset_pa_filename_fix(opt, pa, xset)
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106 pa <- fix[[1]]
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107 xset <- fix[[2]]
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108 xa <- NULL
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109 }else{
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110
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111 xa <- loadRData(opt$xset, 'xa')
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112 fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet)
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113 pa <- fix[[1]]
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114 xa@xcmsSet <- fix[[2]]
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115 xset <- NULL
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116 }
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117
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118
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119
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120 if(is.null(opt$grp_peaklist)){
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121 grpPeaklist = NA
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122 }else{
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123 grpPeaklist = opt$grp_peaklist
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124 }
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125
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126
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127
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128 dbPth <- msPurity::createDatabase(pa,
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129 xset=xset,
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130 xsa=xa,
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131 outDir=opt$outDir,
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132 grpPeaklist=grpPeaklist,
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133 dbName='createDatabase_output.sqlite'
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134 )
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135
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136
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137
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138
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139
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140 if (!is.null(opt$eic)){
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141
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142 if (is.null(xset)){
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143 xset <- xa@xcmsSet
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144 }
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145 # previous check should have matched filelists together
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146 xset@filepaths <- unname(pa@fileList)
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147
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148 convert2Raw <- function(x, xset){
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149 sid <- unique(x$sample)
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150 # for each file get list of peaks
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151 x$rt_raw <- xset@rt$raw[[sid]][match(x$rt, xset@rt$corrected[[sid]])]
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152 x$rtmin_raw <- xset@rt$raw[[sid]][match(x$rtmin, xset@rt$corrected[[sid]])]
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153 x$rtmax_raw <- xset@rt$raw[[sid]][match(x$rtmax, xset@rt$corrected[[sid]])]
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154 return(x)
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155
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156 }
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157
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158 xset@peaks <- as.matrix(plyr::ddply(data.frame(xset@peaks), ~ sample, convert2Raw, xset=xset))
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159 closeAllConnections()
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160 # Saves the EICS into the previously created database
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161 px <- msPurity::purityX(xset, saveEIC = TRUE,
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162 cores=1, sqlitePth=dbPth,
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163 rtrawColumns = TRUE)
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164
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165 }
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166
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167 closeAllConnections()