annotate galaxy/tools/LC-MSMS/XSeekerPreparator.R @ 6:207e36770d18 draft

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author lain
date Wed, 20 Jan 2021 17:47:51 +0000
parents a174cbbb12dd
children 5be8a770a11d
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3 TOOL_NAME <- "XSeekerPreparator"
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4 VERSION <- "1.1.3"
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5
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6 OUTPUT_SPECIFIC_TOOL <- "XSeeker_Galaxy"
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7
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8 ENRICHED_RDATA_VERSION <- paste("1.1.2", OUTPUT_SPECIFIC_TOOL, sep="-")
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9 ENRICHED_RDATA_DOC <- sprintf("
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10 Welcome to the enriched <Version %s> of the output of CAMERA/xcms.
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11 This doc was generated by the tool: %s - Version %s
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12 To show the different variables contained in this rdata, type:
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13 - `load('this_rdata.rdata', rdata_env <- new.env())`
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14 - `names(rdata_env)`
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15
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16 Sections
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17 ######
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18
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19
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20 This tools helpers
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21 ------
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22 The version number is somewhat special because the evolution of the
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23 rdata's format is non-linear.
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24 There may be different branches, each evolving separatly.
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25 To reflect these branches's diversions, there may be a prepended
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26 branch name following this format:
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27 major.minor.patch-branch_name
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28 Like this, we can process rdata with the same tool, and output
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29 rdata formated differently, for each tool.
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30
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31
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32 - enriched_rdata:
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33 - Description: flag created by that tool to tell it was enriched.
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34 - Retrieval method: enriched_rdata <- TRUE
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35
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36 - enriched_rdata_version:
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37 - Description: A flag created by that tool to tell which version of
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38 this tool has enriched the rdata.
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39 - Retrieval method: enriched_rdata_version <- sprintf(\"%s\", ENRICHED_RDATA_VERSION)
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40
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41 - enriched_rdata_doc:
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42 - Description: Contains the documentation string.
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43
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44 Data from original mzxml file
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45 ------
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46 - tic:
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47 - Description: Those are the tic values from the original mzxml
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48 file, extracted using xcms 2.
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49 - Retrieval method: xcms::xcmsRaw('original_file.mzxml')@tic
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50 - xcms version: 2.0
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51
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52 - mz:
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53 - Description: Those are the m/z values from the original mzxml
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54 file, extracted using xcms 2.
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55 - Retrieval method: xcms::xcmsRaw('original_file.mzxml')@env$mz
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56 - xcms version: 2.0
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57
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58 - scanindex:
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59 - Description: Those are the scanindex values from the original mzxml
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60 file, extracted using xcms 2.
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61 - Retrieval method: xcms::xcmsRaw('original_file.mzxml')@scanindex
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62 - xcms version: 2.0
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63
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64 - scantime:
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65 - Description: Those are the scantime values from the original mzxml
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66 file, extracted using xcms 2.
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67 - Retrieval method: xcms::xcmsRaw('original_file.mzxml')@scantime
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68 - xcms version: 2.0
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69
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70 - intensity:
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71 - Description: Those are the intensity values from the original mzxml
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72 file, extracted using xcms 2.
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73 - Retrieval method: xcms::xcmsRaw('original_file.mzxml')@env$intensity
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74 - xcms version: 2.0
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75
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76 - polarity:
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77 - Description: Those are the polarity values from the original mzxml
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78 file, extracted using xcms 2.
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79 - Retrieval method: as.character(xcms::xcmsRaw('original_file.mzxml')@polarity[[1]])
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80 - xcms version: 2.0
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81
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82 Data taken from incoming rdata
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83 ------
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84 - variableMetadata:
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85 - Description: Unmodified copy of variableMetadata from incoming rdata.
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86 - Retrieval method: rdata_file$variableMetadata
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87
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88 - process_params:
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89 - Description: Those are the processing parameters values from the
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90 curent rdata. They have been simplified to allow easy access like:
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91 for (params in process_params) {
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92 if (params[[\"xfunction\"]] == \"annotatediff\") {
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93 process_peak_picking_params(params)
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94 }
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95 }
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96 - Retrieval method:
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97 ## just he same list, but simplified
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98 process_params <- list()
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99 for (list_name in names(rdata_file$listOFlistArguments)) {
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100 param_list <- list()
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101 for (param_name in names(rdata_file$listOFlistArguments[[list_name]])) {
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102 param_list[[param_name]] <- rdata_file$listOFlistArguments[[list_name]][[param_name]]
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103 }
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104 process_params[[length(process_params)+1]] <- param_list
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105 }
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106 ", ENRICHED_RDATA_VERSION, TOOL_NAME, VERSION, ENRICHED_RDATA_VERSION)
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107
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108
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109
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110 get_models <- function(path) {
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111 if (is.null(path)) {
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112 stop("No models to define the database schema")
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113 } else {
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114 message(sprintf("Loading models from %s", path))
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115 }
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116 ## galaxy mangles the "@" to a "__at__"
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117 if (substr(path, 1, 9) == "git__at__") {
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118 path <- sub("^git__at__", "git@", path, perl=TRUE)
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119 }
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120 if (
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121 substr(path, 1, 4) == "git@"
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122 || substr(path, length(path)-4, 4) == ".git"
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123 ) {
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124 return (get_models_from_git(path))
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125 }
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126 if (substr(path, 1, 4) == "http") {
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127 return (get_models_from_url(path))
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128 }
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129 return (source(path)$value)
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130 }
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131
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132 get_models_from_git <- function (url, target_file="models.R", rm=TRUE) {
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133 tmp <- tempdir()
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134 message(sprintf("Cloning %s", url))
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135 system2("git", c("clone", url, tmp))
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136 result <- search_tree(file.path(tmp, dir), target_file)
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137 if (!is.null(result)) {
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138 models <- source(result)$value
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139 if (rm) {
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140 unlink(tmp, recursive=TRUE)
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141 }
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142 return (models)
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143 }
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144 if (rm) {
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145 unlink(tmp, recursive=TRUE)
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146 }
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147 stop(sprintf(
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148 "Could not find any file named \"%s\" in this repo",
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149 target_file
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150 ))
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151 }
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152
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153 get_models_from_url <- function (url, target_file="models.R", rm=TRUE) {
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154 tmp <- tempdir()
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155 message(sprintf("Downloading %s", url))
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156 result <- file.path(tmp, target_file)
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157 if (download.file(url, destfile=result) == 0) {
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158 models <- source(result)$value
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159 if (rm) {
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160 unlink(tmp, recursive=TRUE)
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161 }
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162 return (models)
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163 }
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164 if (rm) {
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165 unlink(tmp, recursive=TRUE)
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166 }
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167 stop("Could not download any file at this adress.")
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168 }
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169
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170 search_tree <- function(path, target) {
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171 target <- tolower(target)
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172 for (file in list.files(path)) {
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173 if (is.dir(file)) {
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174 result <- search_tree(file.path(path, file), target)
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175 if (!is.null(result)) {
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176 return (result)
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177 }
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178 } else if (tolower(file) == target) {
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179 return (file.path(path, file))
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180 }
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181 }
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182 return (NULL)
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183 }
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184
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185 create_database <- function(orm) {
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186 orm$recreate_database(no_exists=FALSE)
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187 set_database_version(orm, "created")
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188 }
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189
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190 insert_adducts <- function(orm) {
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191 message("Creating adducts...")
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192 adducts <- list(
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193 list("[M-H2O-H]-",1,-1,-48.992020312000001069,1,0,0.5,"H0","H1O3"),
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194 list("[M-H-Cl+O]-",1,-1,-19.981214542000000022,2,0,0.5,"O1","H1Cl1"),
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195 list("[M-Cl+O]-",1,-1,-18.973389510000000512,3,0,0.5,"O1","Cl1"),
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196 list("[M-3H]3-",1,-3,-3.0218293560000000219,4,0,1.0,"H0","H3"),
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197 list("[2M-3H]3-",2,-3,-3.0218293560000000219,4,0,0.5,"H0","H3"),
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198 list("[3M-3H]3-",3,-3,-3.0218293560000000219,4,0,0.5,"H0","H3"),
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199 list("[M-2H]2-",1,-2,-2.0145529039999998666,5,0,1.0,"H0","H2"),
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200 list("[2M-2H]2-",2,-2,-2.0145529039999998666,5,0,0.5,"H0","H2"),
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201 list("[3M-2H]2-",3,-2,-2.0145529039999998666,5,0,0.5,"H0","H2"),
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202 list("[M-H]-",1,-1,-1.0072764519999999333,6,1,1.0,"H0","H1"),
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lain
parents:
diff changeset
203 list("[2M-H]-",2,-1,-1.0072764519999999333,6,0,0.5,"H0","H1"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
204 list("[3M-H]-",3,-1,-1.0072764519999999333,6,0,0.5,"H0","H1"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
205 list("[M]+",1,1,-0.00054858000000000000945,7,1,1.0,"H0","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
206 list("[M]-",1,-1,0.00054858000000000000945,8,1,1.0,"H0","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
207 list("[M+H]+",1,1,1.0072764519999999333,9,1,1.0,"H1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
208 list("[2M+H]+",2,1,1.0072764519999999333,9,0,0.5,"H1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
209 list("[3M+H]+",3,1,1.0072764519999999333,9,0,0.25,"H1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
210 list("[M+2H]2+",1,2,2.0145529039999998666,10,0,0.75,"H2","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
211 list("[2M+2H]2+",2,2,2.0145529039999998666,10,0,0.5,"H2","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
212 list("[3M+2H]2+",3,2,2.0145529039999998666,10,0,0.25,"H2","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
213 list("[M+3H]3+",1,3,3.0218293560000000219,11,0,0.75,"H3","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
214 list("[2M+3H]3+",2,3,3.0218293560000000219,11,0,0.5,"H3","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
215 list("[3M+3H]3+",3,3,3.0218293560000000219,11,0,0.25,"H3","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
216 list("[M-2H+NH4]-",1,-1,16.019272654000001665,12,0,0.25,"N1H4","H2"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
217 list("[2M-2H+NH4]-",2,-1,16.019272654000001665,12,0,0.0,"N1H4","H2"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
218 list("[3M-2H+NH4]-",3,-1,16.019272654000001665,12,0,0.25,"N1H4","H2"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
219 list("[M+NH4]+",1,1,18.033825558000000199,13,1,1.0,"N1H4","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
220 list("[2M+NH4]+",2,1,18.033825558000000199,13,0,0.5,"N1H4","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
221 list("[3M+NH4]+",3,1,18.033825558000000199,13,0,0.25,"N1H4","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
222 list("[M+H+NH4]2+",1,2,19.041102009999999467,14,0,0.5,"N1H5","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
223 list("[2M+H+NH4]2+",2,2,19.041102009999999467,14,0,0.5,"N1H5","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
224 list("[3M+H+NH4]2+",3,2,19.041102009999999467,14,0,0.25,"N1H5","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
225 list("[M+Na-2H]-",1,-1,20.974668176000001551,15,0,0.75,"Na1","H2"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
226 list("[2M-2H+Na]-",2,-1,20.974668176000001551,15,0,0.25,"Na1","H2"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
227 list("[3M-2H+Na]-",3,-1,20.974668176000001551,15,0,0.25,"Na1","H2"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
228 list("[M+Na]+",1,1,22.989221080000000086,16,1,1.0,"Na1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
229 list("[2M+Na]+",2,1,22.989221080000000086,16,0,0.5,"Na1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
230 list("[3M+Na]+",3,1,22.989221080000000086,16,0,0.25,"Na1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
231 list("[M+H+Na]2+",1,2,23.996497531999999353,17,0,0.5,"Na1H1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
232 list("[2M+H+Na]2+",2,2,23.996497531999999353,17,0,0.5,"Na1H1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
233 list("[3M+H+Na]2+",3,2,23.996497531999999353,17,0,0.25,"Na1H1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
234 list("[M+2H+Na]3+",1,3,25.003773983999998619,18,0,0.25,"H2Na1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
235 list("[M+CH3OH+H]+",1,1,33.033491200000000276,19,0,0.25,"C1O1H5","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
236 list("[M-H+Cl]2-",1,-2,33.962124838000001148,20,0,1.0,"Cl1","H1"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
237 list("[2M-H+Cl]2-",2,-2,33.962124838000001148,20,0,0.5,"Cl1","H1"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
238 list("[3M-H+Cl]2-",3,-2,33.962124838000001148,20,0,0.5,"Cl1","H1"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
239 list("[M+Cl]-",1,-1,34.969401290000000416,21,1,1.0,"Cl1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
240 list("[2M+Cl]-",2,-1,34.969401290000000416,21,0,0.5,"Cl1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
241 list("[3M+Cl]-",3,-1,34.969401290000000416,21,0,0.5,"Cl1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
242 list("[M+K-2H]-",1,-1,36.948605415999999479,22,0,0.5,"K1","H2"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
243 list("[2M-2H+K]-",2,-1,36.948605415999999479,22,0,0.0,"K1","H2"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
244 list("[3M-2H+K]-",3,-1,36.948605415999999479,22,0,0.0,"K1","H2"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
245 list("[M+K]+",1,1,38.963158319999998013,23,1,1.0,"K1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
246 list("[2M+K]+",2,1,38.963158319999998013,23,0,0.5,"K1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
247 list("[3M+K]+",3,1,38.963158319999998013,23,0,0.25,"K1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
248 list("[M+H+K]2+",1,2,39.970434771999997281,24,0,0.5,"K1H1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
249 list("[2M+H+K]2+",2,2,39.970434771999997281,24,0,0.5,"K1H1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
250 list("[3M+H+K]2+",3,2,39.970434771999997281,24,0,0.25,"K1H1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
251 list("[M+ACN+H]+",1,1,42.033825557999996646,25,0,0.25,"C2H4N1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
252 list("[2M+ACN+H]+",2,1,42.033825557999996646,25,0,0.25,"C2H4N1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
253 list("[M+2Na-H]+",1,1,44.971165708000000902,26,0,0.5,"Na2","H1"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
254 list("[2M+2Na-H]+",2,1,44.971165708000000902,26,0,0.25,"Na2","H1"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
255 list("[3M+2Na-H]+",3,1,44.971165708000000902,26,0,0.25,"Na2","H1"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
256 list("[2M+FA-H]-",2,-1,44.998202851999998586,27,0,0.25,"C1O2H2","H1"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
257 list("[M+FA-H]-",1,-1,44.998202851999998586,27,0,0.5,"C1O2H2","H1"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
258 list("[M+2Na]2+",1,2,45.978442160000000172,28,0,0.5,"Na2","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
259 list("[2M+2Na]2+",2,2,45.978442160000000172,28,0,0.5,"Na2","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
260 list("[3M+2Na]2+",3,2,45.978442160000000172,28,0,0.25,"Na2","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
261 list("[M+H+2Na]3+",1,3,46.985718611999999438,29,0,0.25,"H1Na2","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
262 list("[M+H+FA]+",1,1,47.012755755999997122,30,0,0.25,"C1O2H3","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
263 list("[M+Hac-H]-",1,-1,59.013852915999997607,31,0,0.25,"C2O2H4","H1"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
264 list("[2M+Hac-H]-",2,-1,59.013852915999997607,31,0,0.25,"C2O2H4","H1"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
265 list("[M+IsoProp+H]+",1,1,61.064791327999998317,32,0,0.25,"C3H9O1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
266 list("[M+Na+K]2+",1,2,61.9523793999999981,33,0,0.5,"Na1K1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
267 list("[2M+Na+K]2+",2,2,61.9523793999999981,33,0,0.5,"Na1K1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
268 list("[3M+Na+K]2+",3,2,61.9523793999999981,33,0,0.25,"Na1K1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
269 list("[M+NO3]-",1,-1,61.988366450000000895,34,0,0.5,"N1O3","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
270 list("[M+ACN+Na]+",1,1,64.015770185999997464,35,0,0.25,"C2H3N1Na1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
271 list("[2M+ACN+Na]+",2,1,64.015770185999997464,35,0,0.25,"C2H3N1Na1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
272 list("[M+NH4+FA]+",1,1,64.039304861999994502,36,0,0.25,"N1C1O2H6","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
273 list("[M-2H+Na+FA]-",1,-1,66.980147479999999405,37,0,0.5,"NaC1O2H2","H2"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
274 list("[M+3Na]3+",1,3,68.967663239999993153,38,0,0.25,"Na3","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
275 list("[M+Na+FA]+",1,1,68.99470038399999794,39,0,0.25,"Na1C1O2H2","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
276 list("[M+2Cl]2-",1,-2,69.938802580000000832,40,0,1.0,"Cl2","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
277 list("[2M+2Cl]2-",2,-2,69.938802580000000832,40,0,0.5,"Cl2","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
278 list("[3M+2Cl]2-",3,-2,69.938802580000000832,40,0,0.5,"Cl2","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
279 list("[M+2K-H]+",1,1,76.919040187999996758,41,0,0.5,"K2","H1"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
280 list("[2M+2K-H]+",2,1,76.919040187999996758,41,0,0.25,"K2","H1"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
281 list("[3M+2K-H]+",3,1,76.919040187999996758,41,0,0.25,"K2","H1"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
282 list("[M+2K]2+",1,2,77.926316639999996028,42,0,0.5,"K2","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
283 list("[2M+2K]2+",2,2,77.926316639999996028,42,0,0.5,"K2","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
284 list("[3M+2K]2+",3,2,77.926316639999996028,42,0,0.25,"K2","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
285 list("[M+Br]-",1,-1,78.918886479999997619,43,1,1.0,"Br1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
286 list("[M+Cl+FA]-",1,-1,80.974880593999998268,44,0,0.5,"Cl1C1O2H2","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
287 list("[M+AcNa-H]-",1,-1,80.995797543999998426,45,0,0.25,"C2H3Na1O2","H1"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
288 list("[M+2ACN+2H]2+",1,2,84.067651115999993292,46,0,0.25,"C4H8N2","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
289 list("[M+K+FA]+",1,1,84.968637623999995868,47,0,0.25,"K1C1O2H2","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
290 list("[M+Cl+Na+FA-H]-",1,-1,102.95682522200000619,48,0,0.5,"Cl1Na1C1O2H2","H1"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
291 list("[2M+3H2O+2H]+",2,1,104.03153939599999944,49,0,0.25,"H8O6","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
292 list("[M+TFA-H]-",1,-1,112.98558742000000165,50,0,0.5,"C2F3O2H1","H1"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
293 list("[M+H+TFA]+",1,1,115.00014032400000019,51,0,0.25,"C2F3O2H2","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
294 list("[M+3ACN+2H]2+",1,2,125.09420022199999778,52,0,0.25,"C6H11N3","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
295 list("[M+NH4+TFA]+",1,1,132.02668943000000468,53,0,0.25,"N1C2F3O2H5","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
296 list("[M+Na+TFA]+",1,1,136.98208495200000811,54,0,0.25,"Na1C2F3O2H1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
297 list("[M+Cl+TFA]-",1,-1,148.96226516199999423,55,0,0.5,"Cl1C2F3O2H1","H0"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
298 list("[M+K+TFA]+",1,1,152.95602219200000604,56,0,0.25,"K1C2F3O2H1","H0")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
299 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
300 dummy_adduct <- orm$adduct()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
301 for (adduct in adducts) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
302 i <- 0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
303 dummy_adduct$set_name(adduct[[i <- i+1]])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
304 dummy_adduct$set_multi(adduct[[i <- i+1]])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
305 dummy_adduct$set_charge(adduct[[i <- i+1]])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
306 dummy_adduct$set_mass(adduct[[i <- i+1]])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
307 dummy_adduct$set_oidscore(adduct[[i <- i+1]])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
308 dummy_adduct$set_quasi(adduct[[i <- i+1]])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
309 dummy_adduct$set_ips(adduct[[i <- i+1]])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
310 dummy_adduct$set_formula_add(adduct[[i <- i+1]])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
311 dummy_adduct$set_formula_ded(adduct[[i <- i+1]])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
312 dummy_adduct$save()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
313 dummy_adduct$clear(unset_id=TRUE)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
314 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
315 message("Adducts created")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
316 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
317
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
318 insert_base_data <- function(orm, path, archetype=FALSE) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
319 if (archetype) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
320 ## not implemented yet
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
321 return ()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
322 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
323 base_data <- readLines(path)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
324 for (sql in strsplit(paste(base_data, collapse=" "), ";")[[1]]) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
325 orm$execute(sql)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
326 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
327 set_database_version(orm, "enriched")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
328 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
329
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
330 insert_compounds <- function(orm, compounds_path) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
331 compounds <- read.csv(file=compounds_path, sep="\t")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
332 if (is.null(compounds <- translate_compounds(compounds))) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
333 stop("Could not find asked compound's attributes in csv file.")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
334 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
335 dummy_compound <- orm$compound()
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lain
parents:
diff changeset
336 compound_list <- list()
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lain
parents:
diff changeset
337 for (i in seq_len(nrow(compounds))) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
338 dummy_compound$set_mz(compounds[i, "mz"])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
339 dummy_compound$set_name(compounds[i, "name"])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
340 dummy_compound$set_common_name(compounds[i, "common_name"])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
341 dummy_compound$set_formula(compounds[i, "formula"])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
342 # dummy_compound$set_mz(compounds[i, "mz"])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
343 # dummy_compound$set_mz(compounds[i, "mz"])
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lain
parents:
diff changeset
344 compound_list[[length(compound_list)+1]] <- as.list(
a174cbbb12dd " master branch Updating"
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parents:
diff changeset
345 dummy_compound,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
346 c("mz", "name", "common_name", "formula")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
347 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
348 dummy_compound$clear(unset_id=TRUE)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
349 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
350 dummy_compound$save(bulk=compound_list)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
351 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
352
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
353 translate_compounds <- function(compounds) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
354 recognized_headers <- list(
a174cbbb12dd " master branch Updating"
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parents:
diff changeset
355 c("HMDB_ID", "MzBank", "X.M.H..", "X.M.H...1", "MetName", "ChemFormula", "INChIkey")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
356 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
357 header_translators <- list(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
358 hmdb_header_translator
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
359 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
360 for (index in seq_along(recognized_headers)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
361 headers <- recognized_headers[[index]]
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
362 if (identical(colnames(compounds), headers)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
363 return (header_translators[[index]](compounds))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
364 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
365 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
366 if (is.null(translator <- guess_translator(colnames(compounds)))) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
367 return (NULL)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
368 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
369 return (csv_header_translator(translator, compounds))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
370 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
371
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
372 guess_translator <- function(header) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
373 result <- list(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
374 # HMDB_ID=NULL,<
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
375 mz=NULL,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
376 name=NULL,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
377 common_name=NULL,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
378 formula=NULL,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
379 # inchi_key=NULL
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
380 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
381 asked_cols <- names(result)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
382 for (asked_col in asked_cols) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
383 for (col in header) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
384 if ((twisted <- tolower(col)) == asked_col
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
385 || gsub("-", "_", twisted) == asked_col
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
386 || gsub(" ", "_", twisted) == asked_col
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
387 || tolower(gsub("(.)([A-Z])", "\\1_\\2", col)) == asked_col
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
388 ) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
389 result[[asked_col]] <- col
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
390 next
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
391 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
392 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
393 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
394 if (any(mapply(is.null, result))) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
395 return (NULL)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
396 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
397 return (result)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
398 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
399
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
400 hmdb_header_translator <- function(compounds) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
401 return (csv_header_translator(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
402 list(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
403 HMDB_ID="HMDB_ID",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
404 mz="MzBank",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
405 name="MetName",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
406 common_name="MetName",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
407 formula="ChemFormula",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
408 inchi_key="INChIkey"
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
409 ), compounds
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
410 ))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
411 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
412
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
413 csv_header_translator <- function(translation_table, csv) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
414 header_names <- names(translation_table)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
415 result <- data.frame(1:nrow(csv))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
416 # colnames(result) <- header_names
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
417 for (i in seq_along(header_names)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
418 result[, header_names[[i]]] <- csv[, translation_table[[i]]]
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
419 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
420 print(result[, "mz"])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
421 result[, "mz"] <- as.numeric(result[, "mz"])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
422 print(result[, "mz"])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
423 return (result)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
424 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
425
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
426 set_database_version <- function(orm, version) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
427 orm$set_tag(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
428 version,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
429 tag_name="database_version",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
430 tag_table_name="XSeeker_tagging_table"
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
431 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
432 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
433
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
434 process_rdata <- function(orm, rdata, options) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
435 mzml_tmp_dir <- gather_mzml_files(rdata)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
436 samples <- names(rdata$singlefile)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
437 if (!is.null(options$samples)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
438 samples <- samples[options$samples %in% samples]
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
439 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
440 show_percent <- (
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
441 is.null(options$`not-show-percent`)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
442 || options$`not-show-percent` == FALSE
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
443 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
444 error <- tryCatch({
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
445 process_sample_list(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
446 orm, rdata, samples,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
447 show_percent=show_percent
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
448 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
449 NULL
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
450 }, error=function(e) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
451 message(e)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
452 e
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
453 })
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
454 if (!is.null(mzml_tmp_dir)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
455 unlink(mzml_tmp_dir, recursive=TRUE)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
456 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
457 if (!is.null(error)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
458 stop(error)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
459 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
460 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
461
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
462 gather_mzml_files <- function(rdata) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
463 if (is.null(rdata$singlefile)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
464 message("Extracting mxml files")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
465 tmp <- tempdir()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
466 rdata$singlefile <- utils::unzip(rdata$zipfile, exdir=tmp)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
467 names(rdata$singlefile) <- tools::file_path_sans_ext(basename(rdata$singlefile))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
468 message("Extracted")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
469 return (tmp)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
470 } else {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
471 message(sprintf("Not a zip file, loading files directly from path: %s", paste(rdata$singlefile, collapse=" ; ")))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
472 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
473 return (NULL)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
474 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
475
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
476 process_sample_list <- function(orm, radta, sample_names, show_percent) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
477 file_grouping_var <- find_grouping_var(rdata$variableMetadata)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
478 message("Processing samples.")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
479 message(sprintf("File grouping variable: %s", file_grouping_var))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
480 if(is.null(file_grouping_var)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
481 stop("Malformed variableMetada.")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
482 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
483
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
484 process_arg_list <- rdata$listOFlistArguments
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
485 process_params <- list()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
486 for (list_name in names(process_arg_list)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
487 param_list <- list()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
488 for (param_name in names(process_arg_list[[list_name]])) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
489 param_list[[param_name]] <- process_arg_list[[list_name]][[param_name]]
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
490 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
491 process_params[[length(process_params)+1]] <- param_list
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
492 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
493 message("Parameters from previous processes extracted.")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
494
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
495 var_meta <- rdata$variableMetadata
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
496 align_group <- rep(0, nrow(var_meta))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
497 var_meta <- cbind(var_meta, align_group)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
498 context <- new.env()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
499 context$clusters <- list()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
500 context$groupidx <- rdata$xa@xcmsSet@groupidx
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
501 context$peaks <- rdata$xa@xcmsSet@peaks
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
502 context$show_percent <- show_percent
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
503
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
504 indices <- as.numeric(unique(var_meta[, file_grouping_var]))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
505 smol_xcms_set <- orm$smol_xcms_set()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
506 mz_tab_info <- new.env()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
507 xcms_set <- rdata$xa@xcmsSet
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
508 g <- xcms::groups(xcms_set)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
509 mz_tab_info$group_length <- nrow(g)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
510 mz_tab_info$dataset_path <- xcms::filepaths(xcms_set)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
511 mz_tab_info$sampnames <- xcms::sampnames(xcms_set)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
512 mz_tab_info$sampclass <- xcms::sampclass(xcms_set)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
513 mz_tab_info$rtmed <- g[,"rtmed"]
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
514 mz_tab_info$mzmed <- g[,"mzmed"]
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
515 mz_tab_info$smallmolecule_abundance_assay <- xcms::groupval(xcms_set, value="into")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
516 blogified <- blob::blob(fst::compress_fst(serialize(mz_tab_info, NULL), compression=100))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
517 smol_xcms_set$set_raw(blogified)$save()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
518 for (no in indices) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
519 sample_name <- names(rdata$singlefile)[[no]]
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
520 sample_path <- rdata$singlefile[[no]]
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
521 if (
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
522 is.na(no)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
523 || is.null(sample_path)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
524 || !(sample_name %in% sample_names)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
525 ) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
526 next
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
527 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
528 ms_file=xcms::xcmsRaw(sample_path)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
529 env <- new.env()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
530 env$variableMetadata <- var_meta[var_meta[, file_grouping_var]==no,]
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
531 env$tic <- ms_file@tic
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
532 env$mz <- ms_file@env$mz
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
533 env$scanindex <- ms_file@scanindex
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
534 env$scantime <- ms_file@scantime
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
535 env$intensity <- ms_file@env$intensity
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
536 env$polarity <- as.character(ms_file@polarity[[1]])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
537 env$sample_name <- sample_name
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
538 env$dataset_path <- sample_path
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
539 env$process_params <- process_params
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
540 env$enriched_rdata <- TRUE
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
541 env$enriched_rdata_version <- ENRICHED_RDATA_VERSION
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
542 env$tool_name <- TOOL_NAME
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
543 env$enriched_rdata_doc <- ENRICHED_RDATA_DOC
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
544 context$sample_no <- no
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
545 add_sample_to_database(orm, env, context, smol_xcms_set)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
546 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
547 message("Features enrichment")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
548 complete_features(orm, context)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
549 message("Features enrichment done.")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
550 return (NULL)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
551 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
552
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
553 find_grouping_var <- function(var_meta) {
6
207e36770d18 " master branch Updating"
lain
parents: 0
diff changeset
554 known_colnames = c(
207e36770d18 " master branch Updating"
lain
parents: 0
diff changeset
555 "name", "namecustom", "mz", "mzmin", "mzmax",
207e36770d18 " master branch Updating"
lain
parents: 0
diff changeset
556 "rt", "rtmin", "rtmax", "npeaks", "isotopes", "adduct", "pcgroup"
207e36770d18 " master branch Updating"
lain
parents: 0
diff changeset
557 )
207e36770d18 " master branch Updating"
lain
parents: 0
diff changeset
558 col_names <- colnames(var_meta)
207e36770d18 " master branch Updating"
lain
parents: 0
diff changeset
559 classes = list()
207e36770d18 " master branch Updating"
lain
parents: 0
diff changeset
560 for (name in col_names) {
207e36770d18 " master branch Updating"
lain
parents: 0
diff changeset
561 if (!(name %in% known_colnames)) {
207e36770d18 " master branch Updating"
lain
parents: 0
diff changeset
562 classes[[length(classes)+1]] = name
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
563 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
564 }
6
207e36770d18 " master branch Updating"
lain
parents: 0
diff changeset
565 if (length(classes) > 1) {
207e36770d18 " master branch Updating"
lain
parents: 0
diff changeset
566 stop(sprintf("Only one class expected in the variable metadata. Found %d .", length(classes)))
207e36770d18 " master branch Updating"
lain
parents: 0
diff changeset
567 }
207e36770d18 " master branch Updating"
lain
parents: 0
diff changeset
568 if (length(classes) === 0) {
207e36770d18 " master branch Updating"
lain
parents: 0
diff changeset
569 stop("Could not find any class column in your variableMetadata.")
207e36770d18 " master branch Updating"
lain
parents: 0
diff changeset
570 }
207e36770d18 " master branch Updating"
lain
parents: 0
diff changeset
571 return (classes[[1]])
0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
572 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
573
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
574 add_sample_to_database <- function(orm, env, context, smol_xcms_set) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
575 message(sprintf("Processing sample %s", env$sample_name))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
576 sample <- (
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
577 orm$sample()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
578 $set_name(env$sample_name)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
579 $set_path(env$dataset_path)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
580 $set_kind("enriched_rdata")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
581 $set_polarity(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
582 if (is.null(env$polarity) || identical(env$polarity, character(0))) ""
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
583 else env$polarity
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
584 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
585 $set_smol_xcms_set(smol_xcms_set)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
586 $set_raw(blob::blob(fst::compress_fst(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
587 serialize(env, NULL),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
588 compression=100
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
589 )))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
590 $save()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
591 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
592 load_variable_metadata(orm, sample, env$variableMetadata, context)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
593 load_process_params(orm, sample, env$process_params)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
594 message(sprintf("Sample %s inserted.", env$sample_name))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
595 return (sample)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
596 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
597
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
598
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
599 load_variable_metadata <- function(orm, sample, var_meta, context) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
600 all_clusters <- orm$cluster()$all()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
601
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
602 next_feature_id <- get_next_id(orm$feature()$all(), "featureID")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
603 next_cluster_id <- get_next_id(all_clusters, "clusterID")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
604 next_pc_group <- get_next_id(all_clusters, "pc_group")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
605 next_align_group <- get_next_id(all_clusters, "align_group")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
606 message("Extracting features")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
607 invisible(create_features(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
608 orm, sample, var_meta, context,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
609 next_feature_id, next_cluster_id,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
610 next_pc_group, next_align_group
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
611 ))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
612 message("Extracting features done.")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
613 return (NULL)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
614 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
615
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
616 get_next_id <- function(models, attribute) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
617 if ((id <- models$max(attribute)) == Inf || id == -Inf) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
618 return (1)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
619 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
620 return (id + 1)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
621 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
622
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
623 create_features <- function(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
624 orm, sample, var_meta, context,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
625 next_feature_id, next_cluster_id,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
626 next_pc_group, next_align_group
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
627 ) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
628 field_names <- as.list(names(orm$feature()$fields__))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
629 field_names[field_names=="id"] <- NULL
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
630
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
631 features <- list()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
632 dummy_feature <- orm$feature()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
633
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
634 if (show_percent <- context$show_percent) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
635 percent <- -1
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
636 total <- nrow(var_meta)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
637 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
638 for (row in seq_len(nrow(var_meta))) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
639 if (show_percent && (row / total) * 100 > percent) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
640 percent <- percent + 1
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
641 message("\r", sprintf("\r%d %%", percent), appendLF=FALSE)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
642 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
643
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
644 curent_var_meta <- var_meta[row, ]
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
645
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
646 peak_list <- context$peaks[context$groupidx[[row]], ]
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
647 sample_peak_list <- peak_list[peak_list[, "sample"] == context$sample_no, , drop=FALSE]
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
648 if (!identical(sample_peak_list, numeric(0)) && !is.null(nrow(sample_peak_list)) && nrow(sample_peak_list) != 0) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
649 if (!is.na(int_o <- extract_peak_var(sample_peak_list, "into"))) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
650 dummy_feature$set_int_o(int_o)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
651 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
652 if (!is.na(int_b <- extract_peak_var(sample_peak_list, "intb"))) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
653 dummy_feature$set_int_b(int_b)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
654 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
655 if (!is.na(max_o <- extract_peak_var(sample_peak_list, "maxo"))) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
656 dummy_feature$set_max_o(max_o)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
657 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
658 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
659
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
660 set_feature_fields_from_var_meta(dummy_feature, curent_var_meta)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
661
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
662 dummy_feature$set_featureID(next_feature_id)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
663 next_feature_id <- next_feature_id + 1
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
664 fake_iso <- dummy_feature$get_iso()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
665 iso <- extract_iso(fake_iso)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
666 clusterID <- extract_clusterID(fake_iso, next_cluster_id)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
667 context$clusterID <- clusterID
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
668 dummy_feature$set_iso(iso)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
669 create_associated_cluster(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
670 sample, dummy_feature, clusterID,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
671 context, curent_var_meta, next_pc_group,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
672 next_align_group
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
673 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
674 next_align_group <- next_align_group + 1
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
675 features[[length(features)+1]] <- as.list(dummy_feature, field_names)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
676 dummy_feature$clear()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
677 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
678 message("")## +\n for previous message
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
679 message("Saving features")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
680 dummy_feature$save(bulk=features)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
681 message("Saved.")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
682 return (context$clusters)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
683 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
684
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
685 extract_peak_var <- function(peak_list, var_name, selector=max) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
686 value <- peak_list[, var_name]
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
687 names(value) <- NULL
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
688 return (selector(value))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
689 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
690
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
691 set_feature_fields_from_var_meta <- function(feature, var_meta) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
692 if (!is.null(mz <- var_meta[["mz"]]) && !is.na(mz)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
693 feature$set_mz(mz)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
694 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
695 if (!is.null(mzmin <- var_meta[["mzmin"]]) && !is.na(mzmin)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
696 feature$set_mz_min(mzmin)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
697 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
698 if (!is.null(mzmax <- var_meta[["mzmax"]]) && !is.na(mzmax)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
699 feature$set_mz_max(mzmax)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
700 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
701 if (!is.null(rt <- var_meta[["rt"]]) && !is.na(rt)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
702 feature$set_rt(rt)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
703 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
704 if (!is.null(rtmin <- var_meta[["rtmin"]]) && !is.na(rtmin)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
705 feature$set_rt_min(rtmin)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
706 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
707 if (!is.null(rtmax <- var_meta[["rtmax"]]) && !is.na(rtmax)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
708 feature$set_rt_max(rtmax)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
709 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
710 if (!is.null(isotopes <- var_meta[["isotopes"]]) && !is.na(isotopes)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
711 feature$set_iso(isotopes)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
712 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
713 return (feature)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
714 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
715
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
716 extract_iso <- function(weird_data) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
717 if (grepl("^\\[\\d+\\]", weird_data)[[1]]) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
718 return (sub("^\\[\\d+\\]", "", weird_data, perl=TRUE))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
719 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
720 return (weird_data)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
721 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
722
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
723 extract_clusterID <- function(weird_data, next_cluster_id){
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
724 if (grepl("^\\[\\d+\\]", weird_data)[[1]]) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
725 clusterID <- stringr::str_extract(weird_data, "^\\[\\d+\\]")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
726 clusterID <- as.numeric(stringr::str_extract(clusterID, "\\d+"))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
727 } else {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
728 clusterID <- 0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
729 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
730 return (clusterID + next_cluster_id)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
731 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
732
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
733 create_associated_cluster <- function(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
734 sample, feature, grouping_variable,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
735 context, curent_var_meta, next_pc_group, next_align_group
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
736 ) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
737 pcgroup <- as.numeric(curent_var_meta[["pcgroup"]])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
738 adduct <- as.character(curent_var_meta[["adduct"]])
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
739 annotation <- curent_var_meta[["isotopes"]]
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
740 grouping_variable <- as.character(grouping_variable)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
741 if (is.null(cluster <- context$clusters[[grouping_variable]])) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
742 cluster <- context$clusters[[grouping_variable]] <- orm$cluster(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
743 pc_group=pcgroup + next_pc_group,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
744 adduct=adduct,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
745 align_group=next_align_group,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
746 # curent_group=curent_group,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
747 clusterID=context$clusterID,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
748 annotation=annotation
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
749 )$set_sample(sample)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
750 } else {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
751 if (context$clusterID != 0 && cluster$get_clusterID() == 0) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
752 cluster$set_clusterID(context$clusterID)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
753 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
754 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
755 cluster$save()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
756 feature$set_cluster(cluster)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
757 return (feature)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
758 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
759
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
760 complete_features <- function(orm, context) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
761 for (cluster in context$clusters) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
762 features <- orm$feature()$load_by(cluster_id=cluster$get_id())
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
763 if (features$any()) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
764 if (!is.null(rt <- features$mean("rt"))) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
765 cluster$set_mean_rt(rt)$save()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
766 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
767 features_df <- as.data.frame(features)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
768 central_feature <- features_df[grepl("^\\[M\\]", features_df[, "iso"]), ]
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
769 central_feature_into <- central_feature[["int_o"]]
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
770 if (!identical(central_feature_into, numeric(0)) && central_feature_into != 0) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
771 for (feature in as.vector(features)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
772 feature$set_abundance(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
773 feature$get_int_o() / central_feature_into * 100
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
774 )$save()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
775 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
776 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
777 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
778 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
779 return (NULL)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
780 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
781
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
782 load_process_params <- function(orm, sample, params) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
783 for (param_list in params) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
784 if (is.null(param_list[["xfunction"]])) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
785 next
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
786 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
787 if (param_list[["xfunction"]] == "annotatediff") {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
788 load_process_params_peak_picking(orm, sample, param_list)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
789 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
790 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
791 return (sample)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
792 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
793
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
794 load_process_params_peak_picking <- function(orm, sample, peak_picking_params) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
795 return (add_sample_process_parameters(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
796 params=peak_picking_params,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
797 params_translation=list(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
798 ppm="ppm",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
799 maxcharge="maxCharge",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
800 maxiso="maxIso"
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
801 ),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
802 param_model_generator=orm$peak_picking_parameters,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
803 sample_param_setter=sample$set_peak_picking_parameters
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
804 ))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
805 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
806
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
807 add_sample_process_parameters <- function(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
808 params,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
809 params_translation,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
810 param_model_generator,
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
811 sample_param_setter
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
812 ) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
813 model_params <- list()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
814 for (rdata_param_name in names(params_translation)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
815 database_param_name <- params_translation[[rdata_param_name]]
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
816 if (is.null(rdata_param <- params[[rdata_param_name]])) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
817 next
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
818 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
819 model_params[[database_param_name]] <- rdata_param
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
820 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
821 params_models <- do.call(param_model_generator()$load_by, model_params)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
822 if (params_models$any()) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
823 params_model <- params_models$first()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
824 } else {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
825 params_model <- do.call(param_model_generator, model_params)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
826 params_model$save()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
827 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
828 return (sample_param_setter(params_model)$save())
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
829 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
830
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
831
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
832 library(optparse)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
833
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
834 option_list <- list(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
835 optparse::make_option(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
836 c("-v", "--version"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
837 action="store_true",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
838 help="Display this tool's version and exits"
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
839 ),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
840 optparse::make_option(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
841 c("-i", "--input"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
842 type="character",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
843 help="The rdata path to import in XSeeker"
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
844 ),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
845 optparse::make_option(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
846 c("-s", "--samples"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
847 type="character",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
848 help="Samples to visualise in XSeeker"
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
849 ),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
850 optparse::make_option(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
851 c("-B", "--archetype"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
852 type="character",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
853 help="The name of the base database"
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
854 ),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
855 optparse::make_option(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
856 c("-b", "--database"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
857 type="character",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
858 help="The base database's path"
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
859 ),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
860 optparse::make_option(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
861 c("-c", "--compounds-csv"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
862 type="character",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
863 help="The csv containing compounds"
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
864 ),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
865 optparse::make_option(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
866 c("-m", "--models"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
867 type="character",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
868 help="The path or url (must begin with http[s]:// or git@) to the database's models"
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
869 ),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
870 optparse::make_option(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
871 c("-o", "--output"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
872 type="character",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
873 help="The path where to output sqlite"
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
874 ),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
875 optparse::make_option(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
876 c("-P", "--not-show-percent"),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
877 action="store_true",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
878 help="Flag not to show the percents",
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
879 default=FALSE
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
880 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
881 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
882
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
883 options(error=function(){traceback(3)})
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
884
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
885 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
886 args <- parse_args(parser, positional_arguments=0)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
887
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
888 err_code <- 0
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
889
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
890 if (!is.null(args$options$version)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
891 message(sprintf("%s %s", TOOL_NAME, VERSION))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
892 quit()
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
893 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
894
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
895 models <- get_models(args$options$models)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
896 orm <- DBModelR::ORM(
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
897 connection_params=list(dbname=args$options$output),
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
898 dbms="SQLite"
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
899 )
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
900
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
901 invisible(orm$models(models))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
902 invisible(create_database(orm))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
903
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
904 message("Database model created")
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
905
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
906 insert_adducts(orm)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
907
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
908 if (!is.null(args$options$database)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
909 insert_base_data(orm, args$options$database)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
910 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
911 message(sprintf("Base data inserted using %s.", args$options$database))
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
912
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
913 if (!is.null(args$options$archetype)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
914 insert_base_data(orm, args$options$archetype, archetype=TRUE)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
915 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
916 if (!is.null(args$options$`compounds-csv`)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
917 insert_compounds(orm, args$options$`compounds-csv`)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
918 }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
919
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
920 # if (!is.null(args$options$rdata)) {
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
921 # load_rdata_in_base(args$options$rdata, args$options$samples, args$options$`not-show-percent`)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
922 # }
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
923
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
924
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
925 load(args$options$input, rdata <- new.env())
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
926
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
927 process_rdata(orm, rdata, args$options)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
928
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
929 quit(status=err_code)
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
930
a174cbbb12dd " master branch Updating"
lain
parents:
diff changeset
931