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1 #!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
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2
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3 ## 201919016 2DNmrAnnotation_1.0.0.R
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4 ## Marie Tremblay-Franco
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5 ## MetaboHUB: The French Infrastructure for Metabolomics and Fluxomics
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6 ## www.metabohub.fr/en
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7 ## marie.tremblay-franco@toulouse.inra.fr
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8
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9 runExampleL <- FALSE
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10
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11 if(runExampleL) {
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12 ##------------------------------
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13 ## Example of arguments
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14 ##------------------------------
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15 }
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16
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17
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18 ##------------------------------
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19 ## Options
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20 ##------------------------------
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21 strAsFacL <- options()$stringsAsFactors
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22 options(stringsAsFactors = FALSE)
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23
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24 ##------------------------------
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25 ## Constants
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26 ##------------------------------
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27 topEnvC <- environment()
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28 flagC <- "\n"
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29
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30
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31 ##-------------------------
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32 ## Input parameters reading
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33 ##-------------------------
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34
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35 ##------------------------------
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36 ## R libraries laoding
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37 ##------------------------------
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38 library(batch)
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39 library(dplyr)
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40 library(ggplot2)
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41 library(openxlsx)
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42 library(stringr)
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43 library(tidyr)
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44
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45 if(!runExampleL)
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46 argLs <- parseCommandArgs(evaluate=FALSE)
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47 logFile <- argLs[["logOut"]]
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48 sink(logFile)
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49
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50 cat("\tPACKAGE INFO\n")
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51 sessionInfo()
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52
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53 ##------------------------------
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54 ## Functions
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55 ##------------------------------
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56 source_local <- function(fname)
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57 {
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58 argv <- commandArgs(trailingOnly = FALSE)
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59 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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60 source(paste(base_dir, fname, sep="/"))
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61 }
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62 #Import the different functions
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63 source_local("annotationRmn2D.R")
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64 source_local("annotationRmn2DGlobale.R")
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65 source_local("viridis.R")
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66
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67 ## Input parameter values
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68 fileToAnnotate <- argLs[[1]]
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69 # Chosen sequence(s)
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70 cosy <- 0
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71 hmbc <- 0
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72 hsqc <- 0
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73 jres <- 0
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74 tocsy <- 0
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75 ## sequences <- str_split(argLs[[2]], ",")[[1]]
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76 ## for (s in 1:length(sequences))
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77 ## {
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78 ## argv <- commandArgs(trailingOnly = FALSE)
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79 ## currentDir <- dirname(substring(argv[grep("--file=", argv)], 8))
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80 ## if (sequences[s]=="cosy"){
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81 ## cosy <- 1
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82 ## load(paste(currentDir, "BdDReference_COSY.RData", sep="/"))
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83 ## }else if(sequences[s]=="hmbc"){
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84 ## hmbc <- 1
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85 ## load(paste(currentDir, "BdDReference_HMBC.RData", sep="/"))
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86 ## }else if(sequences[s]=="hsqc"){
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87 ## hsqc <- 1
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88 ## load(paste(currentDir, "BdDReference_HSQC.RData", sep="/"))
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89 ## }else if(sequences[s]=="jres"){
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90 ## jres <- 1
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91 ## load(paste(currentDir, "BdDReference_JRES.RData", sep="/"))
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92 ## }else if(sequences[s]=="tocsy"){
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93 ## tocsy <- 1
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94 ## load(paste(currentDir, "BdDReference_TOCSY.RData", sep="/"))
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95 ## }else
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96 ## stop("No chosen sequence", call.=FALSE)
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97 ## }
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98
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99 if (argLs[[2]]=='yes')
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100 {
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101 argv <- commandArgs(trailingOnly = FALSE)
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102 currentDir <- dirname(substring(argv[grep("--file=", argv)], 8))
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103 cosy <- 1
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104 load(paste(currentDir, "BdDReference_COSY.RData", sep="/"))
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105 }
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106
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107 if (argLs[[3]]=='yes')
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108 {
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109 argv <- commandArgs(trailingOnly = FALSE)
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110 currentDir <- dirname(substring(argv[grep("--file=", argv)], 8))
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111 jres <- 1
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112 load(paste(currentDir, "BdDReference_JRES.RData", sep="/"))
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113 }
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114
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115 if (argLs[[4]]=='yes')
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116 {
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117 argv <- commandArgs(trailingOnly = FALSE)
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118 currentDir <- dirname(substring(argv[grep("--file=", argv)], 8))
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119 hmbc <- 1
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120 load(paste(currentDir, "BdDReference_HMBC.RData", sep="/"))
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121 }
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122
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123 if (argLs[[5]]=='yes')
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124 {
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125 argv <- commandArgs(trailingOnly = FALSE)
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126 currentDir <- dirname(substring(argv[grep("--file=", argv)], 8))
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127 hsqc <- 1
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128 load(paste(currentDir, "BdDReference_HSQC.RData", sep="/"))
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129 }
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130
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131 if (argLs[[6]]=='yes')
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132 {
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133 argv <- commandArgs(trailingOnly = FALSE)
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134 currentDir <- dirname(substring(argv[grep("--file=", argv)], 8))
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135 tocsy <- 1
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136 load(paste(currentDir, "BdDReference_TOCSY.RData", sep="/"))
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137 }
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138
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139 if (argLs[[2]]=='no' & argLs[[3]]=='no' & argLs[[4]]=='no' & argLs[[5]]=='no' & argLs[[6]]=='no')
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140 stop("No chosen sequence", call.=FALSE)
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141
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142
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143 # User database
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144
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145
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146 # Allowed chemical shifts
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147 tolPpm1 <- argLs$tolppm1
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148 tolPpm2HJRes <- argLs$tolppmJRES
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149 tolPpm2C <- argLs$tolppm2
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150 # Threshold to remove metabolites (probability score < threshold)
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151 seuil <- argLs$threshold
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152 # Remove metabolites when multiple assignations?
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153 unicite <- str_to_upper(argLs$unicity)
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154
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155 ## Output paramater values
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156 AnnotationGraph <- argLs[["AnnotationGraph"]]
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157
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158 print(argLs)
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159
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160 ## ANNOTATION
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161 st0=Sys.time()
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162 pdf(AnnotationGraph,onefile=TRUE)
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163 annotationMelange <- annotationRmn2DGlobale(fileToAnnotate, tolPpm1=tolPpm1, tolPpm2HJRes=tolPpm2HJRes,
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164 tolPpm2C=tolPpm2C, cosy=cosy, hmbc=hmbc, hsqc=hsqc,
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165 jres=jres, tocsy=tocsy, seuil=seuil, unicite=unicite)
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166 dev.off()
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167
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168 if (cosy==1)
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169 {
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170 write.table(annotationMelange$COSY$liste_resultat, file=argLs[["annotationCOSY"]], quote=FALSE,
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171 row.names=FALSE,sep="\t")
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172 if (nrow(annotationMelange$COSY$listing_ppm_commun) != 0)
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173 write.table(annotationMelange$COSY$listing_ppm_commun, file=argLs[["ppmCommunCOSY"]], quote=FALSE,
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174 row.names=FALSE,sep="\t")
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175 }
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176
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177 if (hmbc==1)
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178 {
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179 write.table(annotationMelange$HMBC$liste_resultat, file=argLs[["annotationHMBC"]], quote=FALSE,
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180 row.names=FALSE,sep="\t")
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181 if (nrow(annotationMelange$HMBC$listing_ppm_commun) != 0)
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182 write.table(annotationMelange$HMBC$listing_ppm_commun, file=argLs[["ppmCommunHMBC"]], quote=FALSE,
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183 row.names=FALSE,sep="\t")
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184 }
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185
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186 if (hsqc==1)
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187 {
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188 write.table(annotationMelange$HSQC$liste_resultat, file=argLs[["annotationHSQC"]], quote=FALSE,
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189 row.names=FALSE,sep="\t")
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190 if (nrow(annotationMelange$HSQC$listing_ppm_commun) != 0)
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191 write.table(annotationMelange$HSQC$listing_ppm_commun, file=argLs[["ppmCommunHSQC"]], quote=FALSE,
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192 row.names=FALSE,sep="\t")
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193 }
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194
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195 if (jres==1)
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196 {
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197 write.table(annotationMelange$JRES$liste_resultat, file=argLs[["annotationJRES"]], quote=FALSE,
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198 row.names=FALSE,sep="\t")
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199 if (nrow(annotationMelange$JRES$listing_ppm_commun) != 0)
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200 write.table(annotationMelange$JRES$listing_ppm_commun, file=argLs[["ppmCommunJRES"]], quote=FALSE,
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201 row.names=FALSE,sep="\t")
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202 }
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203
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204 if (tocsy==1)
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205 {
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206 write.table(annotationMelange$TOCSY$liste_resultat, file=argLs[["annotationTOCSY"]], quote=FALSE,
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207 row.names=FALSE,sep="\t")
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208 if (nrow(annotationMelange$TOCSY$listing_ppm_commun) != 0)
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209 write.table(annotationMelange$TOCSY$listing_ppm_commun, file=argLs[["ppmCommunTOCSY"]], quote=FALSE,
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210 row.names=FALSE,sep="\t")
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211 }
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212
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213 ## Combinaison de sequences
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214 if (cosy + jres + hmbc + hsqc + tocsy > 1)
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215 {
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216 write.table(annotationMelange$combination, file=argLs[["annotationCombination"]], quote=FALSE,
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217 row.names=FALSE,sep="\t")
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218 }
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219 st1=Sys.time()
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220 print(st1-st0)
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221
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222 ## Ending
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223 ##--------
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224 cat("\nEnd of '2D NMR annotation' Galaxy module call: ", as.character(Sys.time()), sep = "")
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225 sink()
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226 options(stringsAsFactors = strAsFacL)
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227 rm(list = ls())
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