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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 ## 06102016_NmrAlignment_wrapper.R
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4 ## Marie Tremblay-Franco
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5 ## marie.tremblay-franco@toulouse.inra.fr
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6
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7 runExampleL <- FALSE
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8
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9 ##------------------------------
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10 ## Options
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11 ##------------------------------
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12 strAsFacL <- options()$stringsAsFactors
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13 options(stringsAsFactors = FALSE)
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14
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15
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16 ##------------------------------
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17 ## Libraries loading
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18 ##------------------------------
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19 # ParseCommandArgs function
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3
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20 library(batch)
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21 # Alignment
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22 library(speaq)
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23
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24
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25 # R script call
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26 source_local <- function(fname)
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27 {
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28 argv <- commandArgs(trailingOnly = FALSE)
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29 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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30 source(paste(base_dir, fname, sep="/"))
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31 }
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32 # Function import
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33 source_local("NmrAlignment_script.R")
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34
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35
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36 ##------------------------------
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37 ## Errors ?????????????????????
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38 ##------------------------------
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39
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40
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41 ##------------------------------
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42 ## Constants
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43 ##------------------------------
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44 topEnvC <- environment()
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45 flagC <- "\n"
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46
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47
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48 ##------------------------------
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49 ## Script
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50 ##------------------------------
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51 if(!runExampleL)
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52 argLs <- parseCommandArgs(evaluate=FALSE)
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53
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54
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55 ## Parameters Loading
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56 ##-------------------
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57 # Inputs
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58 ## Library of spectra to align
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59 if (!is.null(argLs[["zipfile"]])){
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60 fileType="zip"
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61 zipfile= argLs[["zipfile"]]
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62 directory=unzip(zipfile, list=F)
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63 directory=paste(getwd(),strsplit(directory[1],"/")[[1]][2],sep="/")
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64 } else if (!is.null(argLs[["tsvfile"]])){
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65 fileType="tsv"
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66 directory <- read.table(argLs[["tsvfile"]],check.names=FALSE,header=TRUE,sep="\t")
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67 }
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68
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69
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70 ## Spectral width
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71 leftBorder <- argLs[["left_border"]]
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72 rightBorder <- argLs[["right_border"]]
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73
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74 ## Exclusion zone(s)
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75 exclusionZones <- argLs[["zone_exclusion_choices.choice"]]
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76 exclusionZonesBorders <- NULL
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77 if (!is.null(argLs$zone_exclusion_left))
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78 {
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79 for(i in which(names(argLs)=="zone_exclusion_left"))
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80 {
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81 exclusionZonesBorders <- c(exclusionZonesBorders,list(c(argLs[[i]],argLs[[i+1]])))
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82 }
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83 }
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84
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85 ## Reference spectrum
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86 reference <- argLs[["reference"]]
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87
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88 ## Size of a small nDivRange
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89 nDivRange <- argLs[["nDivRange"]]
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90
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91 ## Intensity threshold for peak removal
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92 baselineThresh <- argLs[["baselineThresh"]]
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93
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4
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94 ## Graphical zone(s)
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95 graphicalZones <- argLs[["zone_graphical_choices.choice"]]
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96 graphicalZonesBorders <- NULL
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97 if (!is.null(argLs$zone_exclusion_left))
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98 {
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99 for(i in which(names(argLs)=="zone_graphical_left"))
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100 {
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101 graphicalZonesBorders <- c(graphicalZonesBorders,list(c(argLs[[i]],argLs[[i+1]])))
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102 }
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103 }
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104
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105
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106 # Outputs
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107 logOut <- argLs[["logOut"]]
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108 alignedSpectra <- argLs[["alignedSpectra"]]
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109 graphOut <- argLs[["graphOut"]]
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110
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111
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112 ## Checking R packages
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113 ##--------------------
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114 sink(logOut)
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115 cat("\tPACKAGE INFO\n")
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116 #pkgs=c("xcms","batch")
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117 pkgs=c("batch","speaq")
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118 for(pkg in pkgs) {
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119 suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
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120 cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
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121 }
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122
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123 ## Checking arguments
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124 ##-------------------
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125 error.stock <- "\n"
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126 if(length(error.stock) > 1)
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127 stop(error.stock)
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128
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129
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130 ## Computation
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131 ##------------
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132 directory.alignement <- nmr.alignment(fileType=fileType,directory=directory,leftBorder=leftBorder,rightBorder=rightBorder,exclusionZones=exclusionZones,
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133 exclusionZonesBorders=exclusionZonesBorders, reference=reference, nDivRange=nDivRange,
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134 baselineThresh=baselineThresh, maxshift=50, verbose=FALSE)
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135 directory.raw <- directory.alignement[[1]]
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136 directory.aligned <- directory.alignement[[2]]
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137
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138 ## Saving
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139 ##-------
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140 # Aligned spectra
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141 t.directory.aligned <- t(directory.aligned)
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142 rownames(t.directory.aligned) <- colnames(directory.aligned)
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143 # colnames(t.directory.aligned) <- c("Bucket",colnames(t.directory.aligned))
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144 write.table(t.directory.aligned,file=alignedSpectra,row.names=TRUE,quote=FALSE,sep="\t")
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145
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146
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147 ## Graphical output: overlay of raw and estimated spectra
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148 pdf(graphOut,onefile=TRUE)
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149
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150 graphical.zone.length <- length(graphicalZonesBorders)
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151 par(mfrow=c(2,1))
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152
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153 raw.spectra <- data.frame(directory.raw)
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154 colnames(raw.spectra) <- substr(colnames(raw.spectra),2,7)
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155
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156 aligned.spectra <- data.frame(directory.aligned)
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157 colnames(aligned.spectra) <- substr(colnames(aligned.spectra),2,7)
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158
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159 drawSpec(raw.spectra,xlab="", ylab="Raw spectra", main="")
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160 drawSpec(aligned.spectra,xlab="", ylab="Aligned spectra", main="")
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161
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162 if (graphical.zone.length != 0)
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163 {
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164 # par(mfrow=c(2,1))
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165 for (g in 1:graphical.zone.length)
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166 {
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167 print(paste(g, graphicalZonesBorders[[g]][1], graphicalZonesBorders[[g]][2]))
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168 drawSpec(raw.spectra[,(which(round(as.numeric(colnames(raw.spectra)),2) == graphicalZonesBorders[[g]][1])[1]):(which(round(as.numeric(colnames(raw.spectra)),2) == graphicalZonesBorders[[g]][2])[1])],xlab="", main="")
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169 drawSpec(aligned.spectra[,(which(round(as.numeric(colnames(aligned.spectra)),2) == graphicalZonesBorders[[g]][1])[1]):(which(round(as.numeric(colnames(aligned.spectra)),2) == graphicalZonesBorders[[g]][2])[1])],xlab="", main="")
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170 }
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171 }
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172 dev.off()
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173
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174
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175 ## Ending
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176 ##---------------------
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177 cat("\nEnd of 'NMR alignment' Galaxy module call: ", as.character(Sys.time()), sep = "")
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178 sink()
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179 options(stringsAsFactors = strAsFacL)
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180 rm(list = ls())
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