Mercurial > repos > mmonsoor > probmetab

annotate probmetab.r @ 4:a1b528cba999 draft

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author lecorguille
date Thu, 06 Apr 2017 05:26:35 -0400
parents f24b9c360a60
children 1dd90aa7815d
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1 #!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
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2 # probmetab.r version="1.0.0"
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3 # Author: Misharl Monsoor ABIMS TEAM mmonsoor@sb-roscoff.fr
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6 # ----- LOG -----
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7 log_file=file("log.txt", open = "wt")
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8 sink(log_file)
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9 sink(log_file, type = "out")
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10
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11 # ----- PACKAGE -----
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12 cat("\tPACKAGE INFO\n")
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13 pkgs=c("parallel","BiocGenerics", "Biobase", "Rcpp", "mzR", "igraph", "xcms","snow","CAMERA","batch","ProbMetab")
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14 for(p in pkgs) {
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15 suppressWarnings( suppressPackageStartupMessages( stopifnot( library(p, quietly=TRUE, logical.return=TRUE, character.only=TRUE))))
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16 cat(p,"\t",as.character(packageVersion(p)),"\n",sep="")
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17 }
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19 source_local <- function(fname){
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20 argv <- commandArgs(trailingOnly = FALSE)
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21 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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22 source(paste(base_dir, fname, sep="/"))
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23 }
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24 cat("\n\n")
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26
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27 # ----- ARGUMENTS -----
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28 cat("\tARGUMENTS INFO\n")
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29 listArguments = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
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30 write.table(as.matrix(listArguments), col.names=F, quote=F, sep='\t')
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33
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34 # ----- PROCESSING INFILE -----
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35 cat("\tINFILE PROCESSING INFO\n")
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36
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37 # ----- INFILE PROCESSING -----
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38
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39 if(listArguments[["mode_acquisition"]]=="one") {
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40 load(listArguments[["image"]])
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41 cat("\t\tXA OBJECT INFO\n")
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42 print(xa)
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44 source_local("lib.r")
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45 if (!exists("zipfile")) zipfile=NULL
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46 if (!exists("singlefile")) singlefile=NULL
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47 rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments)
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48 zipfile = rawFilePath$zipfile
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49 singlefile = rawFilePath$singlefile
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50 retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
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51
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52 if (!exists("variableMetadata")) variableMetadata= getVariableMetadata(xa);
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53
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54 } else if(listArguments[["inputs_mode"]]=="two"){
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55
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56 # POSITIVE
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57 load(listArguments[["image_pos"]])
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58
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59 if (!exists("xa")) xaP=xsAnnotate_object
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60 else xaP=xa
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61 cat("\t\tXA-POSITIVE OBJECT INFO\n")
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62 print(xaP)
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63
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64 if (!exists("variableMetadata")) variableMetadataP = getVariableMetadata(xa)
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65 else variableMetadataP = variableMetadata
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66
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67 source_local("lib.r")
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68 if (!exists("zipfile")) zipfile=NULL
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69 if (!exists("singlefile")) singlefile=NULL
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70 rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments)
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71 zipfilePos = rawFilePath$zipfile
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72 singlefilePos = rawFilePath$singlefile
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73 retrieveRawfileInTheWorkingDirectory(singlefilePos, zipfilePos)
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74
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75 # NEGATIVE
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76 load(listArguments[["image_neg"]])
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77
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78 if (!exists("xa")) xaN=xsAnnotate_object
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79 else xaN=xa
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80 cat("\t\tXA-NEGATIVE OBJECT INFO\n")
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81 print(xaP)
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82
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83 if (!exists("variableMetadata")) variableMetadataN = getVariableMetadata(xa)
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84 else variableMetadataN = variableMetadata
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85
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86 source_local("lib.r")
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87 if (!exists("zipfile")) zipfile=NULL
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88 if (!exists("singlefile")) singlefile=NULL
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89 rawFilePath = getRawfilePathFromArguments(singlefile, zipfile, listArguments)
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90 zipfileNeg = rawFilePath$zipfile
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91 singlefileNeg = rawFilePath$singlefile
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92 retrieveRawfileInTheWorkingDirectory(singlefileNeg, zipfileNeg)
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93 }
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94
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95 #Import the different functions
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96 source_local("lib.r")
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97 source_local("export.class.table-color-graph.R")
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98
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99 # ----- PROCESSING INFO -----
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100 cat("\tMAIN PROCESSING INFO\n")
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101
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102 if(listArguments[["mode_acquisition"]]=="one") {
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103 results=probmetab(xa=xa, variableMetadata=variableMetadata,listArguments=listArguments)
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104 } else if(listArguments[["inputs_mode"]]=="two"){
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105 results=probmetab(xaP=xaP, xaN=xaN,variableMetadataP=variableMetadataP, variableMetadataN=variableMetadataN, listArguments=listArguments)
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106 }
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107 #delete the parameters to avoid the passage to the next tool in .RData image
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108 #rm(listArguments)
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109 cat("\tDONE\n")
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110 #saving R data in .Rdata file to save the variables used in the present tool
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111 #save.image(paste("probmetab","RData",sep="."))