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annotate frag4feature.R @ 2:89f33758ad22 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
author tomnl
date Thu, 14 Jun 2018 09:09:58 -0400
parents
children a91e186cf294
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89f33758ad22 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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1 library(optparse)
89f33758ad22 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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2 library(msPurity)
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3 library(xcms)
89f33758ad22 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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4 print(sessionInfo())
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6 xset_pa_filename_fix <- function(opt, pa, xset){
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9 if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
89f33758ad22 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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10 # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
89f33758ad22 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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11 # needs to be done due to Galaxy moving the files around and screwing up any links to files
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13 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
89f33758ad22 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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14 filepaths <- filepaths[filepaths != ""]
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15 new_names <- basename(filepaths)
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17 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
89f33758ad22 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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18 galaxy_names <- galaxy_names[galaxy_names != ""]
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20 nsave <- names(pa@fileList)
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21 old_filenames <- basename(pa@fileList)
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23 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
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24 names(pa@fileList) <- nsave
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26 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
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27 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
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28 }
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29 print(pa@fileList)
89f33758ad22 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f79fa34772bbab836d89cf8bad52d49285409a98
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30 print(xset@filepaths)
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32 if(!all(basename(pa@fileList)==basename(xset@filepaths))){
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33 if(!all(names(pa@fileList)==basename(xset@filepaths))){
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34 print('FILELISTS DO NOT MATCH')
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35 message('FILELISTS DO NOT MATCH')
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36 quit(status = 1)
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37 }else{
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38 xset@filepaths <- unname(pa@fileList)
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39 }
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40 }
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43 return(list(pa, xset))
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44 }
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47 option_list <- list(
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48 make_option(c("-o", "--out_dir"), type="character"),
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49 make_option("--pa", type="character"),
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50 make_option("--xset", type="character"),
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51 make_option("--ppm", default=10),
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52 make_option("--plim", default=0.0),
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53 make_option("--convert2RawRT", action="store_true"),
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54 make_option("--mostIntense", action="store_true"),
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55 make_option("--createDB", action="store_true"),
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56 make_option("--cores", default=4),
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57 make_option("--mzML_files", type="character"),
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58 make_option("--galaxy_names", type="character"),
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59 make_option("--grp_peaklist", type="character")
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60 )
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61
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62 # store options
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63 opt<- parse_args(OptionParser(option_list=option_list))
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64
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65 loadRData <- function(rdata_path, name){
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66 #loads an RData file, and returns the named xset object if it is there
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67 load(rdata_path)
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68 return(get(ls()[ls() %in% name]))
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69 }
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70
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71 # This function retrieve a xset like object
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72 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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73 getxcmsSetObject <- function(xobject) {
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74 # XCMS 1.x
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75 if (class(xobject) == "xcmsSet")
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76 return (xobject)
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77 # XCMS 3.x
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78 if (class(xobject) == "XCMSnExp") {
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79 # Get the legacy xcmsSet object
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80 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
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81 sampclass(xset) <- xset@phenoData$sample_group
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82 return (xset)
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83 }
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84 }
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85
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86 # Requires
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87 pa <- loadRData(opt$pa, 'pa')
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88 xset <- loadRData(opt$xset, c('xset','xdata'))
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89 xset <- getxcmsSetObject(xset)
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90
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91 pa@cores <- opt$cores
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92
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93 print(pa@fileList)
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94 print(xset@filepaths)
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95
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96 if(is.null(opt$mostIntense)){
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97 mostIntense = FALSE
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98 }else{
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99 mostIntense = TRUE
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100 }
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101
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102 if(is.null(opt$convert2RawRT)){
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103 convert2RawRT = FALSE
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104 }else{
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105 convert2RawRT= TRUE
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106 }
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107
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108 if(is.null(opt$createDB)){
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109 createDB = FALSE
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110 }else{
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111 createDB = TRUE
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112 }
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113
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114
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115 fix <- xset_pa_filename_fix(opt, pa, xset)
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116 pa <- fix[[1]]
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117 xset <- fix[[2]]
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118
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119 if(is.null(opt$grp_peaklist)){
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120 grp_peaklist = NA
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121 }else{
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122 grp_peaklist = opt$grp_peaklist
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123 }
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124
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125 print(pa@fileList)
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126 print(names(pa@fileList))
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127 print(xset@filepaths)
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128 saveRDS(pa, 'test_pa.rds')
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129
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130 pa <- msPurity::frag4feature(pa=pa, xset=xset, ppm=opt$ppm, plim=opt$plim,
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131 intense=opt$mostIntense, convert2RawRT=convert2RawRT,
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132 db_name='alldata.sqlite', out_dir=opt$out_dir, grp_peaklist=grp_peaklist,
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133 create_db=createDB)
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134
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135 save(pa, file=file.path(opt$out_dir, 'frag4feature.RData'))
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136
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137 print(head(pa@grped_df))
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138 write.table(pa@grped_df, file.path(opt$out_dir, 'frag4feature.tsv'), row.names=FALSE, sep='\t')