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annotate frag4feature.R @ 0:fe7d7cc95ca5 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
author tomnl
date Tue, 27 Mar 2018 06:03:50 -0400
parents
children 1a88758357ed
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1 library(optparse)
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2 library(msPurity)
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3 library(xcms)
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5 xset_pa_filename_fix <- function(opt, pa, xset){
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8 if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
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9 # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
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10 # needs to be done due to Galaxy moving the files around and screwing up any links to files
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12 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
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13 filepaths <- filepaths[filepaths != ""]
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14 new_names <- basename(filepaths)
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16 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
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17 galaxy_names <- galaxy_names[galaxy_names != ""]
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19 nsave <- names(pa@fileList)
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20 old_filenames <- basename(pa@fileList)
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21 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
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22 names(pa@fileList) <- nsave
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24 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
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25 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
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26 }
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29 if(!all(basename(pa@fileList)==basename(xset@filepaths))){
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30 if(!all(names(pa@fileList)==basename(xset@filepaths))){
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31 print('FILELISTS DO NOT MATCH')
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32 message('FILELISTS DO NOT MATCH')
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33 quit(status = 1)
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34 }else{
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35 xset@filepaths <- unname(pa@fileList)
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36 }
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37 }
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40 return(list(pa, xset))
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41 }
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42
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43
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44 option_list <- list(
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45 make_option(c("-o", "--out_dir"), type="character"),
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46 make_option("--pa", type="character"),
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47 make_option("--xset", type="character"),
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48 make_option("--ppm", default=10),
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49 make_option("--plim", default=0.0),
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50 make_option("--convert2RawRT", action="store_true"),
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51 make_option("--mostIntense", action="store_true"),
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52 make_option("--createDB", action="store_true"),
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53 make_option("--cores", default=4),
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54 make_option("--mzML_files", type="character"),
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55 make_option("--galaxy_names", type="character"),
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56 make_option("--grp_peaklist", type="character")
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57 )
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58
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59 # store options
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60 opt<- parse_args(OptionParser(option_list=option_list))
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61
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62 loadRData <- function(rdata_path, name){
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63 #loads an RData file, and returns the named xset object if it is there
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64 load(rdata_path)
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65 return(get(ls()[ls() == name]))
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66 }
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67
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68 # Requires
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69 pa <- loadRData(opt$pa, 'pa')
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70 xset <- loadRData(opt$xset, 'xset')
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71
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72 pa@cores <- opt$cores
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74 print(pa@fileList)
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75 print(xset@filepaths)
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76
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77 if(is.null(opt$mostIntense)){
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78 mostIntense = FALSE
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79 }else{
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80 mostIntense = TRUE
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81 }
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82
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83 if(is.null(opt$convert2RawRT)){
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84 convert2RawRT = FALSE
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85 }else{
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86 convert2RawRT= TRUE
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87 }
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88
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89 if(is.null(opt$createDB)){
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90 createDB = FALSE
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91 }else{
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92 createDB = TRUE
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93 }
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94
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95
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96 fix <- xset_pa_filename_fix(opt, pa, xset)
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97 pa <- fix[[1]]
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98 xset <- fix[[2]]
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99
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100 if(is.null(opt$grp_peaklist)){
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101 grp_peaklist = NA
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102
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103
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104 }else{
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105 grp_peaklist = opt$grp_peaklist
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106 }
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107
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108 print('heck')
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109 print(pa@fileList)
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110 print(names(pa@fileList))
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111 print(xset@filepaths)
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112 saveRDS(pa, 'test_pa.rds')
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113
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114 pa <- msPurity::frag4feature(pa=pa, xset=xset, ppm=opt$ppm, plim=opt$plim,
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115 intense=opt$mostIntense, convert2RawRT=convert2RawRT,
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116 db_name='alldata.sqlite', out_dir=opt$out_dir, grp_peaklist=grp_peaklist,
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117 create_db=createDB)
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118
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119 save(pa, file=file.path(opt$out_dir, 'frag4feature.RData'))
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120
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121 print(head(pa@grped_df))
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122 write.table(pa@grped_df, file.path(opt$out_dir, 'frag4feature.tsv'), row.names=FALSE, sep='\t')