Mercurial > repos > computational-metabolomics > mspurity_spectralmatching

annotate combineAnnotations.R @ 4:aee10d29e82c draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"
author computational-metabolomics
date Mon, 10 Aug 2020 08:39:40 -0400
parents 07745c473323
children fecfe8c80e25
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5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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1 library(optparse)
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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2 library(msPurity)
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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3 print(sessionInfo())
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4
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5 # Get the parameter
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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6 option_list <- list(
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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7 make_option(c("-s","--sm_resultPth"),type="character"),
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8 make_option(c("-m","--metfrag_resultPth"),type="character"),
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9 make_option(c("-c","--sirius_csi_resultPth"),type="character"),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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10 make_option(c("-p","--probmetab_resultPth"),type="character"),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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11 make_option(c("-l","--ms1_lookup_resultPth"),type="character"),
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12
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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13 make_option("--ms1_lookup_checkAdducts", action="store_true"),
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14 make_option("--ms1_lookup_keepAdducts", type="character", default=NA),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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15 make_option("--ms1_lookup_dbSource", type="character", default="hmdb"),
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17 make_option("--sm_weight", type="numeric"),
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18 make_option("--metfrag_weight", type="numeric"),
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19 make_option("--sirius_csi_weight", type="numeric"),
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20 make_option("--probmetab_weight", type="numeric"),
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21 make_option("--ms1_lookup_weight", type="numeric"),
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22 make_option("--biosim_weight", type="numeric"),
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24 make_option("--summaryOutput", action="store_true"),
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0
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26 make_option("--create_new_database", action="store_true"),
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27 make_option("--outdir", type="character", default="."),
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29 make_option("--compoundDbType", type="character", default="sqlite"),
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30 make_option("--compoundDbPth", type="character", default=NA),
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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31 make_option("--compoundDbHost", type="character", default=NA)
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32 )
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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33 opt <- parse_args(OptionParser(option_list=option_list))
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34
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35 print(opt)
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36
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37 if (!is.null(opt$create_new_database)){
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38 sm_resultPth <- file.path(opt$outdir, 'combined_annotations.sqlite')
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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39 file.copy(opt$sm_resultPth, sm_resultPth)
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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40 }else{
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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41 sm_resultPth <- opt$sm_resultPth
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42 }
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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43
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44 if (is.null(opt$ms1_lookup_checkAdducts)){
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45 opt$ms1_lookup_checkAdducts <- FALSE
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46 }
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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47 if (!is.null(opt$ms1_lookup_keepAdducts)){
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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48 opt$ms1_lookup_keepAdducts <- gsub("__ob__", "[", opt$ms1_lookup_keepAdducts)
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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49 opt$ms1_lookup_keepAdducts <- gsub("__cb__", "]", opt$ms1_lookup_keepAdducts)
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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50 ms1_lookup_keepAdducts <- strsplit(opt$ms1_lookup_keepAdducts, ",")[[1]]
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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51 }
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52
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53 weights <-list('sm'=opt$sm_weight,
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54 'metfrag'=opt$metfrag_weight,
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55 'sirius_csifingerid'= opt$sirius_csi_weight,
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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56 'probmetab'=opt$probmetab_weight,
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57 'ms1_lookup'=opt$ms1_lookup_weight,
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58 'biosim'=opt$biosim_weight
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59 )
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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60 print(weights)
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62 if (is.null(opt$probmetab_resultPth)){
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63 opt$probmetab_resultPth = NA
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64 }
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65
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66 if (round(!sum(unlist(weights),0)==1)){
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67 stop(paste0('The weights should sum to 1 not ', sum(unlist(weights))))
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68 }
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69
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70 if (is.null(opt$summaryOutput)){
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71 summaryOutput = FALSE
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72 }else{
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73 summaryOutput = TRUE
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74 }
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75
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76 if (opt$compoundDbType=='local_config'){
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77 # load in compound config
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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78 # Soure local function taken from workflow4metabolomics
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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79 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
5ff9d40c7a42 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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80 source_local("dbconfig.R")
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81 }else{
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82 compoundDbPth = opt$compoundDbPth
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83 compoundDbType = opt$compoundDbType
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84 compoundDbName = NA
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85 compoundDbHost = NA
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86 compoundDbPort = NA
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87 compoundDbUser = NA
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88 compoundDbPass = NA
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89 }
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90
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91 summary_output <- msPurity::combineAnnotations(
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92 sm_resultPth = sm_resultPth,
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93 compoundDbPth = compoundDbPth,
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94 metfrag_resultPth = opt$metfrag_resultPth,
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95 sirius_csi_resultPth = opt$sirius_csi_resultPth,
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96 probmetab_resultPth = opt$probmetab_resultPth,
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97 ms1_lookup_resultPth = opt$ms1_lookup_resultPth,
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98 ms1_lookup_keepAdducts = ms1_lookup_keepAdducts,
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99 ms1_lookup_checkAdducts = opt$ms1_lookup_checkAdducts,
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100
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101 compoundDbType = compoundDbType,
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102 compoundDbName = compoundDbName,
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103 compoundDbHost = compoundDbHost,
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104 compoundDbPort = compoundDbPort,
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105 compoundDbUser = compoundDbUser,
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106 compoundDbPass = compoundDbPass,
2
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107 weights = weights,
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108 summaryOutput = summaryOutput)
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109 if (summaryOutput){
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110 write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE)
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111 }
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112
0
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114 write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE)
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115
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116
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117 closeAllConnections()
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118