Mercurial > repos > tomnl > mspurity_dimspredictpuritysingle

annotate combineAnnotations.R @ 12:d70fd233784a draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4f88143938cc198436c2691443832c87e2c31cd0
author tomnl
date Tue, 24 Sep 2019 08:07:38 -0400
parents a90832e6acb2
children 1389e565f95e
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1 library(optparse)
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2 library(msPurity)
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3 print(sessionInfo())
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5 # Get the parameter
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6 option_list <- list(
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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"),
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10 make_option(c("-p","--probmetab_resultPth"),type="character"),
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11 make_option(c("-l","--ms1_lookup_resultPth"),type="character"),
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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),
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15 make_option("--ms1_lookup_dbSource", type="character", default="hmdb"),
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17 make_option(c("-sw","--sm_weight"),type="numeric"),
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18 make_option(c("-mw","--metfrag_weight"),type="numeric"),
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19 make_option(c("-cw","--sirius_csi_weight"),type="numeric"),
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20 make_option(c("-pw","--probmetab_weight"),type="numeric"),
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21 make_option(c("-lw","--ms1_lookup_weight"),type="numeric"),
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22 make_option(c("-bw","--biosim_weight"),type="numeric"),
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24 make_option("--create_new_database", action="store_true"),
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25 make_option(c("-o","--outdir"),type="character", default="."),
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27 make_option("--compoundDbType", type="character", default="sqlite"),
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28 make_option("--compoundDbPth", type="character", default=NA),
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29 make_option("--compoundDbHost", type="character", default=NA)
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30 )
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31 opt <- parse_args(OptionParser(option_list=option_list))
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33 print(opt)
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35 if (!is.null(opt$create_new_database)){
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36 sm_resultPth <- file.path(opt$outdir, 'combined_annotations.sqlite')
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37 file.copy(opt$sm_resultPth, sm_resultPth)
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38 }else{
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39 sm_resultPth <- opt$sm_resultPth
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40 }
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42 if (is.null(opt$ms1_lookup_checkAdducts)){
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43 opt$ms1_lookup_checkAdducts <- FALSE
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44 }
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45 if (!is.null(opt$ms1_lookup_keepAdducts)){
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46 opt$ms1_lookup_keepAdducts <- gsub("__ob__", "[", opt$ms1_lookup_keepAdducts)
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47 opt$ms1_lookup_keepAdducts <- gsub("__cb__", "]", opt$ms1_lookup_keepAdducts)
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48 ms1_lookup_keepAdducts <- strsplit(opt$ms1_lookup_keepAdducts, ",")[[1]]
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49 }
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51 weights <-list('sm'=opt$sm_weight,
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52 'metfrag'=opt$metfrag_weight,
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53 'sirius_csifingerid'= opt$sirius_csi_weight,
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54 'probmetab'=opt$probmetab_weight,
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55 'ms1_lookup'=opt$ms1_lookup_weight,
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56 'biosim'=opt$biosim_weight
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57 )
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58 print(weights)
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59 if (round(!sum(unlist(weights),0)==1)){
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61 stop(paste0('The weights should sum to 1 not ', sum(unlist(weights))))
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62 }
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63
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64 if (opt$compoundDbType=='local_config'){
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65 # load in compound config
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66 # Soure local function taken from workflow4metabolomics
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67 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
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68 source_local("dbconfig.R")
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69 }else{
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70 compoundDbType = compoundDbType
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71 compoundDbName = NA
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72 compoundDbHost = NA
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73 compoundDbPort = NA
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74 compoundDbUser = NA
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75 compoundDbPass = NA
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76 }
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80 summary_output <- msPurity::combineAnnotations(
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81 sm_resultPth = sm_resultPth,
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82 compoundDbPth = compoundDbPth,
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83 metfrag_resultPth = opt$metfrag_resultPth,
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84 sirius_csi_resultPth = opt$sirius_csi_resultPth,
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85 probmetab_resultPth = opt$probmetab_resultPth,
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86 ms1_lookup_resultPth = opt$ms1_lookup_resultPth,
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87 ms1_lookup_keepAdducts = ms1_lookup_keepAdducts,
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88 ms1_lookup_checkAdducts = opt$ms1_lookup_checkAdducts,
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90 compoundDbType = compoundDbType,
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91 compoundDbName = compoundDbName,
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92 compoundDbHost = compoundDbHost,
a90832e6acb2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
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93 compoundDbPort = compoundDbPort,
a90832e6acb2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
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94 compoundDbUser = compoundDbUser,
a90832e6acb2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
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parents: 4
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95 compoundDbPass = compoundDbPass,
a90832e6acb2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
tomnl
parents: 4
diff changeset
96 weights = weights)
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fc9bb7e49a3a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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97
fc9bb7e49a3a planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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98 write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE)
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0a3e6c28f1ab planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e05cb49ba56d359fec34f132d1c9ace582e5b483-dirty
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99
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100
0a3e6c28f1ab planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e05cb49ba56d359fec34f132d1c9ace582e5b483-dirty
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101 closeAllConnections()
0a3e6c28f1ab planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e05cb49ba56d359fec34f132d1c9ace582e5b483-dirty
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102