Mercurial > repos > tomnl > anticipated_purity_lcms

annotate create_sqlite_db.R @ 9:5969d72028f3 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
author tomnl
date Wed, 02 May 2018 14:13:46 -0400
parents b83bcc259b76
children 3c4a548b5237
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1 library(msPurity)
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2 library(optparse)
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3 library(xcms)
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4 library(CAMERA)
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5 print(sessionInfo())
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6 print('CREATING DATABASE')
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9 xset_pa_filename_fix <- function(opt, pa, xset){
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12 if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
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13 # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
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14 # needs to be done due to Galaxy moving the files around and screwing up any links to files
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16 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
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17 filepaths <- filepaths[filepaths != ""]
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18 new_names <- basename(filepaths)
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20 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
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21 galaxy_names <- galaxy_names[galaxy_names != ""]
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23 nsave <- names(pa@fileList)
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24 old_filenames <- basename(pa@fileList)
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25 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
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26 names(pa@fileList) <- nsave
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28 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
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29 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
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30 }
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33 if(!all(basename(pa@fileList)==basename(xset@filepaths))){
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34 if(!all(names(pa@fileList)==basename(xset@filepaths))){
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35 print('FILELISTS DO NOT MATCH')
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36 message('FILELISTS DO NOT MATCH')
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37 quit(status = 1)
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38 }else{
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39 xset@filepaths <- unname(pa@fileList)
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40 }
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41 }
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44 return(list(pa, xset))
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45 }
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49 option_list <- list(
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50 make_option(c("-o", "--out_dir"), type="character"),
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51 make_option("--pa", type="character"),
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52 make_option("--xset_xa", type="character"),
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53 make_option("--xcms_camera_option", type="character"),
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54 make_option("--eic", action="store_true"),
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55 make_option("--cores", default=4),
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56 make_option("--mzML_files", type="character"),
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57 make_option("--galaxy_names", type="character"),
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58 make_option("--grp_peaklist", type="character"),
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59 make_option("--db_name", type="character", default='lcms_data.sqlite'),
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60 make_option("--raw_rt_columns", action="store_true")
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61 )
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63 # store options
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64 opt<- parse_args(OptionParser(option_list=option_list))
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66 loadRData <- function(rdata_path, name){
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67 #loads an RData file, and returns the named xset object if it is there
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68 load(rdata_path)
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69 return(get(ls()[ls() == name]))
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70 }
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72 print(paste('pa', opt$pa))
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73 print(opt$xset)
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74 print(opt$xcms_camera_option)
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75 # Requires
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76 pa <- loadRData(opt$pa, 'pa')
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78 print('TESTETSTESTETE')
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79 print(pa@fileList)
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82 if (opt$xcms_camera_option=='xcms'){
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83 xset <- loadRData(opt$xset, 'xset')
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84 fix <- xset_pa_filename_fix(opt, pa, xset)
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85 pa <- fix[[1]]
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86 xset <- fix[[2]]
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87 xa <- NULL
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88 }else{
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89
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90 xa <- loadRData(opt$xset, 'xa')
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91 fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet)
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92 pa <- fix[[1]]
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93 xa@xcmsSet <- fix[[2]]
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94 xset <- NULL
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95 }
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99
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100
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101 if(is.null(opt$grp_peaklist)){
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102 grp_peaklist = NA
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103 }else{
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104 grp_peaklist = opt$grp_peaklist
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105 }
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106
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107
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108 print(pa@fileList)
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109 print(xset@filepaths)
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110
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111
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112 db_pth <- msPurity::create_database(pa, xset=xset, xsa=xa, out_dir=opt$out_dir,
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113 grp_peaklist=grp_peaklist, db_name=opt$db_name)
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114
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115
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116 if (!is.null(opt$eic)){
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117 if (is.null(opt$raw_rt_columns)){
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118 rtrawColumns <- FALSE
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119 }else{
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120 rtrawColumns <- TRUE
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121 }
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122
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123 # Saves the EICS into the previously created database
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124 px <- msPurity::purityX(xset, saveEIC = TRUE,
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125 cores=opt$cores, sqlitePth=db_pth,
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126 rtrawColumns = rtrawColumns)
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127 }
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128
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129
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130
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131 con <- DBI::dbConnect(RSQLite::SQLite(), db_pth)
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132
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133 cmd <- paste('SELECT cpg.grpid, cpg.mz, cpg.mzmin, cpg.mzmax, cpg.rt, cpg.rtmin, cpg.rtmax, c_peaks.cid, ',
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134 'c_peaks.mzmin AS c_peak_mzmin, c_peaks.mzmax AS c_peak_mzmax, ',
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135 'c_peaks.rtmin AS c_peak_rtmin, c_peaks.rtmax AS c_peak_rtmax, s_peak_meta.*, fileinfo.filename, fileinfo.nm_save ',
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136 'FROM c_peak_groups AS cpg ',
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137 'LEFT JOIN c_peak_X_c_peak_group AS cXg ON cXg.grpid=cpg.grpid ',
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138 'LEFT JOIN c_peaks on c_peaks.cid=cXg.cid ',
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139 'LEFT JOIN c_peak_X_s_peak_meta AS cXs ON cXs.cid=c_peaks.cid ',
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140 'LEFT JOIN s_peak_meta ON cXs.pid=s_peak_meta.pid ',
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141 'LEFT JOIN fileinfo ON s_peak_meta.fileid=fileinfo.fileid')
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142
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143 print(cmd)
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144 cpeakgroup_msms <- DBI::dbGetQuery(con, cmd)
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145
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146 write.table(cpeakgroup_msms, file.path(opt$out_dir, 'cpeakgroup_msms.tsv'), row.names=FALSE, sep='\t')