Mercurial > repos > tomnl > create_sqlite_db

annotate create_sqlite_db.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(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('CREATING DATABASE')
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8 xset_pa_filename_fix <- function(opt, pa, xset){
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11 if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){
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12 # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables
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13 # needs to be done due to Galaxy moving the files around and screwing up any links to files
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15 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
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16 filepaths <- filepaths[filepaths != ""]
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17 new_names <- basename(filepaths)
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19 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
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20 galaxy_names <- galaxy_names[galaxy_names != ""]
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22 nsave <- names(pa@fileList)
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23 old_filenames <- basename(pa@fileList)
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24 pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)]
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25 names(pa@fileList) <- nsave
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27 pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)])
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28 pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)])
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29 }
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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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48 option_list <- list(
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49 make_option(c("-o", "--out_dir"), type="character"),
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50 make_option("--pa", type="character"),
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51 make_option("--xset_xa", type="character"),
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52 make_option("--xcms_camera_option", type="character"),
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53 make_option("--eic", action="store_true"),
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54 make_option("--cores", default=4),
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55 make_option("--mzML_files", type="character"),
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56 make_option("--galaxy_names", type="character"),
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57 make_option("--grp_peaklist", type="character"),
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58 make_option("--db_name", type="character", default='lcms_data.sqlite'),
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59 make_option("--raw_rt_columns", action="store_true")
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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() == name]))
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69 }
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70
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71 print(paste('pa', opt$pa))
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72 print(opt$xset)
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73 print(opt$xcms_camera_option)
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74 # Requires
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75 pa <- loadRData(opt$pa, 'pa')
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77 print('TESTETSTESTETE')
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78 print(pa@fileList)
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81 if (opt$xcms_camera_option=='xcms'){
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82 xset <- loadRData(opt$xset, 'xset')
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83 fix <- xset_pa_filename_fix(opt, pa, xset)
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84 pa <- fix[[1]]
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85 xset <- fix[[2]]
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86 xa <- NULL
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87 }else{
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88
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89 xa <- loadRData(opt$xset, 'xa')
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90 fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet)
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91 pa <- fix[[1]]
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92 xa@xcmsSet <- fix[[2]]
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93 xset <- NULL
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94 }
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98
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99
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100 if(is.null(opt$grp_peaklist)){
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101 grp_peaklist = NA
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102 }else{
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103 grp_peaklist = opt$grp_peaklist
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104 }
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105
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106
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107 print(pa@fileList)
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108 print(xset@filepaths)
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109
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110
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111 db_pth <- msPurity::create_database(pa, xset=xset, xsa=xa, out_dir=opt$out_dir,
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112 grp_peaklist=grp_peaklist, db_name=opt$db_name)
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113
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114
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115 if (!is.null(opt$eic)){
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116 if (is.null(opt$raw_rt_columns)){
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117 rtrawColumns <- FALSE
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118 }else{
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119 rtrawColumns <- TRUE
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120 }
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121
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122 # Saves the EICS into the previously created database
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123 px <- msPurity::purityX(xset, saveEIC = TRUE,
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124 cores=opt$cores, sqlitePth=db_pth,
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125 rtrawColumns = rtrawColumns)
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126 }
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127
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128
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129
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130 con <- DBI::dbConnect(RSQLite::SQLite(), db_pth)
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131
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132 cmd <- paste('SELECT cpg.grpid, cpg.mz, cpg.mzmin, cpg.mzmax, cpg.rt, cpg.rtmin, cpg.rtmax, c_peaks.cid, ',
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133 'c_peaks.mzmin AS c_peak_mzmin, c_peaks.mzmax AS c_peak_mzmax, ',
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134 '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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135 'FROM c_peak_groups AS cpg ',
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136 'LEFT JOIN c_peak_X_c_peak_group AS cXg ON cXg.grpid=cpg.grpid ',
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137 'LEFT JOIN c_peaks on c_peaks.cid=cXg.cid ',
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138 'LEFT JOIN c_peak_X_s_peak_meta AS cXs ON cXs.cid=c_peaks.cid ',
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139 'LEFT JOIN s_peak_meta ON cXs.pid=s_peak_meta.pid ',
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140 'LEFT JOIN fileinfo ON s_peak_meta.fileid=fileinfo.fileid')
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141
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142 print(cmd)
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143 cpeakgroup_msms <- DBI::dbGetQuery(con, cmd)
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144
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145 write.table(cpeakgroup_msms, file.path(opt$out_dir, 'cpeakgroup_msms.tsv'), row.names=FALSE, sep='\t')