Mercurial > repos > tomnl > mspurity_frag4feature

annotate spectralMatching.R @ 12:a62b102788eb draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit bbbcc75d51c020446fd00d76f908a6250266cfea
author tomnl
date Fri, 13 Sep 2019 11:55:05 -0400
parents 274dc7b40bc2
children a2ba12977060
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1 library(msPurity)
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2 library(msPurityData)
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3 library(optparse)
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4 print(sessionInfo())
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5 # load in library spectra config
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6 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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7 source_local("dbconfig.R")
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9 option_list <- list(
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10 make_option(c("-o", "--outDir"), type="character"),
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11 make_option("--q_dbPth", type="character"),
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12 make_option("--l_dbPth", type="character"),
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14 make_option("--q_dbType", type="character", default=NA),
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15 make_option("--l_dbType", type="character", default=NA),
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17 make_option("--q_msp", type="character", default=NA),
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18 make_option("--l_msp", type="character", default=NA),
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20 make_option("--q_defaultDb", action="store_true"),
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21 make_option("--l_defaultDb", action="store_true"),
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23 make_option("--q_ppmPrec", type="double"),
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24 make_option("--l_ppmPrec", type="double"),
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26 make_option("--q_ppmProd", type="double"),
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27 make_option("--l_ppmProd", type="double"),
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29 make_option("--q_raThres", type="double", default=NA),
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30 make_option("--l_raThres", type="double", default=NA),
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32 make_option("--q_polarity", type="character", default=NA),
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33 make_option("--l_polarity", type="character", default=NA),
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35 make_option("--q_purity", type="double", default=NA),
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36 make_option("--l_purity", type="double", default=NA),
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38 make_option("--q_xcmsGroups", type="character", default=NA),
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39 make_option("--l_xcmsGroups", type="character", default=NA),
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41 make_option("--q_pids", type="character", default=NA),
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42 make_option("--l_pids", type="character", default=NA),
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44 make_option("--q_rtrangeMin", type="double", default=NA),
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45 make_option("--l_rtrangeMin", type="double", default=NA),
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47 make_option("--q_rtrangeMax", type="double", default=NA),
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48 make_option("--l_rtrangeMax", type="double", default=NA),
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50 make_option("--q_accessions", type="character", default=NA),
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51 make_option("--l_accessions", type="character", default=NA),
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53 make_option("--q_sources", type="character", default=NA),
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54 make_option("--l_sources", type="character", default=NA),
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56 make_option("--q_sourcesUser", type="character", default=NA),
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57 make_option("--l_sourcesUser", type="character", default=NA),
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59 make_option("--q_instrumentTypes", type="character", default=NA),
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60 make_option("--l_instrumentTypes", type="character", default=NA),
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62 make_option("--q_instrumentTypesUser", type="character", default=NA),
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63 make_option("--l_instrumentTypesUser", type="character", default=NA),
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65 make_option("--q_instruments", type="character", default=NA),
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66 make_option("--l_instruments", type="character", default=NA),
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68 make_option("--q_spectraTypes", type="character", default=NA),
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69 make_option("--l_spectraTypes", type="character", default=NA),
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71 make_option("--q_spectraFilter", action="store_true"),
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72 make_option("--l_spectraFilter", action="store_true"),
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74 make_option("--usePrecursors", action="store_true"),
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76 make_option("--mzW", type="double"),
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77 make_option("--raW", type="double"),
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79 make_option("--rttol", type="double", default=NA),
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81 make_option("--updateDb", action="store_true"),
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82 make_option("--copyDb", action="store_true"),
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83 make_option("--cores", default=1)
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86 )
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88 # store options
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89 opt<- parse_args(OptionParser(option_list=option_list))
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91 print(opt)
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92
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93 extractMultiple <- function(optParam){
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94 if (!is.na(optParam)){
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95 param <- trimws(strsplit(optParam, ',')[[1]])
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96 param <- param[param != ""]
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97 }else{
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98 param <- NA
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99 }
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100 return(param)
11
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101
0
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102 }
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103
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104 if(!is.null(opt$q_defaultDb)){
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105 q_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData")
12
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106 q_dbType <- 'sqlite'
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107 }else if (!opt$q_dbType=='local_config'){
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108 q_dbType <- opt$q_dbType
0
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109 q_dbPth <- opt$q_dbPth
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110 }
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111
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112 if(!is.null(opt$l_defaultDb)){
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113 l_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData")
12
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114 l_dbType <- 'sqlite'
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115 }else if (!opt$l_dbType=='local_config'){
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116 l_dbType <- opt$l_dbType
0
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117 l_dbPth <- opt$l_dbPth
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118 }
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119
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120
12
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121
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122
0
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123 q_polarity <- extractMultiple(opt$q_polarity)
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124 l_polarity <- extractMultiple(opt$l_polarity)
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125
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126 q_xcmsGroups <- extractMultiple(opt$q_xcmsGroups)
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127 l_xcmsGroups <- extractMultiple(opt$l_xcmsGroups)
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128
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129 q_pids <- extractMultiple(opt$q_pids)
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130 l_pids <- extractMultiple(opt$l_pids)
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131
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132 q_sources <- extractMultiple(opt$q_sources)
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133 l_sources <- extractMultiple(opt$l_sources)
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134
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135 q_sourcesUser <- extractMultiple(opt$q_sourcesUser)
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136 l_sourcesUser <- extractMultiple(opt$l_sourcesUser)
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137
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138 q_sources <-c(q_sources, q_sourcesUser)
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139 l_sources <-c(l_sources, l_sourcesUser)
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140
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141 q_instrumentTypes <- extractMultiple(opt$q_instrumentTypes)
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142 l_instrumentTypes <- extractMultiple(opt$l_instrumentTypes)
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143
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144 q_instrumentTypes <-c(q_instrumentTypes, q_instrumentTypes)
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145 l_instrumentTypes <-c(l_instrumentTypes, l_instrumentTypes)
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146
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147
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148 if(!is.null(opt$l_spectraFilter)){
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149 l_spectraFilter <- TRUE
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150 }else{
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151 l_spectraFilter <- FALSE
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152 }
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153
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154 if(!is.null(opt$q_spectraFilter)){
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155 q_spectraFilter <- TRUE
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156 }else{
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157 q_spectraFilter <- FALSE
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158 }
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159
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160 if(!is.null(opt$updateDb)){
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161 updateDb <- TRUE
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162 }else{
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163 updateDb <- FALSE
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164 }
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165
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166 if(!is.null(opt$copyDb)){
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167 copyDb <- TRUE
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168 }else{
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169 copyDb <- FALSE
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170 }
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171
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172 if(!is.null(opt$l_rtrangeMax)){
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173 l_rtrangeMax <- opt$l_rtrangeMax
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174 }else{
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175 l_rtrangeMax <- NA
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176 }
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177
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178 if(!is.null(opt$q_rtrangeMax)){
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179 q_rtrangeMax <- opt$q_rtrangeMax
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180 }else{
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181 q_rtrangeMax <- NA
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182 }
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183
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184 if(!is.null(opt$l_rtrangeMin)){
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185 l_rtrangeMin <- opt$l_rtrangeMin
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186 }else{
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187 l_rtrangeMin <- NA
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188 }
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189
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190 if(!is.null(opt$q_rtrangeMin)){
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191 q_rtrangeMin <- opt$q_rtrangeMin
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192 }else{
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193 q_rtrangeMin <- NA
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194 }
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195
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196
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197
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198 sm <- msPurity::spectralMatching(
0
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199 q_purity = opt$q_purity,
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200 l_purity = opt$l_purity,
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201
0
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202 q_ppmProd = opt$q_ppmProd,
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203 l_ppmProd = opt$l_ppmProd,
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204
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205 q_ppmPrec = opt$q_ppmPrec,
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206 l_ppmPrec = opt$l_ppmPrec,
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207
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208 q_raThres = opt$q_raThres,
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209 l_raThres = opt$l_raThres,
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210
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211 q_pol = q_polarity,
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212 l_pol = l_polarity,
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213
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214 q_xcmsGroups = q_xcmsGroups,
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215 l_xcmsGroups = l_xcmsGroups,
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216
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217 q_pids = q_pids,
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218 l_pids = l_pids,
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219
0
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220 q_sources = q_sources,
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221 l_sources = l_sources,
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222
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223 q_instrumentTypes = q_instrumentTypes,
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224 l_instrumentTypes = l_instrumentTypes,
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225
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226 q_spectraFilter= q_spectraFilter,
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227 l_spectraFilter= l_spectraFilter,
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228
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229 l_rtrange=c(l_rtrangeMin, l_rtrangeMax),
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230 q_rtrange=c(q_rtrangeMin, q_rtrangeMax),
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231
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232 q_accessions = opt$q_accessions,
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233 l_accessions= opt$l_accessions,
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234
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235 raW = opt$raW,
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236 mzW = opt$mzW,
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237 rttol=opt$rttol,
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238 cores=opt$cores,
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239
0
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240 copyDb=copyDb,
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241 updateDb=updateDb,
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242 outPth = "db_with_spectral_matching.sqlite",
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243
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244 q_dbPth = q_dbPth,
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245 q_dbType = q_dbType,
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246 q_dbName = q_dbName,
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247 q_dbHost = q_dbHost,
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248 q_dbUser = q_dbUser,
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249 q_dbPass = q_dbPass,
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250 q_dbPort = q_dbPort,
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251
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252 l_dbPth = l_dbPth,
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253 l_dbType = l_dbType,
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254 l_dbName = l_dbName,
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255 l_dbHost = l_dbHost,
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256 l_dbUser = l_dbUser,
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257 l_dbPass = l_dbPass,
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258 l_dbPort = l_dbPort
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259
0
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260 )
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261
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262
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263
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264 write.table(sm$matchedResults, 'matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE)
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265 write.table(sm$xcmsMatchedResults, 'xcms_matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE)
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266
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267
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268 # Add extra details from library spectra in resulting database
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269 # First get all the ids from the l_s_peak_meta from the query database
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270 if(updateDb){
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271 message('Adding extra details to database')
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272 q_con <- DBI::dbConnect(RSQLite::SQLite(),sm$q_dbPth)
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273 if (DBI::dbExistsTable(q_con, "l_s_peak_meta")){
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274 l_s_peak_meta <- DBI::dbGetQuery(q_con, 'SELECT * FROM l_s_peak_meta')
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275 colnames(l_s_peak_meta)[1] <- 'pid'
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276 }
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277
9
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278 l_con <- DBI::dbConnect(RSQLite::SQLite(),l_dbPth)
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279 if (DBI::dbExistsTable(l_con, "s_peaks")){
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280 l_s_peaks <- DBI::dbGetQuery(q_con, sprintf("SELECT * FROM s_peaks WHERE pid in (%s)", paste(unique(l_s_peak_meta$pid), collapse=',')))
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281
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282 }else if(DBI::dbExistsTable(l_con, "library_spectra")){
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283 l_s_peaks <- DBI::dbGetQuery(l_con, sprintf("SELECT * FROM library_spectra
9
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284 WHERE library_spectra_meta_id in (%s)", paste(unique(l_s_peak_meta$pid), collapse=',')))
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285 }else{
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286 l_s_peaks = NULL
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287 }
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288
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289 if (DBI::dbExistsTable(l_con, "source")){
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290 l_source <- DBI::dbGetQuery(l_con, 'SELECT * FROM source')
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291 }else if (DBI::dbExistsTable(l_con, "library_spectra_source")) {
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292 l_source <- DBI::dbGetQuery(l_con, 'SELECT * FROM library_spectra_source')
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293 }else{
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294 l_source = NULL
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295 }
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296
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297 if (!is.null(l_s_peaks)){
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298 DBI::dbWriteTable(q_con, name='l_s_peaks', value=l_s_peaks, row.names=FALSE, append=TRUE)
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299 }
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300
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301 if (!is.null(l_source)){
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302 DBI::dbWriteTable(q_con, name='l_source', value=l_source, row.names=FALSE, append=TRUE)
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303 }
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304
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305 }
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310