Mercurial > repos > tomnl > mspurity_flagremove

annotate spectralMatching.R @ 9:6bd3ff77063c draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 74e7bfbb5e70ec6e665114fa9e9863dafd7bced5
author tomnl
date Tue, 25 Jun 2019 05:59:31 -0400
parents ca0ac330f1a4
children 7e4a5ce0877d
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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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7 option_list <- list(
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8 make_option(c("-o", "--outDir"), type="character"),
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9 make_option("--q_dbPth", type="character"),
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10 make_option("--l_dbPth", type="character"),
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12 make_option("--q_msp", type="character", default=NA),
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13 make_option("--l_msp", type="character", default=NA),
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15 make_option("--q_defaultDb", action="store_true"),
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16 make_option("--l_defaultDb", action="store_true"),
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18 make_option("--q_ppmPrec", type="double"),
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19 make_option("--l_ppmPrec", type="double"),
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21 make_option("--q_ppmProd", type="double"),
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22 make_option("--l_ppmProd", type="double"),
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24 make_option("--q_raThres", type="double", default=NA),
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25 make_option("--l_raThres", type="double", default=NA),
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27 make_option("--q_polarity", type="character", default=NA),
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28 make_option("--l_polarity", type="character", default=NA),
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30 make_option("--q_purity", type="double", default=NA),
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31 make_option("--l_purity", type="double", default=NA),
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33 make_option("--q_xcmsGroups", type="character", default=NA),
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34 make_option("--l_xcmsGroups", type="character", default=NA),
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36 make_option("--q_pids", type="character", default=NA),
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37 make_option("--l_pids", type="character", default=NA),
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39 make_option("--q_rtrangeMin", type="double", default=NA),
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40 make_option("--l_rtrangeMin", type="double", default=NA),
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42 make_option("--q_rtrangeMax", type="double", default=NA),
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43 make_option("--l_rtrangeMax", type="double", default=NA),
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45 make_option("--q_accessions", type="character", default=NA),
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46 make_option("--l_accessions", type="character", default=NA),
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48 make_option("--q_sources", type="character", default=NA),
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49 make_option("--l_sources", type="character", default=NA),
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51 make_option("--q_sourcesUser", type="character", default=NA),
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52 make_option("--l_sourcesUser", type="character", default=NA),
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54 make_option("--q_instrumentTypes", type="character", default=NA),
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55 make_option("--l_instrumentTypes", type="character", default=NA),
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57 make_option("--q_instrumentTypesUser", type="character", default=NA),
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58 make_option("--l_instrumentTypesUser", type="character", default=NA),
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60 make_option("--q_instruments", type="character", default=NA),
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61 make_option("--l_instruments", type="character", default=NA),
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63 make_option("--q_spectraTypes", type="character", default=NA),
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64 make_option("--l_spectraTypes", type="character", default=NA),
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66 make_option("--q_spectraFilter", action="store_true"),
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67 make_option("--l_spectraFilter", action="store_true"),
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69 make_option("--usePrecursors", action="store_true"),
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71 make_option("--mzW", type="double"),
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72 make_option("--raW", type="double"),
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74 make_option("--rttol", type="double", default=NA),
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76 make_option("--updateDb", action="store_true"),
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77 make_option("--copyDb", action="store_true"),
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78 make_option("--cores", default=1)
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81 )
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83 # store options
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84 opt<- parse_args(OptionParser(option_list=option_list))
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86 print(opt)
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88 extractMultiple <- function(optParam){
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89 if (!is.na(optParam)){
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90 param <- trimws(strsplit(optParam, ',')[[1]])
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91 param <- param[param != ""]
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92 }else{
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93 param <- NA
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94 }
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95 return(param)
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96
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97 }
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98
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99 if(!is.null(opt$q_defaultDb)){
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100 q_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData")
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101 }else if (!is.null(opt$q_dbPth)){
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102 q_dbPth <- opt$q_dbPth
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103 }else{
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104 message('No query database available')
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105 exit()
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106 }
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107
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108 if(!is.null(opt$l_defaultDb)){
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109 l_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData")
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110 }else if (!is.null(opt$l_dbPth)){
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111 l_dbPth <- opt$l_dbPth
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112 }else{
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113 message('No library database available')
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114 exit()
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115 }
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116
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117
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118 q_polarity <- extractMultiple(opt$q_polarity)
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119 l_polarity <- extractMultiple(opt$l_polarity)
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120
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121 q_xcmsGroups <- extractMultiple(opt$q_xcmsGroups)
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122 l_xcmsGroups <- extractMultiple(opt$l_xcmsGroups)
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123
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124 q_pids <- extractMultiple(opt$q_pids)
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125 l_pids <- extractMultiple(opt$l_pids)
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126
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127 q_sources <- extractMultiple(opt$q_sources)
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128 l_sources <- extractMultiple(opt$l_sources)
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129
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130 q_sourcesUser <- extractMultiple(opt$q_sourcesUser)
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131 l_sourcesUser <- extractMultiple(opt$l_sourcesUser)
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132
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133 q_sources <-c(q_sources, q_sourcesUser)
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134 l_sources <-c(l_sources, l_sourcesUser)
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135
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136 q_instrumentTypes <- extractMultiple(opt$q_instrumentTypes)
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137 l_instrumentTypes <- extractMultiple(opt$l_instrumentTypes)
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138
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139 q_instrumentTypes <-c(q_instrumentTypes, q_instrumentTypes)
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140 l_instrumentTypes <-c(l_instrumentTypes, l_instrumentTypes)
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141
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142
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143 if(!is.null(opt$l_spectraFilter)){
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144 l_spectraFilter <- TRUE
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145 }else{
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146 l_spectraFilter <- FALSE
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147 }
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148
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149 if(!is.null(opt$q_spectraFilter)){
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150 q_spectraFilter <- TRUE
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151 }else{
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152 q_spectraFilter <- FALSE
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153 }
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154
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155 if(!is.null(opt$updateDb)){
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156 updateDb <- TRUE
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157 }else{
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158 updateDb <- FALSE
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159 }
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160
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161 if(!is.null(opt$copyDb)){
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162 copyDb <- TRUE
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163 }else{
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164 copyDb <- FALSE
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165 }
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166
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167 if(!is.null(opt$l_rtrangeMax)){
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168 l_rtrangeMax <- opt$l_rtrangeMax
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169 }else{
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170 l_rtrangeMax <- NA
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171 }
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172
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173 if(!is.null(opt$q_rtrangeMax)){
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174 q_rtrangeMax <- opt$q_rtrangeMax
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175 }else{
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176 q_rtrangeMax <- NA
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177 }
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178
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179 if(!is.null(opt$l_rtrangeMin)){
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180 l_rtrangeMin <- opt$l_rtrangeMin
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181 }else{
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182 l_rtrangeMin <- NA
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183 }
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184
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185 if(!is.null(opt$q_rtrangeMin)){
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186 q_rtrangeMin <- opt$q_rtrangeMin
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187 }else{
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188 q_rtrangeMin <- NA
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189 }
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190
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191
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192
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193 sm <- msPurity::spectralMatching(q_dbPth = q_dbPth,
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194 l_dbPth = l_dbPth,
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195
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196 q_purity = opt$q_purity,
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197 l_purity = opt$l_purity,
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198
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199 q_ppmProd = opt$q_ppmProd,
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200 l_ppmProd = opt$l_ppmProd,
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201
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202 q_ppmPrec = opt$q_ppmPrec,
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203 l_ppmPrec = opt$l_ppmPrec,
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204
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205 q_raThres = opt$q_raThres,
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206 l_raThres = opt$l_raThres,
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207
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208 q_pol = q_polarity,
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209 l_pol = l_polarity,
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210
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211 q_xcmsGroups = q_xcmsGroups,
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212 l_xcmsGroups = l_xcmsGroups,
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213
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214 q_pids = q_pids,
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215 l_pids = l_pids,
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216
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217 q_sources = q_sources,
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218 l_sources = l_sources,
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219
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220 q_instrumentTypes = q_instrumentTypes,
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221 l_instrumentTypes = l_instrumentTypes,
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222
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223 q_spectraFilter= q_spectraFilter,
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224 l_spectraFilter= l_spectraFilter,
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225
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226 l_rtrange=c(l_rtrangeMin, l_rtrangeMax),
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227 q_rtrange=c(q_rtrangeMin, q_rtrangeMax),
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228
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229 q_accessions = opt$q_accessions,
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230 l_accessions= opt$l_accessions,
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231
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232 raW = opt$raW,
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233 mzW = opt$mzW,
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234 rttol=opt$rttol,
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235 cores=opt$cores,
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236
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237 copyDb=copyDb,
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238 updateDb=updateDb,
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239 outPth = "db_with_spectral_matching.sqlite"
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240 )
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241
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242
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243
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244 write.table(sm$matchedResults, 'matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE)
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245 write.table(sm$xcmsMatchedResults, 'xcms_matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE)
9
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246
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247
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248 # Add extra details from library spectra in resulting database
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249 # First get all the ids from the l_s_peak_meta from the query database
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250 if(updateDb){
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251 message('Adding extra details to database')
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252 q_con <- DBI::dbConnect(RSQLite::SQLite(),sm$q_dbPth)
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253 if (DBI::dbExistsTable(q_con, "l_s_peak_meta")){
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254 l_s_peak_meta <- DBI::dbGetQuery(q_con, 'SELECT * FROM l_s_peak_meta')
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255 colnames(l_s_peak_meta)[1] <- 'pid'
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256 }
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257
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258 l_con <- DBI::dbConnect(RSQLite::SQLite(),l_dbPth)
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259 if (DBI::dbExistsTable(q_con, "s_peaks")){
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260 l_s_peaks <- DBI::dbGetQuery(q_con, sprintf("SELECT * FROM s_peaks WHERE pid in (%s)", paste(unique(l_s_peak_meta$pid), collapse=',')))
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261
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262 }else if(DBI::dbExistsTable(q_con, "library_spectra")){
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263 l_s_peaks <- DBI::dbGetQuery(q_con, sprintf("SELECT * FROM library_spectra
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264 WHERE library_spectra_meta_id in (%s)", paste(unique(l_s_peak_meta$pid), collapse=',')))
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265 }else{
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266 l_s_peaks = NULL
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267 }
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268
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269 if (DBI::dbExistsTable(q_con, "source")){
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270 l_source <- DBI::dbGetQuery(q_con, 'SELECT * FROM source')
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271 }else if (DBI::dbExistsTable(q_con, "library_spectra_source")) {
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272 l_source <- DBI::dbGetQuery(q_con, 'library_spectra_source')
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273 }else{
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274 l_source = NULL
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275 }
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276
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277 if (!is.null(l_s_peaks)){
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278 DBI::dbWriteTable(q_con, name='l_s_peaks', value=l_s_peaks, row.names=FALSE, append=TRUE)
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279 }
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280
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281 if (!is.null(l_source)){
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282 DBI::dbWriteTable(q_con, name='l_source', value=l_source, row.names=FALSE, append=TRUE)
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283 }
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284
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285 }
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286
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287
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288
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289
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290