Mercurial > repos > computational-metabolomics > mspurity_combineannotations
view spectralMatching.R @ 1:cf62d2c0104e draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
author | computational-metabolomics |
---|---|
date | Thu, 05 Dec 2019 07:47:31 -0500 |
parents | 7f3183988100 |
children | 20768ba7f0b4 |
line wrap: on
line source
library(msPurity) library(msPurityData) library(optparse) print(sessionInfo()) # load in library spectra config source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } source_local("dbconfig.R") option_list <- list( make_option(c("-o", "--outDir"), type="character"), make_option("--q_dbPth", type="character"), make_option("--l_dbPth", type="character"), make_option("--q_dbType", type="character", default=NA), make_option("--l_dbType", type="character", default=NA), make_option("--q_msp", type="character", default=NA), make_option("--l_msp", type="character", default=NA), make_option("--q_defaultDb", action="store_true"), make_option("--l_defaultDb", action="store_true"), make_option("--q_ppmPrec", type="double"), make_option("--l_ppmPrec", type="double"), make_option("--q_ppmProd", type="double"), make_option("--l_ppmProd", type="double"), make_option("--q_raThres", type="double", default=NA), make_option("--l_raThres", type="double", default=NA), make_option("--q_polarity", type="character", default=NA), make_option("--l_polarity", type="character", default=NA), make_option("--q_purity", type="double", default=NA), make_option("--l_purity", type="double", default=NA), make_option("--q_xcmsGroups", type="character", default=NA), make_option("--l_xcmsGroups", type="character", default=NA), make_option("--q_pids", type="character", default=NA), make_option("--l_pids", type="character", default=NA), make_option("--q_rtrangeMin", type="double", default=NA), make_option("--l_rtrangeMin", type="double", default=NA), make_option("--q_rtrangeMax", type="double", default=NA), make_option("--l_rtrangeMax", type="double", default=NA), make_option("--q_accessions", type="character", default=NA), make_option("--l_accessions", type="character", default=NA), make_option("--q_sources", type="character", default=NA), make_option("--l_sources", type="character", default=NA), make_option("--q_sourcesUser", type="character", default=NA), make_option("--l_sourcesUser", type="character", default=NA), make_option("--q_instrumentTypes", type="character", default=NA), make_option("--l_instrumentTypes", type="character", default=NA), make_option("--q_instrumentTypesUser", type="character", default=NA), make_option("--l_instrumentTypesUser", type="character", default=NA), make_option("--q_instruments", type="character", default=NA), make_option("--l_instruments", type="character", default=NA), make_option("--q_spectraTypes", type="character", default=NA), make_option("--l_spectraTypes", type="character", default=NA), make_option("--q_spectraFilter", action="store_true"), make_option("--l_spectraFilter", action="store_true"), make_option("--usePrecursors", action="store_true"), make_option("--mzW", type="double"), make_option("--raW", type="double"), make_option("--rttol", type="double", default=NA), make_option("--updateDb", action="store_true"), make_option("--copyDb", action="store_true"), make_option("--cores", default=1) ) # store options opt<- parse_args(OptionParser(option_list=option_list)) print(opt) # check if the sqlite databases have any spectra checkSPeakMeta <- function(dbPth, nme){ if(is.null(dbPth)){ return(TRUE) }else if ((file.exists(dbPth)) & (file.info(dbPth)$size>0)){ con <- DBI::dbConnect(RSQLite::SQLite(), dbPth) if (DBI::dbExistsTable(con, "s_peak_meta")){ spm <- DBI::dbGetQuery(con, 'SELECT * FROM s_peak_meta ORDER BY ROWID ASC LIMIT 1') return(TRUE) }else if(DBI::dbExistsTable(con, "library_spectra_meta")){ spm <- DBI::dbGetQuery(con, 'SELECT * FROM library_spectra_meta ORDER BY ROWID ASC LIMIT 1') return(TRUE) }else{ print(paste("No spectra available for ",nme)) return(FALSE) } }else{ print(paste("file empty or does not exist for", nme)) return(FALSE) } } addQueryNameColumn <- function(sm){ if (is.null(sm$matchedResults) || length(sm$matchedResults)==1 || nrow(sm$matchedResults)==0){ return(sm) } con <- DBI::dbConnect(RSQLite::SQLite(),sm$q_dbPth) if (DBI::dbExistsTable(con, "s_peak_meta")){ spm <- DBI::dbGetQuery(con, 'SELECT pid, name AS query_entry_name FROM s_peak_meta') }else if(DBI::dbExistsTable(con, "library_spectra_meta")){ spm <- DBI::dbGetQuery(con, 'SELECT id AS pid, name AS query_entry_name FROM library_spectra_meta') } print(sm$matchedResults) if ('pid' %in% colnames(sm$matchedResults)){ sm$matchedResults <- merge(sm$matchedResults, spm, by.x='pid', by.y='pid') }else{ sm$matchedResults <- merge(sm$matchedResults, spm, by.x='qpid', by.y='pid') } print(sm$xcmsMatchedResults) if (is.null(sm$xcmsMatchedResults) || length(sm$xcmsMatchedResults)==1 || nrow(sm$xcmsMatchedResults)==0){ return(sm) }else{ if ('pid' %in% colnames(sm$xcmsMatchedResults)){ sm$xcmsMatchedResults<- merge(sm$xcmsMatchedResults, spm, by.x='pid', by.y='pid') }else{ sm$xcmsMatchedResults <- merge(sm$xcmsMatchedResults, spm, by.x='qpid', by.y='pid') } } return(sm) } updateDbF <- function(q_con, l_con){ message('Adding extra details to database') q_con <- DBI::dbConnect(RSQLite::SQLite(),sm$q_dbPth) if (DBI::dbExistsTable(q_con, "l_s_peak_meta")){ l_s_peak_meta <- DBI::dbGetQuery(q_con, 'SELECT * FROM l_s_peak_meta') colnames(l_s_peak_meta)[1] <- 'pid' } l_con <- DBI::dbConnect(RSQLite::SQLite(),l_dbPth) if (DBI::dbExistsTable(l_con, "s_peaks")){ l_s_peaks <- DBI::dbGetQuery(q_con, sprintf("SELECT * FROM s_peaks WHERE pid in (%s)", paste(unique(l_s_peak_meta$pid), collapse=','))) }else if(DBI::dbExistsTable(l_con, "library_spectra")){ l_s_peaks <- DBI::dbGetQuery(l_con, sprintf("SELECT * FROM library_spectra WHERE library_spectra_meta_id in (%s)", paste(unique(l_s_peak_meta$pid), collapse=','))) }else{ l_s_peaks = NULL } if (DBI::dbExistsTable(l_con, "source")){ l_source <- DBI::dbGetQuery(l_con, 'SELECT * FROM source') }else if (DBI::dbExistsTable(l_con, "library_spectra_source")) { l_source <- DBI::dbGetQuery(l_con, 'SELECT * FROM library_spectra_source') }else{ l_source = NULL } if (!is.null(l_s_peaks)){ DBI::dbWriteTable(q_con, name='l_s_peaks', value=l_s_peaks, row.names=FALSE, append=TRUE) } if (!is.null(l_source)){ DBI::dbWriteTable(q_con, name='l_source', value=l_source, row.names=FALSE, append=TRUE) } } extractMultiple <- function(optParam){ if (!is.na(optParam)){ param <- trimws(strsplit(optParam, ',')[[1]]) param <- param[param != ""] }else{ param <- NA } return(param) } if(!is.null(opt$q_defaultDb)){ q_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData") q_dbType <- 'sqlite' }else if (!opt$q_dbType=='local_config'){ q_dbType <- opt$q_dbType q_dbPth <- opt$q_dbPth } if(!is.null(opt$l_defaultDb)){ l_dbPth <- system.file("extdata", "library_spectra", "library_spectra.db", package="msPurityData") l_dbType <- 'sqlite' }else if (!opt$l_dbType=='local_config'){ l_dbType <- opt$l_dbType l_dbPth <- opt$l_dbPth } q_polarity <- extractMultiple(opt$q_polarity) l_polarity <- extractMultiple(opt$l_polarity) q_xcmsGroups <- extractMultiple(opt$q_xcmsGroups) l_xcmsGroups <- extractMultiple(opt$l_xcmsGroups) q_pids <- extractMultiple(opt$q_pids) l_pids <- extractMultiple(opt$l_pids) q_sources <- extractMultiple(opt$q_sources) l_sources <- extractMultiple(opt$l_sources) q_sourcesUser <- extractMultiple(opt$q_sourcesUser) l_sourcesUser <- extractMultiple(opt$l_sourcesUser) q_sources <-c(q_sources, q_sourcesUser) l_sources <-c(l_sources, l_sourcesUser) q_instrumentTypes <- extractMultiple(opt$q_instrumentTypes) l_instrumentTypes <- extractMultiple(opt$l_instrumentTypes) q_instrumentTypes <-c(q_instrumentTypes, q_instrumentTypes) l_instrumentTypes <-c(l_instrumentTypes, l_instrumentTypes) if(!is.null(opt$l_spectraFilter)){ l_spectraFilter <- TRUE }else{ l_spectraFilter <- FALSE } if(!is.null(opt$q_spectraFilter)){ q_spectraFilter <- TRUE }else{ q_spectraFilter <- FALSE } if(!is.null(opt$updateDb)){ updateDb <- TRUE }else{ updateDb <- FALSE } if(!is.null(opt$copyDb)){ copyDb <- TRUE }else{ copyDb <- FALSE } if(!is.null(opt$l_rtrangeMax)){ l_rtrangeMax <- opt$l_rtrangeMax }else{ l_rtrangeMax <- NA } if(!is.null(opt$q_rtrangeMax)){ q_rtrangeMax <- opt$q_rtrangeMax }else{ q_rtrangeMax <- NA } if(!is.null(opt$l_rtrangeMin)){ l_rtrangeMin <- opt$l_rtrangeMin }else{ l_rtrangeMin <- NA } if(!is.null(opt$q_rtrangeMin)){ q_rtrangeMin <- opt$q_rtrangeMin }else{ q_rtrangeMin <- NA } q_check <- checkSPeakMeta(opt$q_dbPth, 'query') l_check <- checkSPeakMeta(opt$l_dbPth, 'library') if (q_check && l_check){ sm <- msPurity::spectralMatching( q_purity = opt$q_purity, l_purity = opt$l_purity, q_ppmProd = opt$q_ppmProd, l_ppmProd = opt$l_ppmProd, q_ppmPrec = opt$q_ppmPrec, l_ppmPrec = opt$l_ppmPrec, q_raThres = opt$q_raThres, l_raThres = opt$l_raThres, q_pol = q_polarity, l_pol = l_polarity, q_xcmsGroups = q_xcmsGroups, l_xcmsGroups = l_xcmsGroups, q_pids = q_pids, l_pids = l_pids, q_sources = q_sources, l_sources = l_sources, q_instrumentTypes = q_instrumentTypes, l_instrumentTypes = l_instrumentTypes, q_spectraFilter= q_spectraFilter, l_spectraFilter= l_spectraFilter, l_rtrange=c(l_rtrangeMin, l_rtrangeMax), q_rtrange=c(q_rtrangeMin, q_rtrangeMax), q_accessions = opt$q_accessions, l_accessions= opt$l_accessions, raW = opt$raW, mzW = opt$mzW, rttol=opt$rttol, cores=opt$cores, copyDb=copyDb, updateDb=updateDb, outPth = "db_with_spectral_matching.sqlite", q_dbPth = q_dbPth, q_dbType = q_dbType, q_dbName = q_dbName, q_dbHost = q_dbHost, q_dbUser = q_dbUser, q_dbPass = q_dbPass, q_dbPort = q_dbPort, l_dbPth = l_dbPth, l_dbType = l_dbType, l_dbName = l_dbName, l_dbHost = l_dbHost, l_dbUser = l_dbUser, l_dbPass = l_dbPass, l_dbPort = l_dbPort ) sm <- addQueryNameColumn(sm) # Get name of the query results (and merged with the data frames) write.table(sm$matchedResults, 'matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE) write.table(sm$xcmsMatchedResults, 'xcms_matched_results.tsv', sep = '\t', row.names = FALSE, col.names = TRUE) if(updateDb){ updateDbF(q_con, l_con) } }