--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spectralMatching.R	Thu Mar 04 12:11:29 2021 +0000
@@ -0,0 +1,377 @@
+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$l_dbPth
+}
+
+q_spectraTypes <- extractMultiple(opt$q_spectraTypes)
+l_spectraTypes <- extractMultiple(opt$l_spectraTypes)
+
+q_polarity <- extractMultiple(opt$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$l_raThres,
+
+        q_pol =  q_polarity,
+        l_pol =  l_polarity,
+
+        q_spectraFilter = q_spectraFilter,
+        l_spectraFilter = l_spectraFilter,
+
+        q_xcmsGroups = q_xcmsGroups,
+        l_xcmsGroups = l_xcmsGroups,
+
+        q_pids = q_pids,
+        l_pids = l_pids,
+
+        q_sources = q_sources,
+        l_sources = l_sources,
+
+        q_instrumentTypes = q_instrumentTypes,
+        l_instrumentTypes = l_instrumentTypes,
+
+        q_spectraTypes = q_spectraTypes,
+        l_spectraTypes = l_spectraTypes,
+
+        l_rtrange = c(l_rtrangeMin, l_rtrangeMax),
+        q_rtrange = c(q_rtrangeMin, q_rtrangeMax),
+
+        q_accessions = opt$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)
+    }
+}