annotate spectralMatching.R @ 9:548fed2ef792 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f

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)
    }
}