Mercurial > repos > workflow4metabolomics > ms2snoop
changeset 6:77abacd33c31 draft
planemo upload commit 1f791337b9b8f08326c01bf4799f50493ef54f80
| author | workflow4metabolomics |
|---|---|
| date | Fri, 30 Sep 2022 16:18:56 +0000 |
| parents | 78d5a12406c2 |
| children | 2a1f120a6874 |
| files | MS2snoop.R MS2snoop.xml README.md macros.xml test-data/compound_fragments_result.txt test-data/smol/out-smol-base.tsv test-data/smol/out-smol-delta-0.05mz.tsv test-data/smol/out-smol-delta-8.542.tsv |
| diffstat | 8 files changed, 2196 insertions(+), 2361 deletions(-) [+] |
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--- a/MS2snoop.R Fri Aug 05 17:25:45 2022 +0000 +++ b/MS2snoop.R Fri Sep 30 16:18:56 2022 +0000 @@ -1,1236 +1,1233 @@ -#' -#' read and process mspurity W4M files -#' create a summary of fragment for each precursor and a graphics of peseudo -#' spectra + correlation on which checking of fragment is based on -#' V3 try to identify and process multiple files for 1 precursor which may -#' occur if different collision energy are used -#' V4 elimination of correlation = NA. Correlation is done with precursor, if -#' precursor is not present correlation with most intense peak -#' author: Jean-Francois Martin -#' V5 is versionned, lintR-compliant, packaged, unit-tested, documented and -#' tested against data from other labs. -#' new maintainer: Lain Pavot - lain.pavot@inrae.fr -#' -#' @import optparse -#' - - -get_version <- function() { - cmd <- commandArgs(trailingOnly = FALSE) - root <- dirname(gsub("--file=", "", cmd[grep("--file=", cmd)])) - readme <- readLines(file.path(root, "README.md")) - version_line <- readme[grepl(" * **@version**: ", readme, fixed = TRUE)] - return(gsub(".*: ", "", version_line)) -} - -defaults <- list( - MS2SNOOP_VERSION = get_version(), - MISSING_PARAMETER_ERROR = 1, - BAD_PARAMETER_VALUE_ERROR = 2, - MISSING_INPUT_FILE_ERROR = 3, - NO_ANY_RESULT_ERROR = 255, - DEFAULT_PRECURSOR_PATH = NULL, - DEFAULT_FRAGMENTS_PATH = NULL, - DEFAULT_COMPOUNDS_PATH = NULL, - DEFAULT_OUTPUT_PATH = "compound_fragments_result.txt", - DEFAULT_TOLMZ = 0.01, - DEFAULT_TOLRT = 20, - DEFAULT_MZDECIMAL = 3, - DEFAULT_R_THRESHOLD = 0.85, - DEFAULT_MINNUMBERSCAN = 8, - DEFAULT_SEUIL_RA = 0.05, - DEFAULT_FRAGMENTS_MATCH_DELTA = 10, - DEFAULT_FRAGMENTS_MATCH_DELTA_UNIT = "ppm", - DEFAULT_PDF_PATH = "" -) -env <- globalenv() -for (default in names(defaults)) { - assign(default, defaults[[default]], envir = env) - lockBinding(default, env) -} - -######################################################################## - -get_formulas <- function( - mzref, - spectra, - nominal_mz_list, - processing_parameters, - background = !TRUE -) { - if (is.vector(mzref) && length(mzref) > 1) { - return(lapply( - mzref, - function(mz) { - return(get_formulas( - mzref = mz, - spectra = spectra, - nominal_mz_list = nominal_mz_list, - processing_parameters = processing_parameters, - background = background - )) - } - )) - } - input <- sprintf( - "%s-%s.ms", - gsub("[[:space:]]", "_", processing_parameters$c_name), - mzref - ) - create_ms_file(input, mzref, spectra, processing_parameters) - output <- sprintf( - "out/%s-%s.out", - gsub("[[:space:]]", "_", processing_parameters$c_name), - mzref - ) - command <- sprintf( - paste( - "sirius", - "--noCite", - "--noSummaries", - "--loglevel=WARNING", - "-i='%s'", - "-o='%s'", - "tree", - ## loglevel is not working taken into account during - ## sirius startup, so we filter outputs... - "2>&1 | grep '^(WARNING|SEVERE)'" - ), - input, - output - ) - verbose_catf( - ">> Sirius is running %swith the command: %s\n", - if (background) "in the background " else "", - command - ) - system( - command, - wait = !background, - ignore.stdout = background, - ignore.stderr = background - ) - return(extract_sirius_results(output, spectra$mz, processing_parameters)) -} - -create_ms_file <- function( - path, - mzref, - spectra, - processing_parameters -) { - file_content <- paste( - sprintf(">compound %s", processing_parameters$c_name), - sprintf(">ionization %s", processing_parameters$ionization), - sprintf(">parentmass %s", mzref), - sprintf(">formula %s", processing_parameters$elemcomposition), - sep = "\n" - ) - displayed_file_content <- sprintf( - "%s\n>collision\n%s", - file_content, - paste( - sprintf( - "%s %s", - spectra[1:3, "mz"], - spectra[1:3, "intensities"] - ), - collapse = "\n" - ) - ) - if (nrow(spectra) > 3) { - displayed_file_content <- sprintf( - "%s\n[... %s more rows of mz and intensities ...]", - displayed_file_content, - nrow(spectra) - 3 - ) - } - catf( - ">> MS file created for %s with content:\n%s\n", - processing_parameters$c_name, - displayed_file_content - ) - file_content <- sprintf( - "%s\n\n>collision\n%s", - file_content, - paste( - sprintf("%s %s", spectra$mz, spectra$intensities), - collapse = "\n" - ) - ) - cat(file_content, file = path, append = FALSE) -} - -extract_sirius_results <- function( - output, - mz_list, - processing_parameters -) { - - delta <- processing_parameters$fragment_match_delta - delta_unit <- tolower(processing_parameters$fragment_match_delta_unit) - - output <- list.dirs(output, recursive = FALSE)[[1]] - - spectra_out_dir <- sprintf("%s/spectra", output) - spectra_filename <- sprintf( - "%s/%s", - spectra_out_dir, - list.files(spectra_out_dir)[[1]] - ) - - trees_out_dir <- sprintf("%s/trees", output) - trees_filename <- sprintf( - "%s/%s", - trees_out_dir, - list.files(trees_out_dir)[[1]] - ) - - if (!is.null(spectra_filename)) { - sirius_results <- get_csv_or_tsv(spectra_filename) - } else { - return(rep(NA, length(mz_list))) - } - if (!is.null(trees_filename)) { - sirius_results <- cbind(sirius_results, extract_sirius_ppm(trees_filename)) - } else { - return(rep(NA, length(mz_list))) - } - - fragment_matchings <- data.frame( - formula = NA, - ppm = NA, - mz = mz_list, - error = NA - ) - - sirius_results <- filter_sirius_with_delta( - sirius_results = sirius_results, - original_mz = fragment_matchings$mz, - delta = delta, - delta_unit = delta_unit - ) - - for (index in seq_len(nrow(sirius_results))) { - result <- sirius_results[index, ] - filter <- which(order(abs(fragment_matchings$mz - result$mz)) == 1) - fragment_matchings[filter, "formula"] <- result$formula - fragment_matchings[filter, "ppm"] <- result$ppm - catf( - "[OK] Fragment with m/z=%s matches %s with a difference of %s ppm\n", - fragment_matchings[filter, "mz"], result$formula, result$ppm - ) - } - return(fragment_matchings) -} - -filter_sirius_with_delta <- function( - sirius_results, - original_mz, - delta, - delta_unit -) { - if (is.numeric(delta) && !is.na(delta) && delta > 0) { - if (delta_unit == "ppm") { - filter <- abs(sirius_results$ppm) <= delta - fine <- which(filter) - not_fine <- which(!filter) - catf( - paste("[KO] fragment %s (m/z=%s) eleminated because ppm=%s is greater", - "than delta=%s\n" - ), - sirius_results[not_fine, ]$formula, - sirius_results[not_fine, ]$mz, - sirius_results[not_fine, ]$ppm, - delta - ) - sirius_results <- sirius_results[fine, ] - } else if (delta_unit == "mz") { - differences <- sapply( - sirius_results$mz, - function(mz) min(abs(original_mz - mz)) - ) - fine <- which(sapply( - sirius_results$mz, - function(mz) any(abs(original_mz - mz) <= delta) - )) - not_fine <- which(sapply( - sirius_results$mz, - function(mz) all(abs(original_mz - mz) > delta) - )) - catf( - paste( - "[KO] fragment %s eleminated because mz difference=%s is", - "greater than delta=%s\n" - ), - sirius_results[not_fine, ]$formula, - differences[not_fine], - delta - ) - sirius_results <- sirius_results[fine, ] - } - } - return(sirius_results) -} - -extract_sirius_ppm <- function(path) { - json <- file(path, "r") - suppressWarnings(json_lines <- readLines(json)) - close(json) - json_lines <- json_lines[ - grepl("\\s+\"(massDeviation|recalibratedMass)\" :", json_lines) - ] - json_lines <- gsub("^\\s+\"[^\"]+\" : \"?", "", json_lines) - ppms <- json_lines[seq(1, length(json_lines), 2)] - mz <- json_lines[seq(2, length(json_lines), 2)] - ppms <- as.numeric(gsub(" ppm .*", "", ppms)) - mz <- as.numeric(gsub(",$", "", mz)) - ordered <- order(mz) - return(list(ppm = ppms[ordered], recalibrated_mz = mz[ordered])) -} - -#' @title plot_pseudo_spectra -#' @param x -#' @param fid -#' @param sum_int -#' @param vmz -#' @param cor_abs_int -#' @param refcol -#' @param c_name -#' @description plot_pseudo_spectra -#' function to compute sum of intensities among scans for all -#' m/z kept (cor > r_threshold & minimum number of scans) -#' and plot pseudo spectra -#' x dataframe scan X fragments with scans number in the 1st column and -#' ions in next with intensities -#' fid file id when several a precursor has been detected in several files -plot_pseudo_spectra <- function( - x, - fid, - sum_int, - vmz, - cor_abs_int, - refcol, - meaned_mz, - processing_parameters -) { - ## du fait de la difference de nombre de colonne entre la dataframe qui - ## inclue les scans en 1ere col, mzRef se decale de 1 - refcol <- refcol - 1 - ## compute relative intensities max=100% - rel_int <- sum_int[-1] - rel_int <- rel_int / max(rel_int) - - if (processing_parameters$do_pdf) { - ## define max value on vertical axis (need to increase in order to plot the - ## label of fragments) - ymax <- max(rel_int) + 0.2 * max(rel_int) - - par(mfrow = c(2, 1)) - plot(vmz, rel_int, type = "h", ylim = c(0, ymax), - main = processing_parameters$c_name - ) - ## low correl coef. will be display in grey - cor_low <- which(round(cor_abs_int, 2) < processing_parameters$r_threshold) - - lbmzcor <- sprintf("%s(r=%s)", vmz, round(cor_abs_int, 2)) - - if (length(cor_low) > 0) { - text( - vmz[cor_low], - rel_int[cor_low], - lbmzcor[cor_low], - cex = 0.5, - col = "grey", - srt = 90, - adj = 0 - ) - if (length(vmz) - length(cor_low) > 1) { - text( - vmz[-c(refcol, cor_low)], - rel_int[-c(refcol, cor_low)], - lbmzcor[-c(refcol, cor_low)], - cex = 0.6, - col = 1, - srt = 90, - adj = 0 - ) - } - } else { - if (length(vmz) > 1) { - text( - vmz[-c(refcol)], - rel_int[-c(refcol)], - lbmzcor[-c(refcol)], - cex = 0.6, - col = 1, - srt = 90, - adj = 0 - ) - } - } - - text( - vmz[refcol], - rel_int[refcol], - lbmzcor[refcol], - cex = 0.8, - col = 2, - srt = 90, - adj = 0 - ) - } - - ## prepare result file - cor_valid <- (round(cor_abs_int, 2) >= processing_parameters$r_threshold) - - do_sirius <- TRUE - verbose_catf("Checking sirius parameters...\n") - if (is.null(processing_parameters$ionization)) { - do_sirius <- FALSE - verbose_catf("[KO] No ionization passed in parameter.\n") - } else { - verbose_catf("[OK] Ionization=%s.\n", processing_parameters$ionization) - } - if (is.na(processing_parameters$elemcomposition)) { - do_sirius <- FALSE - verbose_catf("[KO] Elemental composition is NA.\n") - } else if (length(processing_parameters$elemcomposition) < 1) { - do_sirius <- FALSE - verbose_catf("[KO] No elemental composition is provided.\n") - } else if (processing_parameters$elemcomposition == "") { - do_sirius <- FALSE - verbose_catf("[KO] Elemental composition is an empty string.\n") - } else { - verbose_catf( - "[OK] Elemental composition=%s.\n", - processing_parameters$elemcomposition - ) - } - - cp_res_length <- length(vmz) - ppm <- rep(NA, cp_res_length) - formulas <- rep(NA, cp_res_length) - if (do_sirius) { - verbose_catf("Everything is ok, preparing for sirius.\n") - formulas <- get_formulas( - mzref = processing_parameters$mzref, - spectra = data.frame(mz = meaned_mz, intensities = sum_int[-1]), - nominal_mz_list = vmz, - processing_parameters = processing_parameters - ) - if (nrow(formulas) == 0) { - catf("No formula found.\n") - } else { - ppm <- formulas$ppm - formulas <- formulas$formula - catf( - "Found %s formula for %s fragments\n", - length(formulas[which(!(is.na(formulas)))]), - cp_res_length - ) - } - } else { - verbose_catf("Sirius cannot be run.\n") - } - cp_res <- data.frame( - rep(processing_parameters$c_name, cp_res_length), - rep(processing_parameters$inchikey, cp_res_length), - rep(processing_parameters$elemcomposition, cp_res_length), - formulas, - vmz, - ppm, - rep(fid, cp_res_length), - cor_abs_int, - sum_int[-1], - rel_int, - cor_valid - ) - - colnames(cp_res) <- c( - "compoundName", - "inchikey", - "elemcomposition", - "fragment", - "fragment_mz", - "ppm", - "fileid", - "CorWithPrecursor", - "AbsoluteIntensity", - "relativeIntensity", - "corValid" - ) - return(cp_res) -} - -#' -#' @title extract_fragments -#' -#' @param precursors the precursor list from mspurity -#' @param fragments the fragments list from ms purity -# ' @param mzref -# ' @param rtref -# ' @param c_name -# ' @param inchikey -# ' @param elemcomposition -#' @param processing_parameters -#' @returns -#' -#' @description -#' function for extraction of fragments corresponding to precursors -#' detected by MSPurity -extract_fragments <- function( ## nolint cyclocomp_linter - precursors, - fragments, - processing_parameters -) { - ## filter precursor in the precursors file based on mz and rt in the - ## compound list - catf("processing %s\n", processing_parameters$c_name) - verbose_catf("===\n") - param <- processing_parameters - selected_precursors <- which( - (abs(precursors$precurMtchMZ - param$mzref) <= param$tolmz) - & (abs(precursors$precurMtchRT - param$rtref) <= param$tolrt) - ) - rm(param) - - verbose_catf( - "> %s precursors selected with mz=%s±%s and rt=%s±%s\n", - length(selected_precursors), - processing_parameters$mzref, - processing_parameters$tolmz, - processing_parameters$rtref, - processing_parameters$tolrt - ) - - ## check if there is the precursor in the file - - if (length(selected_precursors) < 1) { - cat("> non detected in precursor file\n") - show_end_processing() - return(NULL) - } - - precursors <- precursors[selected_precursors, ] - - ## check if fragments corresponding to precursor are found in several - ## files (collision energy) - ## this lead to a processing for each fileid - file_ids <- as.character(sort(unique(precursors$fileid))) - if (length(file_ids) > 1) { - catf("> several files detected for this compounds :\n") - } else if (length(file_ids) < 1 || nrow(precursors) < 1) { - return(data.frame()) - } - - res_comp <- data.frame() - for (curent_file_id in file_ids) { - curent_precursors <- precursors[precursors$fileid == curent_file_id, ] - selected_fragments <- fragments[ - fragments$grpid %in% as.character(curent_precursors$grpid) - & fragments$fileid == curent_file_id, - ] - filtered_fragments <- selected_fragments[ - selected_fragments$ra > processing_parameters$seuil_ra, - ] - if (nrow(filtered_fragments) != 0) { - res_comp_by_file <- process_file( - curent_file_id = curent_file_id, - precursor_mz = curent_precursors$mz, - filtered_fragments = filtered_fragments, - processing_parameters = processing_parameters - ) - if (!is.null(res_comp_by_file)) { - res_comp <- rbind(res_comp, res_comp_by_file) - } - } else { - catf("No fragment found for in fragment file\n") - } - } - return(unique(res_comp)) -} - -process_file <- function( - curent_file_id, - precursor_mz, - filtered_fragments, - processing_parameters -) { - mznominal <- round(x = filtered_fragments$mz, digits = 0) - meaned_mz <- round( - aggregate( - data.frame( - mz = filtered_fragments$mz, - mznominal = mznominal - ), - list(mznominal), - FUN = mean - )$mz, - digits = processing_parameters$mzdecimal - ) - filtered_fragments <- data.frame(filtered_fragments, mznominal) - - ## creation of cross table row=scan col=mz X=ra - - vmz <- as.character(sort(unique(filtered_fragments$mznominal))) - - ds_abs_int <- create_ds_abs_int(vmz, filtered_fragments) - - if (global_debug) { - print(ds_abs_int) - } - - ## elimination of mz with less than min_number_scan scans (user defined - ## parameter) - xmz <- rep(NA, ncol(ds_abs_int) - 1) - sum_int <- rep(NA, ncol(ds_abs_int)) - nbxmz <- 0 - nb_scan_check <- min(nrow(ds_abs_int), processing_parameters$min_number_scan) - - for (j in 2:ncol(ds_abs_int)) { - sum_int[j] <- sum(ds_abs_int[j], na.rm = TRUE) - if (sum(!is.na(ds_abs_int[[j]])) < nb_scan_check) { - nbxmz <- nbxmz + 1 - xmz[nbxmz] <- j - } - } - - xmz <- xmz[-which(is.na(xmz))] - if (length(xmz) > 0) { - ds_abs_int <- ds_abs_int[, -c(xmz)] - sum_int <- sum_int[-c(xmz)] - ## liste des mz keeped decale de 1 avec ds_abs_int - vmz <- as.numeric(vmz[-c(xmz - 1)]) - meaned_mz <- meaned_mz[-c(xmz - 1)] - } - - ## mz of precursor in data precursor to check correlation with - mz_prec <- paste0( - "mz", - round(mean(precursor_mz), processing_parameters$mzdecimal) - ) - ## reference ion for correlation computing = precursor OR maximum - ## intensity ion in precursor is not present - refcol <- which(colnames(ds_abs_int) == mz_prec) - if (length(refcol) == 0) { - refcol <- which(sum_int == max(sum_int, na.rm = TRUE)) - } - - if (processing_parameters$do_pdf) { - start_pdf(processing_parameters, curent_file_id) - } - - ## Pearson correlations between absolute intensities computing - cor_abs_int <- rep(NA, length(vmz)) - - if (length(refcol) > 0) { - for (i in 2:length(ds_abs_int)) { - cor_abs_int[i - 1] <- stats::cor( - x = ds_abs_int[[refcol]], - y = ds_abs_int[[i]], - use = "pairwise.complete.obs", - method = "pearson" - ) - debug_catf( - "Correlation between %s and %s: %s\n", - paste(ds_abs_int[[refcol]], collapse = ";"), - paste(ds_abs_int[[i]], collapse = ";"), - paste(cor_abs_int[i - 1], collapse = ";") - ) - if (processing_parameters$do_pdf) { - pdf_plot_ds_abs_int( - processing_parameters$c_name, - ds_abs_int, - refcol, - i, - round(cor_abs_int[i - 1], 2) - ) - } - } - ## plot pseudo spectra - res_comp_by_file <- plot_pseudo_spectra( - x = ds_abs_int, - fid = curent_file_id, - sum_int = sum_int, - vmz = vmz, - cor_abs_int = cor_abs_int, - refcol = refcol, - meaned_mz = meaned_mz, - processing_parameters = processing_parameters - ) - catf( - "%s has been processed and %s fragments have been found.\n", - processing_parameters$c_name, - nrow(res_comp_by_file) - ) - } else { - res_comp_by_file <- NULL - cat(">> non detected in fragments file \n") - } - show_end_processing() - if (processing_parameters$do_pdf) { - end_pdf() - } - return(res_comp_by_file) -} - -create_ds_abs_int <- function(vmz, filtered_fragments) { - verbose_catf( - ">> fragments: %s\n", - paste(vmz, collapse = " ") - ) - ds_abs_int <- create_int_mz(vmz[1], filtered_fragments) - for (mz in vmz[-1]) { - int_mz <- create_int_mz(mz, filtered_fragments) - ds_abs_int <- merge( - x = ds_abs_int, - y = int_mz, - by.x = 1, - by.y = 1, - all.x = TRUE, - all.y = TRUE - ) - } - return(ds_abs_int) -} - -create_int_mz <- function(mz, filtered_fragments) { - ## absolute intensity - int_mz <- filtered_fragments[ - filtered_fragments$mznominal == mz, - c("acquisitionNum", "i") - ] - colnames(int_mz)[2] <- paste0("mz", mz) - ## average intensities of mass in duplicate scans - comp_scans <- aggregate(x = int_mz, by = list(int_mz[[1]]), FUN = mean) - return(comp_scans[, -1]) -} - -show_end_processing <- function() { - verbose_catf("==========\n") - cat("\n") -} - -start_pdf <- function(processing_parameters, curent_file_id) { - if (!dir.exists(processing_parameters$pdf_path)) { - dir.create(processing_parameters$pdf_path, recursive = TRUE) - } - pdf( - file = sprintf( - "%s/%s_processing_file%s.pdf", - processing_parameters$pdf_path, - processing_parameters$c_name, - curent_file_id - ), - width = 8, - height = 11 - ) - par(mfrow = c(3, 2)) -} - -pdf_plot_ds_abs_int <- function(c_name, ds_abs_int, refcol, i, r_coef) { - plot( - ds_abs_int[[refcol]], - ds_abs_int[[i]], - xlab = colnames(ds_abs_int)[refcol], - ylab = colnames(ds_abs_int)[i], - main = sprintf( - "%s corr coeff r=%s", c_name, r_coef - ) - ) -} -end_pdf <- function() { - dev.off() -} - -set_global <- function(var, value) { - assign(var, value, envir = globalenv()) -} - -set_debug <- function() { - set_global("global_debug", TRUE) -} - -unset_debug <- function() { - set_global("global_debug", FALSE) -} - -set_verbose <- function() { - set_global("global_verbose", TRUE) -} - -unset_verbose <- function() { - set_global("global_verbose", FALSE) -} - -verbose_catf <- function(...) { - if (global_verbose) { - cat(sprintf(...), sep = "") - } -} - - -debug_catf <- function(...) { - if (global_debug) { - cat(sprintf(...), sep = "") - } -} - -catf <- function(...) { - cat(sprintf(...), sep = "") -} - -create_parser <- function() { - parser <- optparse::OptionParser() - parser <- optparse::add_option( - parser, - c("-v", "--verbose"), - action = "store_true", - default = FALSE, - help = paste( - "[default %default]", - "Print extra output" - ) - ) - parser <- optparse::add_option( - parser, - c("-V", "--version"), - action = "store_true", - default = FALSE, - help = "Prints version and exits" - ) - parser <- optparse::add_option( - parser, - c("-d", "--debug"), - action = "store_true", - default = FALSE, - help = paste( - "[default %default]", - "Print debug outputs" - ) - ) - parser <- optparse::add_option( - parser, - c("-o", "--output"), - type = "character", - default = DEFAULT_OUTPUT_PATH, - action = "store", - help = "Path to the output file [default %default]" - ) - parser <- optparse::add_option( - parser, - c("-p", "--precursors"), - type = "character", - default = DEFAULT_PRECURSOR_PATH, - action = "store", - help = "Path to the precursors file [default %default]" - ) - parser <- optparse::add_option( - parser, - c("-f", "--fragments"), - type = "character", - default = DEFAULT_FRAGMENTS_PATH, - action = "store", - help = "Path to the fragments file [default %default]" - ) - parser <- optparse::add_option( - parser, - c("-c", "--compounds"), - type = "character", - default = DEFAULT_COMPOUNDS_PATH, - action = "store", - help = "Path to the compounds file [default %default]" - ) - parser <- optparse::add_option( - parser, - c("--tolmz"), - type = "numeric", - action = "store", - default = DEFAULT_TOLMZ, - metavar = "number", - help = paste( - "[default %default]", - "Tolerance for MZ (in Dalton) to match the standard in the compounds" - ) - ) - parser <- optparse::add_option( - parser, - c("--tolrt"), - type = "integer", - action = "store", - default = DEFAULT_TOLRT, - metavar = "number", - help = paste( - "[default %default]", - "RT (in seconds) to match the standard in the compounds" - ) - ) - parser <- optparse::add_option( - parser, - c("--seuil_ra"), - type = "numeric", - action = "store", - default = DEFAULT_SEUIL_RA, - metavar = "number", - help = paste( - "[default %default]", - "relative intensity threshold" - ), - ) - parser <- optparse::add_option( - parser, - c("--mzdecimal"), - type = "integer", - default = DEFAULT_MZDECIMAL, - action = "store", - help = paste( - "[default %default]", - "Number of decimal to write for MZ" - ), - metavar = "number" - ) - parser <- optparse::add_option( - parser, - c("--r_threshold"), - type = "integer", - default = DEFAULT_R_THRESHOLD, - action = "store", - help = paste( - "[default %default]", - "R-Pearson correlation threshold between precursor and fragment", - "absolute intensity" - ), - metavar = "number" - ) - parser <- optparse::add_option( - parser, - c("--min_number_scan"), - type = "numeric", - action = "store", - default = DEFAULT_MINNUMBERSCAN, - help = paste( - "[default %default]", - "Fragments are kept if there are found in a minimum number", - "of min_number_scan scans" - ), - metavar = "number" - ) - parser <- optparse::add_option( - parser, - c("--pdf_path"), - type = "character", - default = DEFAULT_PDF_PATH, - help = paste( - "[default %default]", - "PDF files output path" - ) - ) - parser <- optparse::add_option( - parser, - c("--ionization"), - type = "character", - action = "store", - default = "None", - help = paste( - "[default %default]", - "Which ionization to use for sirius" - ), - metavar = "character" - ) - parser <- optparse::add_option( - parser, - c("--fragment_match_delta"), - type = "numeric", - action = "store", - default = DEFAULT_FRAGMENTS_MATCH_DELTA, - help = paste( - "[default %default]", - "Fragment match delta" - ), - metavar = "numeric" - ) - parser <- optparse::add_option( - parser, - c("--fragment_match_delta_unit"), - type = "character", - action = "store", - default = DEFAULT_FRAGMENTS_MATCH_DELTA_UNIT, - help = paste( - "[default %default]", - "Fragment match delta" - ), - metavar = "character" - ) - return(parser) -} - -stop_with_status <- function(msg, status) { - sink(stderr()) - message(sprintf("Error: %s", msg)) - message(sprintf("Error code: %s", status)) - sink(NULL) - base::quit(status = status) -} - -check_args_validity <- function(args) { ## nolint cyclocomp_linter - if (length(args$output) == 0 || nchar(args$output[1]) == 0) { - stop_with_status( - "Missing output parameters. Please set it with --output.", - MISSING_PARAMETER_ERROR - ) - } - if (length(args$precursors) == 0 || nchar(args$precursors[1]) == 0) { - stop_with_status( - "Missing precursors parameters. Please set it with --precursors.", - MISSING_PARAMETER_ERROR - ) - } - if (length(args$fragments) == 0 || nchar(args$fragments[1]) == 0) { - stop_with_status( - "Missing fragments parameters. Please set it with --fragments.", - MISSING_PARAMETER_ERROR - ) - } - if (length(args$compounds) == 0 || nchar(args$compounds[1]) == 0) { - stop_with_status( - "Missing compounds parameters. Please set it with --compounds.", - MISSING_PARAMETER_ERROR - ) - } - if (!file.exists(args$precursors)) { - stop_with_status( - sprintf( - "Precursors file %s does not exist or cannot be accessed.", - args$precursors - ), - MISSING_INPUT_FILE_ERROR - ) - } - if (!file.exists(args$fragments)) { - stop_with_status( - sprintf( - "Fragments file %s does not exist or cannot be accessed.", - args$fragments - ), - MISSING_INPUT_FILE_ERROR - ) - } - if (!file.exists(args$compounds)) { - stop_with_status( - sprintf( - "Compounds file %s does not exist or cannot be accessed.", - args$compounds - ), - MISSING_INPUT_FILE_ERROR - ) - } - if (in_galaxy_env()) { - check_galaxy_args_validity(args) - } -} - -in_galaxy_env <- function() { - sysvars <- Sys.getenv() - sysvarnames <- names(sysvars) - return( - "_GALAXY_JOB_HOME_DIR" %in% sysvarnames - || "_GALAXY_JOB_TMP_DIR" %in% sysvarnames - || "GALAXY_MEMORY_MB" %in% sysvarnames - || "GALAXY_MEMORY_MB_PER_SLOT" %in% sysvarnames - || "GALAXY_SLOTS" %in% sysvarnames - ) -} - -check_galaxy_args_validity <- function(args) { - if (!file.exists(args$output)) { - stop_with_status( - sprintf( - "Output file %s does not exist or cannot be accessed.", - args$output - ), - MISSING_INPUT_FILE_ERROR - ) - } -} - -get_csv_or_tsv <- function( - path, - sep_stack = c("\t", ",", ";"), - sep_names = c("tab", "comma", "semicolon"), - header = TRUE, - quote = "\"" -) { - sep <- determine_csv_or_tsv_sep( - path = path, - sep_stack = sep_stack, - header = header, - quote = quote - ) - verbose_catf( - "%s separator has been determined for %s.\n", - sep_names[sep_stack == sep], - path - ) - return(read.table( - file = path, - sep = sep, - header = header, - quote = quote - )) -} - -determine_csv_or_tsv_sep <- function( - path, - sep_stack = c("\t", ",", ";"), - header = TRUE, - quote = "\"" -) { - count <- -1 - best_sep <- sep_stack[1] - for (sep in sep_stack) { - tryCatch({ - table <- read.table( - file = path, - sep = sep, - header = header, - quote = quote, - nrows = 1 - ) - if (ncol(table) > count) { - count <- ncol(table) - best_sep <- sep - } - }) - } - return(best_sep) -} - -uniformize_columns <- function(df) { - cols <- colnames(df) - for (func in c(tolower)) { - cols <- func(cols) - } - colnames(df) <- cols - return(df) -} - -handle_galaxy_param <- function(args) { - for (param in names(args)) { - if (is.character(args[[param]])) { - args[[param]] <- gsub("__ob__", "[", args[[param]]) - args[[param]] <- gsub("__cb__", "]", args[[param]]) - } - } - return(args) -} - -zip_pdfs <- function(processing_parameters) { - if (processing_parameters$do_pdf) { - if (zip <- Sys.getenv("R_ZIPCMD", "zip") == "") { - catf("R could not fin the zip executable. Trying luck: zip = \"zip\"") - zip <- "zip" - } else { - catf("Found zip executable at %s .", zip) - } - utils::zip( - processing_parameters$pdf_zip_path, - processing_parameters$pdf_path, - zip = zip - ) - } -} - -main <- function(args) { - if (args$version) { - catf("%s\n", MS2SNOOP_VERSION) - base::quit(status = 0) - } - if (in_galaxy_env()) { - print(sessionInfo()) - cat("\n\n") - } - check_args_validity(args) - args <- handle_galaxy_param(args) - if (args$ionization == "None") { - args$ionization <- NULL - } - if (args$debug) { - set_debug() - } - if (args$verbose) { - set_verbose() - } - precursors <- get_csv_or_tsv(args$precursors) - fragments <- get_csv_or_tsv(args$fragments) - compounds <- get_csv_or_tsv(args$compounds) - - compounds <- uniformize_columns(compounds) - mandatory_columns <- c( - "compound_name", - "mz", - "rtsec", - "inchikey" - ) - presents <- mandatory_columns %in% colnames(compounds) - if (!all(presents)) { - stop_with_status( - sprintf( - "Some columns are missing: %s", - paste(mandatory_columns[which(!presents)], collapse = ", ") - ), - BAD_PARAMETER_VALUE_ERROR - ) - } - - res_all <- data.frame() - processing_parameters <- list( - min_number_scan = args$min_number_scan, - mzdecimal = args$mzdecimal, - r_threshold = args$r_threshold, - seuil_ra = args$seuil_ra, - tolmz = args$tolmz, - tolrt = args$tolrt, - ionization = args$ionization, - do_pdf = nchar(args$pdf_path) > 0, - pdf_zip_path = args$pdf_path, - pdf_path = tempdir(), - fragment_match_delta = args$fragment_match_delta, - fragment_match_delta_unit = args$fragment_match_delta_unit - ) - for (i in seq_len(nrow(compounds))) { - processing_parameters$mzref <- compounds[["mz"]][i] - processing_parameters$rtref <- compounds[["rtsec"]][i] - processing_parameters$c_name <- compounds[["compound_name"]][i] - processing_parameters$inchikey <- compounds[["inchikey"]][i] - processing_parameters$elemcomposition <- compounds[["elemcomposition"]][i] - res_cor <- extract_fragments( - precursors = precursors, - fragments = fragments, - processing_parameters = processing_parameters - ) - if (!is.null(res_cor)) { - res_all <- rbind(res_all, res_cor) - } - } - - if (nrow(res_all) == 0) { - stop_with_status("No result at all!", NO_ANY_RESULT_ERROR) - } - - write.table( - x = res_all, - file = args$output, - sep = "\t", - row.names = FALSE - ) - zip_pdfs(processing_parameters) - unlink(processing_parameters$pdf_path, recursive = TRUE) -} - -global_debug <- FALSE -global_verbose <- FALSE -args <- optparse::parse_args(create_parser()) -main(args) - -warnings() +#' read and process mspurity W4M files +#' create a summary of fragment for each precursor and a graphics of peseudo +#' spectra + correlation on which checking of fragment is based on +#' V3 try to identify and process multiple files for 1 precursor which may +#' occur if different collision energy are used +#' V4 elimination of correlation = NA. Correlation is done with precursor, if +#' precursor is not present correlation with most intense peak +#' author: Jean-Francois Martin +#' V5 is versionned, lintR-compliant, packaged, unit-tested, documented and +#' tested against data from other labs. +#' new maintainer: Lain Pavot - lain.pavot@inrae.fr +#' +#' @import optparse +#' + + +get_version <- function() { + cmd <- commandArgs(trailingOnly = FALSE) + root <- dirname(gsub("--file=", "", cmd[grep("--file=", cmd)])) + readme <- readLines(file.path(root, "README.md")) + version_line <- readme[grepl(" * **@version**: ", readme, fixed = TRUE)] + return(gsub(".*: ", "", version_line)) +} + +defaults <- list( + MS2SNOOP_VERSION = get_version(), + MISSING_PARAMETER_ERROR = 1, + BAD_PARAMETER_VALUE_ERROR = 2, + MISSING_INPUT_FILE_ERROR = 3, + NO_ANY_RESULT_ERROR = 255, + DEFAULT_PRECURSOR_PATH = NULL, + DEFAULT_FRAGMENTS_PATH = NULL, + DEFAULT_COMPOUNDS_PATH = NULL, + DEFAULT_OUTPUT_PATH = "compound_fragments_result.txt", + DEFAULT_TOLMZ = 0.01, + DEFAULT_TOLRT = 20, + DEFAULT_MZDECIMAL = 3, + DEFAULT_R_THRESHOLD = 0.85, + DEFAULT_MINNUMBERSCAN = 8, + DEFAULT_SEUIL_RA = 0.05, + DEFAULT_FRAGMENTS_MATCH_DELTA = 10, + DEFAULT_FRAGMENTS_MATCH_DELTA_UNIT = "ppm", + DEFAULT_PDF_PATH = "" +) +env <- globalenv() +for (default in names(defaults)) { + assign(default, defaults[[default]], envir = env) + lockBinding(default, env) +} + +######################################################################## + +get_formulas <- function( + mzref, + spectra, + processing_parameters, + background = !TRUE +) { + if (is.vector(mzref) && length(mzref) > 1) { + return(lapply( + mzref, + function(mz) { + return(get_formulas( + mzref = mz, + spectra = spectra, + processing_parameters = processing_parameters, + background = background + )) + } + )) + } + input <- sprintf( + "%s-%s.ms", + gsub("[[:space:]]", "_", processing_parameters$c_name), + mzref + ) + create_ms_file(input, mzref, spectra, processing_parameters) + output <- sprintf( + "out/%s-%s.out", + gsub("[[:space:]]", "_", processing_parameters$c_name), + mzref + ) + command <- sprintf( + paste( + "sirius", + "--noCite", + "--noSummaries", + "--loglevel=WARNING", + "-i='%s'", + "-o='%s'", + "tree", + ## loglevel is not working taken into account during + ## sirius startup, so we filter outputs... + "2>&1 | grep '^(WARNING|SEVERE)'" + ), + input, + output + ) + verbose_catf( + ">> Sirius is running %swith the command: %s\n", + if (background) "in the background " else "", + command + ) + system( + command, + wait = !background, + ignore.stdout = background, + ignore.stderr = background + ) + return(extract_sirius_results(output, spectra$mz, processing_parameters)) +} + +create_ms_file <- function( + path, + mzref, + spectra, + processing_parameters +) { + file_content <- paste( + sprintf(">compound %s", processing_parameters$c_name), + sprintf(">ionization %s", processing_parameters$ionization), + sprintf(">parentmass %s", mzref), + sprintf(">formula %s", processing_parameters$elemcomposition), + sep = "\n" + ) + displayed_file_content <- sprintf( + "%s\n>collision\n%s", + file_content, + paste( + sprintf( + "%s %s", + spectra[1:3, "mz"], + spectra[1:3, "intensities"] + ), + collapse = "\n" + ) + ) + if (nrow(spectra) > 3) { + displayed_file_content <- sprintf( + "%s\n[... %s more rows of mz and intensities ...]", + displayed_file_content, + nrow(spectra) - 3 + ) + } + catf( + ">> MS file created for %s with content:\n%s\n", + processing_parameters$c_name, + displayed_file_content + ) + file_content <- sprintf( + "%s\n\n>collision\n%s", + file_content, + paste( + paste(spectra$mz, spectra$intensities), + collapse = "\n" + ) + ) + cat(file_content, file = path, append = FALSE) +} + +extract_sirius_results <- function( + output, + mz_list, + processing_parameters +) { + + delta <- processing_parameters$fragment_match_delta + delta_unit <- tolower(processing_parameters$fragment_match_delta_unit) + + output <- list.dirs(output, recursive = FALSE)[[1]] + + spectra_out_dir <- sprintf("%s/spectra", output) + spectra_filename <- sprintf( + "%s/%s", + spectra_out_dir, + list.files(spectra_out_dir)[[1]] + ) + + trees_out_dir <- sprintf("%s/trees", output) + trees_filename <- sprintf( + "%s/%s", + trees_out_dir, + list.files(trees_out_dir)[[1]] + ) + + if (!is.null(spectra_filename)) { + sirius_results <- get_csv_or_tsv(spectra_filename) + } else { + return(rep(NA, length(mz_list))) + } + if (!is.null(trees_filename)) { + sirius_results <- cbind(sirius_results, extract_sirius_ppm(trees_filename)) + } else { + return(rep(NA, length(mz_list))) + } + + fragment_matchings <- data.frame( + formula = NA, + ppm = NA, + mz = mz_list, + error = NA + ) + + sirius_results <- filter_sirius_with_delta( + sirius_results = sirius_results, + original_mz = fragment_matchings$mz, + delta = delta, + delta_unit = delta_unit + ) + + for (index in seq_len(nrow(sirius_results))) { + result <- sirius_results[index, ] + filter <- which(order(abs(fragment_matchings$mz - result$mz)) == 1) + fragment_matchings[filter, "formula"] <- result$formula + fragment_matchings[filter, "ppm"] <- result$ppm + catf( + "[OK] Fragment with m/z=%s matches %s with a difference of %s ppm\n", + fragment_matchings[filter, "mz"], result$formula, result$ppm + ) + } + return(fragment_matchings) +} + +filter_sirius_with_delta <- function( + sirius_results, + original_mz, + delta, + delta_unit +) { + if (is.numeric(delta) && !is.na(delta) && delta > 0) { + if (delta_unit == "ppm") { + filter <- abs(sirius_results$ppm) <= delta + fine <- which(filter) + not_fine <- which(!filter) + catf( + paste( + "[KO] fragment %s (m/z=%s) eleminated because ppm=%s is greater", + "than delta=%s\n" + ), + sirius_results[not_fine, ]$formula, + sirius_results[not_fine, ]$mz, + sirius_results[not_fine, ]$ppm, + delta + ) + sirius_results <- sirius_results[fine, ] + } else if (delta_unit == "mz") { + differences <- sapply( + sirius_results$mz, + function(mz) min(abs(original_mz - mz)) + ) + fine <- which(sapply( + sirius_results$mz, + function(mz) any(abs(original_mz - mz) <= delta) + )) + not_fine <- which(sapply( + sirius_results$mz, + function(mz) all(abs(original_mz - mz) > delta) + )) + catf( + paste( + "[KO] fragment %s eleminated because mz difference=%s is", + "greater than delta=%s\n" + ), + sirius_results[not_fine, ]$formula, + differences[not_fine], + delta + ) + sirius_results <- sirius_results[fine, ] + } + } + return(sirius_results) +} + +extract_sirius_ppm <- function(path) { + json <- file(path, "r") + suppressWarnings(json_lines <- readLines(json)) + close(json) + json_lines <- json_lines[ + grepl("\\s+\"(massDeviation|recalibratedMass)\" :", json_lines) + ] + json_lines <- gsub("^\\s+\"[^\"]+\" : \"?", "", json_lines) + ppms <- json_lines[seq(1, length(json_lines), 2)] + mz <- json_lines[seq(2, length(json_lines), 2)] + ppms <- as.numeric(gsub(" ppm .*", "", ppms)) + mz <- as.numeric(gsub(",$", "", mz)) + ordered <- order(mz) + return(list(ppm = ppms[ordered], recalibrated_mz = mz[ordered])) +} + +#' @title plot_pseudo_spectra +#' @param x +#' @param fid +#' @param sum_int +#' @param vmz +#' @param cor_abs_int +#' @param refcol +#' @param c_name +#' @description plot_pseudo_spectra +#' function to compute sum of intensities among scans for all +#' m/z kept (cor > r_threshold & minimum number of scans) +#' and plot pseudo spectra +#' x dataframe scan X fragments with scans number in the 1st column and +#' ions in next with intensities +#' fid file id when several a precursor has been detected in several files +plot_pseudo_spectra <- function( + x, + fid, + sum_int, + vmz, + cor_abs_int, + refcol, + meaned_mz, + processing_parameters +) { + ## du fait de la difference de nombre de colonne entre la dataframe qui + ## inclue les scans en 1ere col, mzRef se decale de 1 + refcol <- refcol - 1 + ## compute relative intensities max=100% + rel_int <- sum_int[-1] + rel_int <- rel_int / max(rel_int) + + if (processing_parameters$do_pdf) { + ## define max value on vertical axis (need to increase in order to plot the + ## label of fragments) + ymax <- max(rel_int) + 0.2 * max(rel_int) + + par(mfrow = c(2, 1)) + plot(vmz, rel_int, type = "h", ylim = c(0, ymax), + main = processing_parameters$c_name + ) + ## low correl coef. will be display in grey + cor_low <- which(round(cor_abs_int, 2) < processing_parameters$r_threshold) + + lbmzcor <- sprintf("%s(r=%s)", vmz, round(cor_abs_int, 2)) + + if (length(cor_low) > 0) { + text( + vmz[cor_low], + rel_int[cor_low], + lbmzcor[cor_low], + cex = 0.5, + col = "grey", + srt = 90, + adj = 0 + ) + if (length(vmz) - length(cor_low) > 1) { + text( + vmz[-c(refcol, cor_low)], + rel_int[-c(refcol, cor_low)], + lbmzcor[-c(refcol, cor_low)], + cex = 0.6, + col = 1, + srt = 90, + adj = 0 + ) + } + } else { + if (length(vmz) > 1) { + text( + vmz[-c(refcol)], + rel_int[-c(refcol)], + lbmzcor[-c(refcol)], + cex = 0.6, + col = 1, + srt = 90, + adj = 0 + ) + } + } + + text( + vmz[refcol], + rel_int[refcol], + lbmzcor[refcol], + cex = 0.8, + col = 2, + srt = 90, + adj = 0 + ) + } + + ## prepare result file + cor_valid <- (round(cor_abs_int, 2) >= processing_parameters$r_threshold) + + do_sirius <- TRUE + verbose_catf("Checking sirius parameters...\n") + if (is.null(processing_parameters$ionization)) { + do_sirius <- FALSE + verbose_catf("[KO] No ionization passed in parameter.\n") + } else { + verbose_catf("[OK] Ionization=%s.\n", processing_parameters$ionization) + } + if (is.na(processing_parameters$elemcomposition)) { + do_sirius <- FALSE + verbose_catf("[KO] Elemental composition is NA.\n") + } else if (length(processing_parameters$elemcomposition) < 1) { + do_sirius <- FALSE + verbose_catf("[KO] No elemental composition is provided.\n") + } else if (processing_parameters$elemcomposition == "") { + do_sirius <- FALSE + verbose_catf("[KO] Elemental composition is an empty string.\n") + } else { + verbose_catf( + "[OK] Elemental composition=%s.\n", + processing_parameters$elemcomposition + ) + } + + cp_res_length <- length(vmz) + ppm <- rep(NA, cp_res_length) + formulas <- rep(NA, cp_res_length) + if (do_sirius) { + verbose_catf("Everything is ok, preparing for sirius.\n") + formulas <- get_formulas( + mzref = processing_parameters$mzref, + spectra = data.frame(mz = meaned_mz, intensities = sum_int[-1]), + processing_parameters = processing_parameters + ) + if (nrow(formulas) == 0) { + catf("No formula found.\n") + } else { + ppm <- formulas$ppm + formulas <- formulas$formula + catf( + "Found %s formula for %s fragments\n", + length(formulas[which(!(is.na(formulas)))]), + cp_res_length + ) + } + } else { + verbose_catf("Sirius cannot be run.\n") + } + cp_res <- data.frame( + rep(processing_parameters$c_name, cp_res_length), + rep(processing_parameters$inchikey, cp_res_length), + rep(processing_parameters$elemcomposition, cp_res_length), + formulas, + meaned_mz, + ppm, + rep(fid, cp_res_length), + cor_abs_int, + sum_int[-1], + rel_int, + cor_valid + ) + + colnames(cp_res) <- c( + "compoundName", + "inchikey", + "elemcomposition", + "fragment", + "fragment_mz", + "ppm", + "fileid", + "CorWithPrecursor", + "AbsoluteIntensity", + "relativeIntensity", + "corValid" + ) + return(cp_res) +} + +#' +#' @title extract_fragments +#' +#' @param precursors the precursor list from mspurity +#' @param fragments the fragments list from ms purity +# ' @param mzref +# ' @param rtref +# ' @param c_name +# ' @param inchikey +# ' @param elemcomposition +#' @param processing_parameters +#' @returns +#' +#' @description +#' function for extraction of fragments corresponding to precursors +#' detected by MSPurity +extract_fragments <- function( ## nolint cyclocomp_linter + precursors, + fragments, + processing_parameters +) { + ## filter precursor in the precursors file based on mz and rt in the + ## compound list + catf("processing %s\n", processing_parameters$c_name) + verbose_catf("===\n") + param <- processing_parameters + selected_precursors <- which( + (abs(precursors$precurMtchMZ - param$mzref) <= param$tolmz) + & (abs(precursors$precurMtchRT - param$rtref) <= param$tolrt) + ) + rm(param) + + verbose_catf( + "> %s precursors selected with mz=%s±%s and rt=%s±%s\n", + length(selected_precursors), + processing_parameters$mzref, + processing_parameters$tolmz, + processing_parameters$rtref, + processing_parameters$tolrt + ) + + ## check if there is the precursor in the file + + if (length(selected_precursors) < 1) { + cat("> non detected in precursor file\n") + show_end_processing() + return(NULL) + } + + precursors <- precursors[selected_precursors, ] + + ## check if fragments corresponding to precursor are found in several + ## files (collision energy) + ## this lead to a processing for each fileid + file_ids <- as.character(sort(unique(precursors$fileid))) + if (length(file_ids) > 1) { + catf("> several files detected for this compounds :\n") + } else if (length(file_ids) < 1 || nrow(precursors) < 1) { + return(data.frame()) + } + + res_comp <- data.frame() + for (curent_file_id in file_ids) { + curent_precursors <- precursors[precursors$fileid == curent_file_id, ] + selected_fragments <- fragments[ + fragments$grpid %in% as.character(curent_precursors$grpid) + & fragments$fileid == curent_file_id, + ] + filtered_fragments <- selected_fragments[ + selected_fragments$ra > processing_parameters$seuil_ra, + ] + if (nrow(filtered_fragments) != 0) { + res_comp_by_file <- process_file( + curent_file_id = curent_file_id, + precursor_mz = curent_precursors$mz, + filtered_fragments = filtered_fragments, + processing_parameters = processing_parameters + ) + if (!is.null(res_comp_by_file)) { + res_comp <- rbind(res_comp, res_comp_by_file) + } + } else { + catf("No fragment found for in fragment file\n") + } + } + return(unique(res_comp)) +} + +process_file <- function( + curent_file_id, + precursor_mz, + filtered_fragments, + processing_parameters +) { + mznominal <- round(x = filtered_fragments$mz, digits = 0) + meaned_mz <- round( + aggregate( + data.frame( + mz = filtered_fragments$mz, + mznominal = mznominal + ), + list(mznominal), + FUN = mean + )$mz, + digits = processing_parameters$mzdecimal + ) + filtered_fragments <- data.frame(filtered_fragments, mznominal) + + ## creation of cross table row=scan col=mz X=ra + + vmz <- as.character(sort(unique(filtered_fragments$mznominal))) + + ds_abs_int <- create_ds_abs_int(vmz, filtered_fragments) + + if (global_debug) { + print(ds_abs_int) + } + + ## elimination of mz with less than min_number_scan scans (user defined + ## parameter) + xmz <- rep(NA, ncol(ds_abs_int) - 1) + sum_int <- rep(NA, ncol(ds_abs_int)) + nbxmz <- 0 + nb_scan_check <- min(nrow(ds_abs_int), processing_parameters$min_number_scan) + + for (j in 2:ncol(ds_abs_int)) { + sum_int[j] <- sum(ds_abs_int[j], na.rm = TRUE) + if (sum(!is.na(ds_abs_int[[j]])) < nb_scan_check) { + nbxmz <- nbxmz + 1 + xmz[nbxmz] <- j + } + } + + xmz <- xmz[-which(is.na(xmz))] + if (length(xmz) > 0) { + ds_abs_int <- ds_abs_int[, -c(xmz)] + sum_int <- sum_int[-c(xmz)] + ## liste des mz keeped decale de 1 avec ds_abs_int + vmz <- as.numeric(vmz[-c(xmz - 1)]) + meaned_mz <- meaned_mz[-c(xmz - 1)] + } + + ## mz of precursor in data precursor to check correlation with + mz_prec <- paste0( + "mz", + round(mean(precursor_mz), processing_parameters$mzdecimal) + ) + ## reference ion for correlation computing = precursor OR maximum + ## intensity ion in precursor is not present + refcol <- which(colnames(ds_abs_int) == mz_prec) + if (length(refcol) == 0) { + refcol <- which(sum_int == max(sum_int, na.rm = TRUE)) + } + + if (processing_parameters$do_pdf) { + start_pdf(processing_parameters, curent_file_id) + } + + ## Pearson correlations between absolute intensities computing + cor_abs_int <- rep(NA, length(vmz)) + + if (length(refcol) > 0) { + for (i in 2:length(ds_abs_int)) { + cor_abs_int[i - 1] <- stats::cor( + x = ds_abs_int[[refcol]], + y = ds_abs_int[[i]], + use = "pairwise.complete.obs", + method = "pearson" + ) + debug_catf( + "Correlation between %s and %s: %s\n", + paste(ds_abs_int[[refcol]], collapse = ";"), + paste(ds_abs_int[[i]], collapse = ";"), + paste(cor_abs_int[i - 1], collapse = ";") + ) + if (processing_parameters$do_pdf) { + pdf_plot_ds_abs_int( + processing_parameters$c_name, + ds_abs_int, + refcol, + i, + round(cor_abs_int[i - 1], 2) + ) + } + } + ## plot pseudo spectra + res_comp_by_file <- plot_pseudo_spectra( + x = ds_abs_int, + fid = curent_file_id, + sum_int = sum_int, + vmz = vmz, + cor_abs_int = cor_abs_int, + refcol = refcol, + meaned_mz = meaned_mz, + processing_parameters = processing_parameters + ) + catf( + "%s has been processed and %s fragments have been found.\n", + processing_parameters$c_name, + nrow(res_comp_by_file) + ) + } else { + res_comp_by_file <- NULL + cat(">> non detected in fragments file \n") + } + show_end_processing() + if (processing_parameters$do_pdf) { + end_pdf() + } + return(res_comp_by_file) +} + +create_ds_abs_int <- function(vmz, filtered_fragments) { + verbose_catf( + ">> fragments: %s\n", + paste(vmz, collapse = " ") + ) + ds_abs_int <- create_int_mz(vmz[1], filtered_fragments) + for (mz in vmz[-1]) { + int_mz <- create_int_mz(mz, filtered_fragments) + ds_abs_int <- merge( + x = ds_abs_int, + y = int_mz, + by.x = 1, + by.y = 1, + all.x = TRUE, + all.y = TRUE + ) + } + return(ds_abs_int) +} + +create_int_mz <- function(mz, filtered_fragments) { + ## absolute intensity + int_mz <- filtered_fragments[ + filtered_fragments$mznominal == mz, + c("acquisitionNum", "i") + ] + colnames(int_mz)[2] <- paste0("mz", mz) + ## average intensities of mass in duplicate scans + comp_scans <- aggregate(x = int_mz, by = list(int_mz[[1]]), FUN = mean) + return(comp_scans[, -1]) +} + +show_end_processing <- function() { + verbose_catf("==========\n") + cat("\n") +} + +start_pdf <- function(processing_parameters, curent_file_id) { + if (!dir.exists(processing_parameters$pdf_path)) { + dir.create(processing_parameters$pdf_path, recursive = TRUE) + } + pdf( + file = sprintf( + "%s/%s_processing_file%s.pdf", + processing_parameters$pdf_path, + processing_parameters$c_name, + curent_file_id + ), + width = 8, + height = 11 + ) + par(mfrow = c(3, 2)) +} + +pdf_plot_ds_abs_int <- function(c_name, ds_abs_int, refcol, i, r_coef) { + plot( + ds_abs_int[[refcol]], + ds_abs_int[[i]], + xlab = colnames(ds_abs_int)[refcol], + ylab = colnames(ds_abs_int)[i], + main = sprintf( + "%s corr coeff r=%s", c_name, r_coef + ) + ) +} +end_pdf <- function() { + dev.off() +} + +set_global <- function(var, value) { + assign(var, value, envir = globalenv()) +} + +set_debug <- function() { + set_global("global_debug", TRUE) +} + +unset_debug <- function() { + set_global("global_debug", FALSE) +} + +set_verbose <- function() { + set_global("global_verbose", TRUE) +} + +unset_verbose <- function() { + set_global("global_verbose", FALSE) +} + +verbose_catf <- function(...) { + if (global_verbose) { + cat(sprintf(...), sep = "") + } +} + + +debug_catf <- function(...) { + if (global_debug) { + cat(sprintf(...), sep = "") + } +} + +catf <- function(...) { + cat(sprintf(...), sep = "") +} + +create_parser <- function() { + parser <- optparse::OptionParser() + parser <- optparse::add_option( + parser, + c("-v", "--verbose"), + action = "store_true", + default = FALSE, + help = paste( + "[default %default]", + "Print extra output" + ) + ) + parser <- optparse::add_option( + parser, + c("-V", "--version"), + action = "store_true", + default = FALSE, + help = "Prints version and exits" + ) + parser <- optparse::add_option( + parser, + c("-d", "--debug"), + action = "store_true", + default = FALSE, + help = paste( + "[default %default]", + "Print debug outputs" + ) + ) + parser <- optparse::add_option( + parser, + c("-o", "--output"), + type = "character", + default = DEFAULT_OUTPUT_PATH, + action = "store", + help = "Path to the output file [default %default]" + ) + parser <- optparse::add_option( + parser, + c("-p", "--precursors"), + type = "character", + default = DEFAULT_PRECURSOR_PATH, + action = "store", + help = "Path to the precursors file [default %default]" + ) + parser <- optparse::add_option( + parser, + c("-f", "--fragments"), + type = "character", + default = DEFAULT_FRAGMENTS_PATH, + action = "store", + help = "Path to the fragments file [default %default]" + ) + parser <- optparse::add_option( + parser, + c("-c", "--compounds"), + type = "character", + default = DEFAULT_COMPOUNDS_PATH, + action = "store", + help = "Path to the compounds file [default %default]" + ) + parser <- optparse::add_option( + parser, + c("--tolmz"), + type = "numeric", + action = "store", + default = DEFAULT_TOLMZ, + metavar = "number", + help = paste( + "[default %default]", + "Tolerance for MZ (in Dalton) to match the standard in the compounds" + ) + ) + parser <- optparse::add_option( + parser, + c("--tolrt"), + type = "integer", + action = "store", + default = DEFAULT_TOLRT, + metavar = "number", + help = paste( + "[default %default]", + "RT (in seconds) to match the standard in the compounds" + ) + ) + parser <- optparse::add_option( + parser, + c("--seuil_ra"), + type = "numeric", + action = "store", + default = DEFAULT_SEUIL_RA, + metavar = "number", + help = paste( + "[default %default]", + "relative intensity threshold" + ), + ) + parser <- optparse::add_option( + parser, + c("--mzdecimal"), + type = "integer", + default = DEFAULT_MZDECIMAL, + action = "store", + help = paste( + "[default %default]", + "Number of decimal to write for MZ" + ), + metavar = "number" + ) + parser <- optparse::add_option( + parser, + c("--r_threshold"), + type = "integer", + default = DEFAULT_R_THRESHOLD, + action = "store", + help = paste( + "[default %default]", + "R-Pearson correlation threshold between precursor and fragment", + "absolute intensity" + ), + metavar = "number" + ) + parser <- optparse::add_option( + parser, + c("--min_number_scan"), + type = "numeric", + action = "store", + default = DEFAULT_MINNUMBERSCAN, + help = paste( + "[default %default]", + "Fragments are kept if there are found in a minimum number", + "of min_number_scan scans" + ), + metavar = "number" + ) + parser <- optparse::add_option( + parser, + c("--pdf_path"), + type = "character", + default = DEFAULT_PDF_PATH, + help = paste( + "[default %default]", + "PDF files output path" + ) + ) + parser <- optparse::add_option( + parser, + c("--ionization"), + type = "character", + action = "store", + default = "None", + help = paste( + "[default %default]", + "Which ionization to use for sirius" + ), + metavar = "character" + ) + parser <- optparse::add_option( + parser, + c("--fragment_match_delta"), + type = "numeric", + action = "store", + default = DEFAULT_FRAGMENTS_MATCH_DELTA, + help = paste( + "[default %default]", + "Fragment match delta" + ), + metavar = "numeric" + ) + parser <- optparse::add_option( + parser, + c("--fragment_match_delta_unit"), + type = "character", + action = "store", + default = DEFAULT_FRAGMENTS_MATCH_DELTA_UNIT, + help = paste( + "[default %default]", + "Fragment match delta" + ), + metavar = "character" + ) + return(parser) +} + +stop_with_status <- function(msg, status) { + sink(stderr()) + message(sprintf("Error: %s", msg)) + message(sprintf("Error code: %s", status)) + sink(NULL) + base::quit(status = status) +} + +check_args_validity <- function(args) { ## nolint cyclocomp_linter + if (length(args$output) == 0 || nchar(args$output[1]) == 0) { + stop_with_status( + "Missing output parameters. Please set it with --output.", + MISSING_PARAMETER_ERROR + ) + } + if (length(args$precursors) == 0 || nchar(args$precursors[1]) == 0) { + stop_with_status( + "Missing precursors parameters. Please set it with --precursors.", + MISSING_PARAMETER_ERROR + ) + } + if (length(args$fragments) == 0 || nchar(args$fragments[1]) == 0) { + stop_with_status( + "Missing fragments parameters. Please set it with --fragments.", + MISSING_PARAMETER_ERROR + ) + } + if (length(args$compounds) == 0 || nchar(args$compounds[1]) == 0) { + stop_with_status( + "Missing compounds parameters. Please set it with --compounds.", + MISSING_PARAMETER_ERROR + ) + } + if (!file.exists(args$precursors)) { + stop_with_status( + sprintf( + "Precursors file %s does not exist or cannot be accessed.", + args$precursors + ), + MISSING_INPUT_FILE_ERROR + ) + } + if (!file.exists(args$fragments)) { + stop_with_status( + sprintf( + "Fragments file %s does not exist or cannot be accessed.", + args$fragments + ), + MISSING_INPUT_FILE_ERROR + ) + } + if (!file.exists(args$compounds)) { + stop_with_status( + sprintf( + "Compounds file %s does not exist or cannot be accessed.", + args$compounds + ), + MISSING_INPUT_FILE_ERROR + ) + } + if (in_galaxy_env()) { + check_galaxy_args_validity(args) + } +} + +in_galaxy_env <- function() { + sysvars <- Sys.getenv() + sysvarnames <- names(sysvars) + return( + "_GALAXY_JOB_HOME_DIR" %in% sysvarnames + || "_GALAXY_JOB_TMP_DIR" %in% sysvarnames + || "GALAXY_MEMORY_MB" %in% sysvarnames + || "GALAXY_MEMORY_MB_PER_SLOT" %in% sysvarnames + || "GALAXY_SLOTS" %in% sysvarnames + ) +} + +check_galaxy_args_validity <- function(args) { + if (!file.exists(args$output)) { + stop_with_status( + sprintf( + "Output file %s does not exist or cannot be accessed.", + args$output + ), + MISSING_INPUT_FILE_ERROR + ) + } +} + +get_csv_or_tsv <- function( + path, + sep_stack = c("\t", ",", ";"), + sep_names = c("tab", "comma", "semicolon"), + header = TRUE, + quote = "\"" +) { + sep <- determine_csv_or_tsv_sep( + path = path, + sep_stack = sep_stack, + header = header, + quote = quote + ) + verbose_catf( + "%s separator has been determined for %s.\n", + sep_names[sep_stack == sep], + path + ) + return(read.table( + file = path, + sep = sep, + header = header, + quote = quote + )) +} + +determine_csv_or_tsv_sep <- function( + path, + sep_stack = c("\t", ",", ";"), + header = TRUE, + quote = "\"" +) { + count <- -1 + best_sep <- sep_stack[1] + for (sep in sep_stack) { + tryCatch({ + table <- read.table( + file = path, + sep = sep, + header = header, + quote = quote, + nrows = 1 + ) + if (ncol(table) > count) { + count <- ncol(table) + best_sep <- sep + } + }) + } + return(best_sep) +} + +uniformize_columns <- function(df) { + cols <- colnames(df) + for (func in c(tolower)) { + cols <- func(cols) + } + colnames(df) <- cols + return(df) +} + +handle_galaxy_param <- function(args) { + for (param in names(args)) { + if (is.character(args[[param]])) { + args[[param]] <- gsub("__ob__", "[", args[[param]]) + args[[param]] <- gsub("__cb__", "]", args[[param]]) + } + } + return(args) +} + +zip_pdfs <- function(processing_parameters) { + if (processing_parameters$do_pdf) { + if (zip <- Sys.getenv("R_ZIPCMD", "zip") == "") { + catf("R could not fin the zip executable. Trying luck: zip = \"zip\"") + zip <- "zip" + } else { + catf("Found zip executable at %s .", zip) + } + utils::zip( + processing_parameters$pdf_zip_path, + processing_parameters$pdf_path, + zip = zip + ) + } +} + +main <- function(args) { + if (args$version) { + catf("%s\n", MS2SNOOP_VERSION) + base::quit(status = 0) + } + if (in_galaxy_env()) { + print(sessionInfo()) + cat("\n\n") + } + check_args_validity(args) + args <- handle_galaxy_param(args) + if (args$ionization == "None") { + args$ionization <- NULL + } + if (args$debug) { + set_debug() + } + if (args$verbose) { + set_verbose() + } + precursors <- get_csv_or_tsv(args$precursors) + fragments <- get_csv_or_tsv(args$fragments) + compounds <- get_csv_or_tsv(args$compounds) + + compounds <- uniformize_columns(compounds) + mandatory_columns <- c( + "compound_name", + "mz", + "rtsec", + "inchikey" + ) + presents <- mandatory_columns %in% colnames(compounds) + if (!all(presents)) { + stop_with_status( + sprintf( + "Some columns are missing: %s", + paste(mandatory_columns[which(!presents)], collapse = ", ") + ), + BAD_PARAMETER_VALUE_ERROR + ) + } + + res_all <- data.frame() + processing_parameters <- list( + min_number_scan = args$min_number_scan, + mzdecimal = args$mzdecimal, + r_threshold = args$r_threshold, + seuil_ra = args$seuil_ra, + tolmz = args$tolmz, + tolrt = args$tolrt, + ionization = args$ionization, + do_pdf = nchar(args$pdf_path) > 0, + pdf_zip_path = args$pdf_path, + pdf_path = tempdir(), + fragment_match_delta = args$fragment_match_delta, + fragment_match_delta_unit = args$fragment_match_delta_unit + ) + for (i in seq_len(nrow(compounds))) { + processing_parameters$mzref <- compounds[["mz"]][i] + processing_parameters$rtref <- compounds[["rtsec"]][i] + processing_parameters$c_name <- compounds[["compound_name"]][i] + processing_parameters$inchikey <- compounds[["inchikey"]][i] + processing_parameters$elemcomposition <- compounds[["elemcomposition"]][i] + res_cor <- extract_fragments( + precursors = precursors, + fragments = fragments, + processing_parameters = processing_parameters + ) + if (!is.null(res_cor)) { + res_all <- rbind(res_all, res_cor) + } + } + + if (nrow(res_all) == 0) { + stop_with_status("No result at all!", NO_ANY_RESULT_ERROR) + } + + write.table( + x = res_all, + file = args$output, + sep = "\t", + row.names = FALSE + ) + zip_pdfs(processing_parameters) + unlink(processing_parameters$pdf_path, recursive = TRUE) +} + +global_debug <- FALSE +global_verbose <- FALSE +args <- optparse::parse_args(create_parser()) +main(args) + +warnings()
--- a/MS2snoop.xml Fri Aug 05 17:25:45 2022 +0000 +++ b/MS2snoop.xml Fri Sep 30 16:18:56 2022 +0000 @@ -1,9 +1,4 @@ -<tool - id="ms2snoop" - name="MS2 Snoop" - version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" - profile="21.09" -> +<tool id="ms2snoop" name="MS2 Snoop" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> <description> MS1/MS2 spectra and associated adducts extraction and cleaning </description> @@ -33,11 +28,13 @@ <regex match="Error in\s+.*:\s+.*" /> </stdio> <version_command> - Rscript '$__tool_directory__/MS2snoop.R' --version | head -n 1 +<![CDATA[ +@COMMAND_RSCRIPT@ '$__tool_directory__/MS2snoop.R' --version | head -n 1 +]]> </version_command> <command> - <![CDATA[ -Rscript '$__tool_directory__/MS2snoop.R' +<![CDATA[ +@COMMAND_RSCRIPT@ '$__tool_directory__/MS2snoop.R' --output '$frag_result_txt' --compounds '$compound_txt' --fragments '$peaklist_frag_tsv' @@ -54,77 +51,34 @@ $advenced.pdf $advenced.debug $advenced.verbose - ]]> +]]> </command> <inputs> - <param - argument="--compound_txt" - type="data" - format="tabular,csv,tsv" + <param argument="--compound_txt" type="data" format="tabular,csv,tsv" label="list of compounds" - help=" - The table must fit the format: - compound_name [MANDATORY] ; - inchikey [MANDATORY] ; - elemcomposition [OPTIONAL] ; - mz [MANDATORY] ; - rtsec [MANDATORY]. - " + help="The table must fit the format: compound_name, inchikey, [elemcomposition], mz, rtsec." /> - <param - argument="--peaklist_frag_tsv" - type="data" - format="tabular,csv,tsv" + <param argument="--peaklist_frag_tsv" type="data" format="tabular,csv,tsv" label="MSpurity fragments file" /> - <param - argument="--peaklist_preco_tsv" - type="data" - format="tabular,csv,tsv" + <param argument="--peaklist_preco_tsv" type="data" format="tabular,csv,tsv" label="MSpurity precursors file" /> - <param - argument="--tolmz" - type="float" - min="0.0001" - max="10" - value="0.01" + <param argument="--tolmz" type="float" min="0.0001" max="10" value="0.01" label="MZ Tolerence" help="M/z tolerance to determine if a precursor matches a compound" /> - <param - argument="--tolrt" - type="integer" - min="0" - max="30" - value="20" + <param argument="--tolrt" type="integer" min="0" max="30" value="20" label="RT Tolerence (in seconds)" - help=" - Retention time tolerance to determine if a - precursor matches a compound - " + help="Retention time tolerance to determine if a precursor matches a compound" /> - <param - argument="--seuil_ra" - type="float" - min="0" - max="1" - value="0.05" + <param argument="--seuil_ra" type="float" min="0" max="1" value="0.05" label="R-Pearson correlation threshold used to filter fragments" /> - <param - argument="--mzdecimal" - type="integer" - min="0" - max="5" - value="0" + <param argument="--mzdecimal" type="integer" min="0" max="5" value="3" label="Number of decimal to output M/z values with" /> - <param - argument="--r_threshold" - type="float" - min="0" - value="0.85" + <param argument="--r_threshold" type="float" min="0" value="0.85" label=" Minimun correlation with absolute intensity value to reach for a fragment to be considered as valid. @@ -132,26 +86,15 @@ displayed in grey. " /> - <param - argument="--min_number_scan" - type="integer" - min="0" - max="25" - value="8" + <param argument="--min_number_scan" type="integer" min="0" max="25" value="8" label="Present in at least X scan" - help=" - Mininum scan number in which a fragment must be found, - to be kept. - " + help="Mininum scan number in which a fragment must be found, to be kept." /> <section title="Sirius Parameters" name="sirius"> - <param - argument="--ionization" - type="select" + <param argument="--ionization" type="select" optional="true" label="Which ionization" help="Select the ionization to use in sirius" - optional="true" > <option value="[M+H]+" selected="true">[M+H]+</option> <option value="[M-H]-">[M-H]-</option> @@ -166,12 +109,7 @@ <option value="[M+Br]-">[M+Br]-</option> </param> - <param - argument="--fragment_match_delta" - type="float" - min="0" - max="25" - value="10" + <param argument="--fragment_match_delta" type="float" min="0" max="25" value="10" label="Fragment match delta" help=" Delta that determines if a fragment found by sirius @@ -180,12 +118,9 @@ associated even when M/z difference is aberant. " /> - <param - argument="--fragment_match_delta_unit" - type="select" + <param argument="--fragment_match_delta_unit" type="select" optional="true" label="Delta unit" help="Select the unit of the fragment match delta" - optional="true" > <option value="ppm" selected="true">PPM</option> <option value="mz">M/z</option> @@ -193,71 +128,33 @@ </section> <section title="Advenced Options" name="advenced"> - <param - argument="--pdf" - type="boolean" - value="" - optional="true" + <param argument="--pdf" type="boolean" truevalue="--pdf_path '$pdf_output'" falsevalue="" value="" optional="true" label="Output PDF" help="The tool will output some pdf in a zip file" - truevalue="--pdf_path '$pdf_output'" - falsevalue="" /> - <param - argument="--verbose" - type="boolean" - value="" - optional="true" + <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" value="" optional="true" label="Verbose logs" help="The tool will print more logs" - truevalue="--verbose" - falsevalue="" /> - <param - argument="--debug" - type="boolean" - value="" - optional="true" + <param argument="--debug" type="boolean" truevalue="--debug" falsevalue="" value="" optional="true" label="Debug statements" help="The tool will print debug statements" - truevalue="--debug" - falsevalue="" /> </section> </inputs> <outputs> - <data - name="frag_result_txt" - format="tsv" - label="${tool.name} on ${peaklist_frag_tsv.name}" - /> - <data - name="pdf_output" - format="zip" - label="${tool.name} PDFs for ${peaklist_frag_tsv.name}" - > + <data name="frag_result_txt" format="tsv" label="${tool.name} on ${peaklist_frag_tsv.name}" /> + <data name="pdf_output" format="zip" label="${tool.name} PDFs for ${peaklist_frag_tsv.name}"> <filter>advenced['pdf']</filter> </data> </outputs> <tests> <test> <!-- Regular test with no option --> - <param - name="compound_txt" - value="compounds_pos.txt" - /> - <param - name="peaklist_frag_tsv" - value="peaklist_fragments.tsv" - /> - <param - name="peaklist_preco_tsv" - value="peaklist_precursors.tsv" - /> - <output - name="frag_result_txt" - file="compound_fragments_result.txt" - /> + <param name="compound_txt" value="compounds_pos.txt" /> + <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> + <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> + <output name="frag_result_txt" file="compound_fragments_result.txt" /> <assert_stdout> <expand macro="has_regular_stdout"/> <expand macro="has_not_verbose_stdout"/> @@ -267,23 +164,11 @@ <test> <!-- Regular files with verbose output --> - <param - name="compound_txt" - value="compounds_pos.txt" - /> - <param - name="peaklist_frag_tsv" - value="peaklist_fragments.tsv" - /> - <param - name="peaklist_preco_tsv" - value="peaklist_precursors.tsv" - /> + <param name="compound_txt" value="compounds_pos.txt" /> + <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> + <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> <param name="verbose" value="--verbose" /> - <output - name="frag_result_txt" - file="compound_fragments_result.txt" - /> + <output name="frag_result_txt" file="compound_fragments_result.txt" /> <assert_stdout> <expand macro="has_regular_stdout"/> <expand macro="has_verbose_stdout"/> @@ -293,23 +178,11 @@ <test> <!-- Regular test with debug outputs --> - <param - name="compound_txt" - value="compounds_pos.txt" - /> - <param - name="peaklist_frag_tsv" - value="peaklist_fragments.tsv" - /> - <param - name="peaklist_preco_tsv" - value="peaklist_precursors.tsv" - /> + <param name="compound_txt" value="compounds_pos.txt" /> + <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> + <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> <param name="debug" value="--debug" /> - <output - name="frag_result_txt" - file="compound_fragments_result.txt" - /> + <output name="frag_result_txt" file="compound_fragments_result.txt" /> <assert_stdout> <expand macro="has_smol_stdout"/> <expand macro="has_debug_stdout"/> @@ -319,24 +192,12 @@ <test> <!-- Regular test with both verbose and debug outputs --> - <param - name="compound_txt" - value="compounds_pos.txt" - /> - <param - name="peaklist_frag_tsv" - value="peaklist_fragments.tsv" - /> - <param - name="peaklist_preco_tsv" - value="peaklist_precursors.tsv" - /> + <param name="compound_txt" value="compounds_pos.txt" /> + <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> + <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> <param name="debug" value="--debug" /> <param name="verbose" value="--verbose" /> - <output - name="frag_result_txt" - file="compound_fragments_result.txt" - /> + <output name="frag_result_txt" file="compound_fragments_result.txt" /> <assert_stdout> <expand macro="has_smol_stdout"/> <expand macro="has_debug_stdout"/> @@ -349,23 +210,11 @@ This test mixes tsv, csv, and so, and ms2snoop is expected handle them like usual. --> - <param - name="compound_txt" - value="compounds_pos.csv" - /> - <param - name="peaklist_frag_tsv" - value="peaklist_fragments.tsv" - /> - <param - name="peaklist_preco_tsv" - value="peaklist_precursors.csv" - /> + <param name="compound_txt" value="compounds_pos.csv" /> + <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> + <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" /> <param name="verbose" value="--verbose" /> - <output - name="frag_result_txt" - file="compound_fragments_result.txt" - /> + <output name="frag_result_txt" file="compound_fragments_result.txt" /> <assert_stdout> <expand macro="has_regular_stdout"/> <expand macro="has_verbose_stdout"/> @@ -432,26 +281,17 @@ This test uses old format for molecules file. Is is expected to fail --> - <param - name="compound_txt" - value="compounds_pos_old_format.txt" - /> - <param - name="peaklist_frag_tsv" - value="peaklist_fragments.tsv" - /> - <param - name="peaklist_preco_tsv" - value="peaklist_precursors.csv" - /> + <param name="compound_txt" value="compounds_pos_old_format.txt" /> + <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> + <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" /> <assert_stderr> <has_line line="Error: Some columns are missing: compound_name, rtsec, inchikey" /> </assert_stderr> </test> </tests> - <help><![CDATA[ - + <help> +<![CDATA[ @AUTHORS@ ============== @@ -508,14 +348,9 @@ | and fragment (Name + m/z + ret Time) | TSV,CSV | +----------------------------------------------+------------+ - @PARAMETERS@ - - @OUTPUTS@ - - @CHANGELOG@ - - ]]></help> +]]> + </help> </tool>
--- a/README.md Fri Aug 05 17:25:45 2022 +0000 +++ b/README.md Fri Sep 30 16:18:56 2022 +0000 @@ -5,7 +5,7 @@ ----------- * **@name**: MS2 Snoop - * **@version**: 2.1.0 + * **@version**: 2.2.0 * **@authors**: Jean François Martin (INRAE), Kevin Wagner (INRAE) * **@maintainers**: Lain Pavot (PFEM - INRAE - MetaboHUB) * **@init date**: 2022, April
--- a/macros.xml Fri Aug 05 17:25:45 2022 +0000 +++ b/macros.xml Fri Sep 30 16:18:56 2022 +0000 @@ -1,18 +1,18 @@ <macros> - <token name="@AUTHORS@"> + <token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript</token> + + <token name="@AUTHORS@"> .. class:: infomark -**Authors** Jean-Francois Martin (jean-francois.martin@inrae.fr), Lain Pavot (lain.pavot@inrae.fr), Kevin Wagner (kevin.wagner@inrae.fr) +**Authors** Jean-Francois Martin (jean-francois.martin@inrae.fr), Kevin Wagner (kevin.wagner@inrae.fr), Lain Pavot (lain.pavot@inrae.fr) .. class:: infomark --------------------------------------------------- - - - </token> - <token name="@PARAMETERS@"> - <![CDATA[ + </token> + <token name="@PARAMETERS@"> + <![CDATA[ ---------- Parameters ---------- @@ -55,9 +55,9 @@ | minNumberScan <- 8 ]]> - </token> - <token name="@OUTPUTS@"> - <![CDATA[ + </token> + <token name="@OUTPUTS@"> +<![CDATA[ ------------ Output files ------------ @@ -75,12 +75,16 @@ fragments. At the end the pdf file a graph of the spectra with validated fragments. ]]> - </token> - <token name="@CHANGELOG@"> + </token> + <token name="@CHANGELOG@"> +<![CDATA[ -------------- Changelog/News -------------- +2.2.0 + | Fix: Replace nominal values by real values in the M/z column of + output files 2.1.0 | Adds support for sirius to match fragments with their formula @@ -122,7 +126,6 @@ input files. | chore: add some tests in an external macro.xml file - 1.0.1 | Bug fix, new parameters and some improvement in the xml. | fix: the program crashed when there were no result on the first @@ -132,105 +135,105 @@ 1.0.0 | First version, published on the toolshed. - - </token> +]]> + </token> - <token name="@TOOL_VERSION@">2.1.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@TOOL_VERSION@">2.2.0</token> + <token name="@VERSION_SUFFIX@">0</token> - <xml name="has_smol_stdout"> - <has_line line="processing 2-diethylamino-6-methyl pyrimidin-4-ol one" /> - </xml> + <xml name="has_smol_stdout"> + <has_line line="processing 2-diethylamino-6-methyl pyrimidin-4-ol one" /> + </xml> - <xml name="has_regular_stdout"> - <has_line line="processing 2-diethylamino-6-methyl pyrimidin-4-ol one" /> - <has_line line="processing 5-hydroxy-thiabendazole" /> - <has_line line="processing acetamiprid-N-desmethyl" /> - <has_line line="processing Acetochlor" /> - <has_line line="processing Avermectin B1a (Abamectin)" /> - <has_line line="processing Benzophenone-3 (Oxybenzone)" /> - <has_line line="processing Butocarboxim" /> - <has_line line="processing Carbendazim" /> - <has_line line="processing Cefoperazone" /> - <has_line line="processing Chlorfenvinphos" /> - <has_line line="processing Chlormequat" /> - <has_line line="processing Desisopropylatrazine" /> - <has_line line="processing Dichlorvos" /> - <has_line line="processing Dimethyldithiophosphate" /> - <has_line line="processing Emamectin B1a" /> - <has_line line="processing Fluopyram" /> - <has_line line="processing Hydroxy-tebuconazole" /> - <has_line line="processing Isoproturon" /> - <has_line line="processing Ivermectin B1a " /> - <has_line line="processing Malathion dicarboxilic acid" /> - <has_line line="processing Methamidophos" /> - <has_line line="processing Metolachlor" /> - <has_line line="processing N,N-diethyl-m-toluamide ou DEET" /> - <has_line line="processing Nigericin" /> - <has_line line="processing Omethoate" /> - <has_line line="processing Prochloraz" /> - <has_line line="processing p-Toluenesulfonamide" /> - <has_line line="processing Rifaximin" /> - <has_line line="processing Spinosad A (Spinosyn A)" /> - <has_line line="processing TCMTB" /> - <has_line line="processing Trichlorfon (Dylox)" /> - <has_line line="processing Tylosin" /> - <has_line line="> non detected in precursor file" min="6" /> - </xml> + <xml name="has_regular_stdout"> + <has_line line="processing 2-diethylamino-6-methyl pyrimidin-4-ol one" /> + <has_line line="processing 5-hydroxy-thiabendazole" /> + <has_line line="processing acetamiprid-N-desmethyl" /> + <has_line line="processing Acetochlor" /> + <has_line line="processing Avermectin B1a (Abamectin)" /> + <has_line line="processing Benzophenone-3 (Oxybenzone)" /> + <has_line line="processing Butocarboxim" /> + <has_line line="processing Carbendazim" /> + <has_line line="processing Cefoperazone" /> + <has_line line="processing Chlorfenvinphos" /> + <has_line line="processing Chlormequat" /> + <has_line line="processing Desisopropylatrazine" /> + <has_line line="processing Dichlorvos" /> + <has_line line="processing Dimethyldithiophosphate" /> + <has_line line="processing Emamectin B1a" /> + <has_line line="processing Fluopyram" /> + <has_line line="processing Hydroxy-tebuconazole" /> + <has_line line="processing Isoproturon" /> + <has_line line="processing Ivermectin B1a " /> + <has_line line="processing Malathion dicarboxilic acid" /> + <has_line line="processing Methamidophos" /> + <has_line line="processing Metolachlor" /> + <has_line line="processing N,N-diethyl-m-toluamide ou DEET" /> + <has_line line="processing Nigericin" /> + <has_line line="processing Omethoate" /> + <has_line line="processing Prochloraz" /> + <has_line line="processing p-Toluenesulfonamide" /> + <has_line line="processing Rifaximin" /> + <has_line line="processing Spinosad A (Spinosyn A)" /> + <has_line line="processing TCMTB" /> + <has_line line="processing Trichlorfon (Dylox)" /> + <has_line line="processing Tylosin" /> + <has_line line="> non detected in precursor file" min="6" /> + </xml> - <xml name="has_not_debug_stdout"> - <has_line negate="true" line=" acquisitionNum mz68 mz71 mz74 mz81 mz82 mz83" /> - <has_line negate="true" line=" acquisitionNum mz67 mz71 mz84 mz85 mz86 mz87" /> - <has_line negate="true" line=" mz243 mz248 mz256 mz257 mz258" /> - </xml> + <xml name="has_not_debug_stdout"> + <has_line negate="true" line=" acquisitionNum mz68 mz71 mz74 mz81 mz82 mz83" /> + <has_line negate="true" line=" acquisitionNum mz67 mz71 mz84 mz85 mz86 mz87" /> + <has_line negate="true" line=" mz243 mz248 mz256 mz257 mz258" /> + </xml> - <xml name="has_debug_stdout"> - <has_line line=" acquisitionNum mz68 mz71 mz74 mz81 mz82 mz83" /> - <has_line line=" mz243 mz248 mz256 mz257 mz258" /> - </xml> + <xml name="has_debug_stdout"> + <has_line line=" acquisitionNum mz68 mz71 mz74 mz81 mz82 mz83" /> + <has_line line=" mz243 mz248 mz256 mz257 mz258" /> + </xml> - <xml name="has_not_verbose_stdout"> - <has_line negate="true" line=">> fragments: 68 71 74 81 82 83 84 94 97 99 102 103 104 105 109 111 112 117 118 120 121 123 124 126 128 134 136 137 139 140 141 144 146 147 148 149 150 151 152 154 162 163 164 165 166 167 168 180 181 182 183" /> - <has_line negate="true" line=">> fragments: 67 71 84 85 86 87 88 89 91 92 95 96 98 99 105 107 110 112 114 116 118 119 120 123 124 126 127 128 129 130 132 134 135 136 139 140 141 142 143 144 145 146 147 148 155 156 157 158 159 160 161 162 164 168 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--- a/test-data/compound_fragments_result.txt Fri Aug 05 17:25:45 2022 +0000 +++ b/test-data/compound_fragments_result.txt Fri Sep 30 16:18:56 2022 +0000 @@ -1,743 +1,743 @@ "compoundName" "inchikey" "elemcomposition" "fragment" "fragment_mz" "ppm" "fileid" "CorWithPrecursor" "AbsoluteIntensity" "relativeIntensity" "corValid" -"2-diethylamino-6-methyl pyrimidin-4-ol one" NA NA NA 84 NA "7" 0.601436519480403 406.383798606 0.00344160476662782 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" NA NA NA 123 NA "7" -0.167860259307508 295.871994004 0.00250569650751035 FALSE -"2-diethylamino-6-methyl pyrimidin-4-ol one" NA NA NA 126 NA "7" 0.907929868611774 430.137959956 0.00364277527394095 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" NA NA NA 137 NA "7" 0.676403388268515 430.806630151 0.00364843814371653 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" NA NA NA 146 NA "7" -0.125051837812104 538.358772757 0.00455928145962519 FALSE -"2-diethylamino-6-methyl pyrimidin-4-ol one" NA NA NA 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789.382863066 0.00185201000490732 TRUE -"Hydroxy-tebuconazole" NA NA NA 193 NA "3" 0.834581905027916 786.770006146 0.00184587985262806 TRUE -"Hydroxy-tebuconazole" NA NA NA 207 NA "3" 0.912806973260801 1817.33848199 0.00426374729985384 TRUE -"Hydroxy-tebuconazole" NA NA NA 213 NA "3" 0.533276651096227 209.824030864 0.000492278490719679 TRUE -"Hydroxy-tebuconazole" NA NA NA 219 NA "3" 0.973387546070147 5785.704654759 0.0135741265834354 TRUE -"Hydroxy-tebuconazole" NA NA NA 225 NA "3" 0.158710766132164 598.46658039 0.00140409191324474 TRUE -"Hydroxy-tebuconazole" NA NA NA 234 NA "3" 0.533892369953371 498.037124195 0.00116846942083577 TRUE -"Hydroxy-tebuconazole" NA NA NA 236 NA "3" 0.757916887845443 401.455109619 0.000941873600660352 TRUE -"Hydroxy-tebuconazole" NA NA NA 237 NA "3" 0.819617372910582 1804.698136231 0.00423409116224753 TRUE -"Hydroxy-tebuconazole" NA NA NA 242 NA "3" 0.0281666681525705 492.2943644595 0.00115499604944205 TRUE -"Hydroxy-tebuconazole" NA NA NA 249 NA "3" 0.148844380563395 668.821608301 0.00156915530856678 TRUE -"Hydroxy-tebuconazole" NA NA NA 251 NA "3" -0.0957358039667109 294.37336396 0.000690643844375629 FALSE -"Hydroxy-tebuconazole" NA NA NA 252 NA "3" 0.571270701114537 262.84086132 0.000616663887245291 TRUE -"Hydroxy-tebuconazole" NA NA NA 261 NA "3" 0.307249106849353 301.249457372 0.000706776185714076 TRUE -"Hydroxy-tebuconazole" NA NA NA 262 NA "3" -0.0664296147654578 356.3203392 0.000835980693306733 FALSE -"Hydroxy-tebuconazole" NA NA NA 264 NA "3" -0.234448577231542 1060.76663015 0.00248871682402531 FALSE -"Hydroxy-tebuconazole" NA NA NA 266 NA "3" 0.442854013871549 224.958957681 0.000527787287781417 TRUE -"Hydroxy-tebuconazole" NA NA NA 268 NA "3" 0.333877814717464 167.482578998 0.00039293912556858 TRUE -"Hydroxy-tebuconazole" NA NA NA 276 NA "3" 0.814390714374443 472.387895585 0.00110829250260451 TRUE -"Hydroxy-tebuconazole" NA NA NA 278 NA "3" 0.275231308762053 379.986748698 0.000891505621983662 TRUE -"Hydroxy-tebuconazole" NA NA NA 280 NA "3" 0.650641022624376 416.402436187 0.000976942259540319 TRUE -"Hydroxy-tebuconazole" NA NA NA 282 NA "3" 0.782140125615591 155.801819332 0.000365534320145864 TRUE -"Hydroxy-tebuconazole" NA NA NA 288 NA "3" 0.702501554923525 901.789572159 0.00211573292011017 TRUE -"Hydroxy-tebuconazole" NA NA NA 292 NA "3" -0.282700274468723 1574.001168335 0.00369284164615631 FALSE -"Hydroxy-tebuconazole" NA NA NA 296 NA "3" -0.00403563274731662 354.472442154 0.000831645251055126 TRUE -"Hydroxy-tebuconazole" NA NA NA 306 NA "3" 0.939487898745732 6832.34144213 0.0160296926875516 TRUE -"Hydroxy-tebuconazole" NA NA NA 307 NA "3" 0.647420935806109 170.978830823 0.000401141854133558 TRUE -"Hydroxy-tebuconazole" NA NA NA 324 NA "3" 1 426230.3448547 1 TRUE -"Hydroxy-tebuconazole" NA NA NA 325 NA "3" 0.526687588803207 740.769098256 0.0017379548575044 TRUE -"Isoproturon" NA NA NA 72 NA "2" 0.993086605464471 59907.1442268 0.115787147683237 TRUE -"Isoproturon" NA NA NA 120 NA "2" 0.927282017838371 790.062006494 0.00152701363761405 TRUE -"Isoproturon" NA NA NA 134 NA "2" 0.71269989274101 432.2311039 0.000835406315999436 TRUE -"Isoproturon" NA NA NA 137 NA "2" 0.213034502535958 770.65881154 0.00148951158959186 TRUE -"Isoproturon" NA NA NA 147 NA "2" -0.543816345969317 1151.6802063 0.00222594095999428 FALSE -"Isoproturon" NA NA NA 149 NA "2" 0.500520723996853 390.29506684 0.000754353310068573 TRUE -"Isoproturon" NA NA NA 161 NA "2" 0.400505614578046 614.84665681 0.00118836144792821 TRUE -"Isoproturon" NA NA NA 162 NA "2" 0.804730923860733 2048.22309885 0.00395875840011529 TRUE -"Isoproturon" NA NA NA 165 NA "2" 0.985177338187729 41795.7801207 0.0807819205510825 TRUE -"Isoproturon" NA NA NA 174 NA "2" -0.672244697055266 2538.22496785 0.00490582271945875 FALSE -"Isoproturon" NA NA NA 175 NA "2" -0.891117335203028 41310.6113296 0.0798441974933163 FALSE -"Isoproturon" NA NA NA 179 NA "2" 0.106337033555785 305.46005153 0.000590386147667693 TRUE -"Isoproturon" NA NA NA 189 NA "2" -0.557815616548336 2256.78026215 0.00436185287873026 FALSE -"Isoproturon" NA NA NA 193 NA "2" -0.457037805653279 900.73918538 0.00174092793819098 FALSE -"Isoproturon" NA NA NA 207 NA "2" 1 517390.275393 1 TRUE -"Malathion dicarboxilic acid" NA NA NA 99 NA "5" 0.0390122357382497 146.313006405 0.00728513388971739 TRUE -"Malathion dicarboxilic acid" NA NA NA 101 NA "5" -0.00307888841729598 435.762945656 0.0216972604232751 TRUE -"Malathion dicarboxilic acid" NA NA NA 105 NA "5" 0.592401757892981 89.451040273 0.00445389525494049 TRUE -"Malathion dicarboxilic acid" NA NA NA 111 NA "5" 0.238541386362055 129.625732421 0.00645425064690212 TRUE -"Malathion dicarboxilic acid" NA NA NA 113 NA "5" -0.181700362244182 214.697242755 0.0106900828412605 FALSE -"Malathion dicarboxilic acid" NA NA NA 115 NA "5" -0.231992590984375 169.733005041 0.00845124912412097 FALSE -"Malathion dicarboxilic acid" NA NA NA 125 NA "5" -0.250900317999769 976.859200016 0.0486392169662613 FALSE -"Malathion dicarboxilic acid" NA NA NA 127 NA "5" -0.120496404762161 251.457530026 0.0125204301300888 FALSE -"Malathion dicarboxilic acid" NA NA NA 133 NA "5" -0.00480587756063445 106.381536014 0.00529688885696561 TRUE -"Malathion dicarboxilic acid" NA NA NA 135 NA "5" -0.090209154235706 265.367501262 0.0132130274961485 FALSE -"Malathion dicarboxilic acid" NA NA NA 143 NA "5" -0.131857430656449 2027.15360119 0.100934877647263 FALSE -"Malathion dicarboxilic acid" NA NA NA 145 NA "5" -0.00327881805976476 340.208190446 0.0169394524702548 TRUE -"Malathion dicarboxilic acid" NA NA NA 155 NA "5" -0.103996527690727 89.39838505 0.00445127347606401 FALSE -"Malathion dicarboxilic acid" NA NA NA 157 NA "5" 0.0930278278084389 283.279369826 0.014104885054885 TRUE -"Malathion dicarboxilic acid" NA NA NA 159 NA "5" -0.0612368257690917 11570.4075283 0.576107142306516 FALSE -"Malathion dicarboxilic acid" NA NA NA 171 NA "5" -0.19710660695736 343.725625045 0.0171145905706306 FALSE -"Malathion dicarboxilic acid" NA NA NA 173 NA "5" 0.0378284550947032 276.705667733 0.0137775710239911 TRUE -"Malathion dicarboxilic acid" NA NA NA 174 NA "5" -0.540544488822746 145.849533325 0.00726205690206577 FALSE -"Malathion dicarboxilic acid" NA NA NA 175 NA "5" 0.184070758387235 1172.409335654 0.0583759379542223 TRUE -"Malathion dicarboxilic acid" NA NA NA 177 NA "5" -0.140789116062933 180.05658699 0.00896527503724966 FALSE -"Malathion dicarboxilic acid" NA NA NA 183 NA "5" -0.260101643573225 92.657263754 0.00461353770856342 FALSE -"Malathion dicarboxilic acid" NA NA NA 185 NA "5" 0.435155306012117 212.018755439 0.0105567171262197 TRUE -"Malathion dicarboxilic acid" NA NA NA 187 NA "5" -0.0466843753550633 941.066299451 0.0468570372453718 FALSE -"Malathion dicarboxilic acid" NA NA NA 189 NA "5" -0.395771460619492 146.580297463 0.00729844269385517 FALSE -"Malathion dicarboxilic acid" NA NA NA 190 NA "5" -0.103737669048405 148.989129555 0.0074183818895511 FALSE -"Malathion dicarboxilic acid" NA NA NA 193 NA "5" -0.153009009646862 1596.369196382 0.0794855058946147 FALSE -"Malathion dicarboxilic acid" NA NA NA 197 NA "5" -0.244011968974358 179.884572989 0.00895671021407378 FALSE -"Malathion dicarboxilic acid" NA NA NA 199 NA "5" 0.150914124088504 276.667024113 0.0137756469028716 TRUE -"Malathion dicarboxilic acid" NA NA NA 201 NA "5" -0.10556131251179 239.864170096 0.0119431801548682 FALSE -"Malathion dicarboxilic acid" NA NA NA 203 NA "5" -0.0442733202671276 1407.858670707 0.0700992971568763 FALSE -"Malathion dicarboxilic acid" NA NA NA 205 NA "5" -0.206299059029665 130.40357304 0.00649298044402344 FALSE -"Malathion dicarboxilic acid" NA NA NA 213 NA "5" 0.034041946036616 282.143243319 0.0140483156908721 TRUE -"Malathion dicarboxilic acid" NA NA NA 215 NA "5" -0.0174569064315414 4632.372268515 0.23065244185969 FALSE -"Malathion dicarboxilic acid" NA NA NA 216 NA "5" 0.11460473836849 152.968408575 0.00761651588431708 TRUE -"Malathion dicarboxilic acid" NA NA NA 217 NA "5" -0.0749466491463488 149.235903278 0.00743066910622917 FALSE -"Malathion dicarboxilic acid" NA NA NA 219 NA "5" -0.229702200918307 275.246332175 0.0137049086189782 FALSE -"Malathion dicarboxilic acid" NA NA NA 229 NA "5" -0.0736331507746074 508.844859597 0.0253361134621037 FALSE -"Malathion dicarboxilic acid" NA NA NA 231 NA "5" -0.398924747325029 548.515546309 0.027311373702427 FALSE -"Malathion dicarboxilic acid" NA NA NA 233 NA "5" -0.0593443075085707 5883.46527449 0.292946152316215 FALSE -"Malathion dicarboxilic acid" NA NA NA 239 NA "5" -0.250539714331339 289.00519777 0.0143899822190159 FALSE -"Malathion dicarboxilic acid" NA NA NA 243 NA "5" -0.0531886469417714 3332.41069708 0.165925495622409 FALSE -"Malathion dicarboxilic acid" NA NA NA 245 NA "5" -0.230543139716182 369.79291249 0.0184125181017819 FALSE -"Malathion dicarboxilic acid" NA NA NA 247 NA "5" -0.0791167715438849 453.035788533 0.0225572999789294 FALSE -"Malathion dicarboxilic acid" NA NA NA 257 NA "5" 0.106470337603423 20083.7772675 1 TRUE -"Malathion dicarboxilic acid" NA NA NA 261 NA "5" 0.355868386838636 138.486630433 0.00689544743443765 TRUE -"Malathion dicarboxilic acid" NA NA NA 275 NA "5" 1 7538.973325 0.375376266356017 TRUE -"Methamidophos" NA NA NA 94 NA "10" 0.976908842717177 9354.73397623 0.0482149771671354 TRUE -"Methamidophos" NA NA NA 100 NA "10" 0.513584871583348 164.780854231 0.000849292469942643 TRUE -"Methamidophos" NA NA NA 110 NA "10" 0.284212959905891 434.336410282 0.0022386013496283 TRUE -"Methamidophos" NA NA NA 112 NA "10" 0.703154152581651 915.166019881 0.00471683201946947 TRUE -"Methamidophos" NA NA NA 114 NA "10" -0.0808744594898649 205.122636803 0.00105721694225077 FALSE -"Methamidophos" NA NA NA 124 NA "10" -0.178837358040908 522.942952646 0.00269528589328229 FALSE -"Methamidophos" NA NA NA 125 NA "10" 0.944616104231969 4800.928386691 0.0247443329904978 TRUE -"Methamidophos" NA NA NA 142 NA "10" 1 194021.3295923 1 TRUE -"Methamidophos" NA NA NA 143 NA "10" 0.462998313752461 215.166582594 0.0011089841670817 TRUE -"Metolachlor" NA NA NA 176 NA "2" 0.791796112912307 995.27586705 0.00140948787866654 TRUE -"Metolachlor" NA NA NA 196 NA "2" 0.390316117761383 165.330739505 0.000234137771263337 TRUE -"Metolachlor" NA NA NA 212 NA "2" 0.793947617278503 3303.57566825 0.00467845148748308 TRUE -"Metolachlor" NA NA NA 220 NA "2" 0.784265545338331 134.73387814 0.000190807166506454 TRUE -"Metolachlor" NA NA NA 222 NA "2" 0.837765555939223 149.329081531 0.000211476573800797 TRUE -"Metolachlor" NA NA NA 224 NA "2" 0.333881608192525 1240.410666011 0.0017566424106045 TRUE -"Metolachlor" NA NA NA 238 NA "2" 0.0957538782410419 278.464510935 0.000394355339856714 TRUE -"Metolachlor" NA NA NA 240 NA "2" 0.702714684679668 309.572997085 0.000438410496425569 TRUE -"Metolachlor" NA NA NA 241 NA "2" 0.310895385493475 198.540365455 0.000281168515985718 TRUE -"Metolachlor" NA NA NA 243 NA "2" 0.131240121206885 350.776814924 0.000496762440566436 TRUE -"Metolachlor" NA NA NA 248 NA "2" 0.61859332075056 330.1702237165 0.000467579837542316 TRUE -"Metolachlor" NA NA NA 252 NA "2" 0.917041451436126 706125.8788487 1 TRUE -"Metolachlor" NA NA NA 253 NA "2" 0.855704337813672 610.27153687 0.000864253180842224 TRUE -"Metolachlor" NA NA NA 256 NA "2" 0.912087870841402 160.856989391 0.000227802144361666 TRUE -"Metolachlor" NA NA NA 266 NA "2" -0.228646021214337 2686.12464523 0.00380403087564158 FALSE -"Metolachlor" NA NA NA 267 NA "2" -0.172706372060116 90.919785974 0.000128758609048913 FALSE -"Metolachlor" NA NA NA 284 NA "2" 1 27717.1231987 0.0392523826543382 TRUE -"Metolachlor" NA NA NA 285 NA "2" 0.516690728602645 786.727229625 0.00111414586717558 TRUE -"Metolachlor" NA NA NA 105 NA "6" 0.147510907385547 67.732931137 0.000302088164521329 TRUE -"Metolachlor" NA NA NA 212 NA "6" 0.56820247221881 1215.116215726 0.00541940561447594 TRUE -"Metolachlor" NA NA NA 224 NA "6" -0.111227845735124 339.173356055 0.00151270962093686 FALSE -"Metolachlor" NA NA NA 252 NA "6" 0.993045070992658 224215.7723866 1 TRUE -"Metolachlor" NA NA NA 266 NA "6" -0.146787460104817 628.791106722 0.00280440176009482 FALSE -"Metolachlor" NA NA NA 284 NA "6" 1 155026.670419 0.691417328802802 TRUE -"Metolachlor" NA NA NA 285 NA "6" 0.118321686070868 459.575310689 0.00204970107944318 TRUE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 72 NA "1" 0.831213054372806 1933.43451305 0.00181816864864583 TRUE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 91 NA "1" 0.822308544953969 1277.57458017 0.00120140921882462 TRUE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 100 NA "1" 0.904831380805312 4819.97843154 0.0045326250318924 TRUE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 119 NA "1" 0.996276922706082 196757.537712 0.185027413154208 TRUE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 159 NA "1" 0.318506076968014 5745.2918091 0.00540277385870641 TRUE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 160 NA "1" -0.60812844929883 81418.296387 0.076564369218524 FALSE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 174 NA "1" -0.0254778159834255 6464.1887357 0.00607881219604324 FALSE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 178 NA "1" 0.189033868824133 1156.2770652 0.00108734311656538 TRUE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 192 NA "1" 1 1063396.68462 1 TRUE -"N,N-diethyl-m-toluamide ou DEET" NA NA NA 193 NA "1" 0.843516913487705 669.860601479 0.000629925418394897 TRUE -"Nigericin" NA NA NA 303 NA "8" 0.69388156788724 256.771903521 2.6267948084131e-05 TRUE -"Nigericin" NA NA NA 345 NA "8" 0.488441108859454 170.187350269 1.74102867959473e-05 TRUE -"Nigericin" NA NA NA 361 NA "8" -0.298158261851774 270.481686601 2.76704686296107e-05 FALSE -"Nigericin" NA NA NA 377 NA "8" 0.921913240362568 212.930380819 2.17829291764015e-05 TRUE -"Nigericin" NA NA NA 399 NA "8" -0.00219607480717936 155.459186543 1.59035851871495e-05 TRUE -"Nigericin" NA NA NA 419 NA "8" -0.128312924215981 334.087566385 3.41773953030539e-05 FALSE -"Nigericin" NA NA NA 485 NA "8" -0.153312907002539 192.458596704 1.96886511228122e-05 FALSE -"Nigericin" NA NA NA 491 NA "8" -0.422922944471844 124.569573874 1.27435558739663e-05 FALSE -"Nigericin" NA NA NA 501 NA "8" 0.330721867433802 1962.279740704 0.000200742611043264 TRUE -"Nigericin" NA NA NA 502 NA "8" 0.746783956260905 200.27525187 2.04883004975159e-05 TRUE -"Nigericin" NA NA NA 507 NA "8" -0.354836880533629 218.69433498 2.23725857805091e-05 FALSE -"Nigericin" NA NA NA 509 NA "8" -0.728921794848418 199.1876421 2.03770372456477e-05 FALSE -"Nigericin" NA NA NA 523 NA "8" 0.0880948030696946 240.14782524 2.45672930699186e-05 TRUE -"Nigericin" NA NA NA 525 NA "8" 0.117962948439402 576.361316696 5.89621720175225e-05 TRUE -"Nigericin" NA NA NA 559 NA "8" 0.84810344800213 103.529180519 1.05911086913109e-05 TRUE -"Nigericin" NA NA NA 567 NA "8" -0.752351991905382 249.41364288 2.55151927948768e-05 FALSE -"Nigericin" NA NA NA 568 NA "8" -0.532840101817629 259.228322029 2.65192414419954e-05 FALSE -"Nigericin" NA NA NA 573 NA "8" 0.244836394250901 221.88957263 2.26994608612938e-05 TRUE -"Nigericin" NA NA NA 580 NA "8" 0.992118727855313 194.64446546 1.99122670489084e-05 TRUE -"Nigericin" NA NA NA 583 NA "8" -0.188987118257525 7100.821918505 0.000726419125115431 FALSE -"Nigericin" NA NA NA 589 NA "8" -0.259152968299446 295.832520469 3.0263876937929e-05 FALSE -"Nigericin" NA NA NA 597 NA "8" -0.0565070203738975 733.689611459 7.50569683029789e-05 FALSE -"Nigericin" NA NA NA 599 NA "8" 0.972283168725802 643.235493679 6.58034478154985e-05 TRUE -"Nigericin" NA NA NA 605 NA "8" 0.429575707714564 667.355635634 6.82709554671057e-05 TRUE -"Nigericin" NA NA NA 607 NA "8" 0.386766245051255 160.19072342 1.63876247699032e-05 TRUE -"Nigericin" NA NA NA 641 NA "8" -0.367379921280677 128.127842899 1.31075693222306e-05 FALSE -"Nigericin" NA NA NA 643 NA "8" -0.327136371457191 200.36151887 2.04971256728809e-05 FALSE -"Nigericin" NA NA NA 649 NA "8" 0.0943387745709055 318.911627299 3.26248859569277e-05 TRUE -"Nigericin" NA NA NA 659 NA "8" 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154.957 NA "6" 1 74403.5832217 1 TRUE +"Chlorfenvinphos" NA NA NA 169.937 NA "6" 0.400965038923134 251.752763748 0.00338361074624395 TRUE +"Chlorfenvinphos" NA NA NA 177.012 NA "6" 0.152941035271053 308.496086376 0.00414625308376313 TRUE +"Chlorfenvinphos" NA NA NA 180.942 NA "6" -0.0396586829705516 354.258750916 0.00476131303865322 FALSE +"Chlorfenvinphos" NA NA NA 184.93 NA "6" 0.21416204967555 620.034171576 0.00833339127940232 TRUE +"Chlorfenvinphos" NA NA NA 186.967 NA "6" 0.0344669511741455 255.646638389 0.00343594525047605 TRUE +"Chlorfenvinphos" NA NA NA 194.987 NA "6" 0.0600010541304002 215.919657704 0.00290200617167355 TRUE +"Chlorfenvinphos" NA NA NA 204.959 NA "6" 0.974358430327003 4144.892359716 0.0557082358166203 TRUE +"Chlorfenvinphos" NA NA NA 215.074 NA "6" -0.450618424806283 111.581706056 0.00149968188660377 FALSE +"Chlorfenvinphos" NA NA NA 216.952 NA "6" -0.105278812587947 184.536623947 0.00248021151611929 FALSE +"Chlorfenvinphos" NA NA NA 227.058 NA "6" 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315.15 NA "6" -0.535392132745364 228.835577496 0.00307559888364704 FALSE +"Chlorfenvinphos" NA NA NA 317.058 NA "6" 0.108398080800289 371.096517574 0.00498761620751847 TRUE +"Chlorfenvinphos" NA NA NA 327.106 NA "6" -0.0292180991930868 857.215583061 0.0115211599487992 FALSE +"Chlorfenvinphos" NA NA NA 331.034 NA "6" 0.935671136523579 10942.34945269 0.147067506414108 TRUE +"Chlorfenvinphos" NA NA NA 341.156 NA "6" 0.3027544679085 681.509114277 0.0091596275981267 TRUE +"Chlorfenvinphos" NA NA NA 359.083 NA "6" 0.963091521050382 70775.23458992 0.951234221865785 TRUE +"Chlorfenvinphos" NA NA NA 359.907 NA "6" 0.316260785934268 336.06626725 0.0045168021847634 TRUE +"Chlormequat" NA NA NA 103.875 NA "3" 0.258848039085982 1344.00603488 0.0035075545862099 TRUE +"Chlormequat" NA NA NA 121.939 NA "3" 1 383174.65968 1 TRUE +"Chlormequat" NA NA NA 103.891 NA "7" -0.238480528781348 249.84195518 0.00659545474896182 FALSE +"Chlormequat" NA NA NA 121.989 NA "7" 1 37880.9293202 1 TRUE 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TRUE +"Dichlorvos" NA NA NA 76.87 NA "8" 0.673126587009387 741.86317154 0.00161896017936163 TRUE +"Dichlorvos" NA NA NA 78.905 NA "8" 0.878900088282318 1378.256703748 0.00300775507655178 TRUE +"Dichlorvos" NA NA NA 94.966 NA "8" 0.23830151975066 167.451852342 0.000365428412276191 TRUE +"Dichlorvos" NA NA NA 98.879 NA "8" 0.0952811367061809 779.789044359 0.00170172541184249 TRUE +"Dichlorvos" NA NA NA 104.915 NA "8" 0.421334905224525 170.538307904 0.000372163951715189 TRUE +"Dichlorvos" NA NA NA 106.991 NA "8" 0.259129043686515 193.227040286 0.000421677333233239 TRUE +"Dichlorvos" NA NA NA 108.907 NA "8" 0.967088540122942 63244.728942055 0.138018305315196 TRUE +"Dichlorvos" NA NA NA 111.003 NA "8" 0.669971084873578 362.689319128 0.000791493078068717 TRUE +"Dichlorvos" NA NA NA 116.962 NA "8" 0.427724412537125 150.021759756 0.000327390904954265 TRUE +"Dichlorvos" NA NA NA 119.018 NA "8" 0.352320220252662 842.015996927 0.00183752263450484 TRUE +"Dichlorvos" NA NA NA 121.012 NA "8" 0.347913703205373 778.073791986 0.00169798223466916 TRUE +"Dichlorvos" NA NA NA 123.095 NA "8" 0.375380270767784 270.12158084 0.000589483478548166 TRUE +"Dichlorvos" NA NA NA 126.93 NA "8" 0.948284758535013 7147.09441171 0.0155970287980156 TRUE +"Dichlorvos" NA NA NA 133.034 NA "8" 0.111433255667834 852.743870701 0.00186093396036062 TRUE +"Dichlorvos" NA NA NA 135.079 NA "8" 0.0748728027193132 220.929068083 0.000482131176490902 TRUE +"Dichlorvos" NA NA NA 136.984 NA "8" 0.453769927098964 505.667025571 0.00110351181972854 TRUE +"Dichlorvos" NA NA NA 138.985 NA "8" 0.467524552074558 137.935647968 0.000301015510597557 TRUE +"Dichlorvos" NA NA NA 143.009 NA "8" 0.278796612798532 266.444155698 0.000581458272424074 TRUE +"Dichlorvos" NA NA NA 144.921 NA "8" 0.994170372012309 44316.40897363 0.0967112321692371 TRUE +"Dichlorvos" NA NA NA 145.872 NA "8" 0.346301417994264 207.562618724 0.000452961714948885 TRUE +"Dichlorvos" NA NA NA 147.046 NA "8" -0.183799172220307 819.102781302 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NA NA NA 177.061 NA "8" 0.0961702542234717 389.493910798 0.000849988455926194 TRUE +"Dichlorvos" NA NA NA 177.991 NA "8" 0.493220332481887 482.049106835 0.00105197068462459 TRUE +"Dichlorvos" NA NA NA 179.031 NA "8" -0.0861608852458405 2525.723908887 0.00551186066301337 FALSE +"Dichlorvos" NA NA NA 185.101 NA "8" 0.0918293472268129 668.89163876 0.00145971517255995 TRUE +"Dichlorvos" NA NA NA 188.967 NA "8" -0.197479261216347 5542.6118852 0.0120955834930694 FALSE +"Dichlorvos" NA NA NA 190.968 NA "8" 0.387244221989 1667.67687608 0.00363935366788881 TRUE +"Dichlorvos" NA NA NA 192.082 NA "8" 0.819756995871118 124.725039958 0.000272186139988758 TRUE +"Dichlorvos" NA NA NA 193.079 NA "8" -0.217736800465349 3528.26782225 0.00769970167745111 FALSE +"Dichlorvos" NA NA NA 203.05 NA "8" -0.00105621012897679 9102.7295684 0.0198647907863461 TRUE +"Dichlorvos" NA NA NA 204.09 NA "8" 0.224749665606753 212.49892521 0.000463734164560272 TRUE +"Dichlorvos" NA NA NA 206.076 NA "8" 0.0812819184416861 745.68288134 0.00162729589179507 TRUE +"Dichlorvos" NA NA NA 219.064 NA "8" 0.850573767933108 128.129454139 0.000279615557170436 TRUE +"Dichlorvos" NA NA NA 220.928 NA "8" 1 458234.353752 1 TRUE +"Dichlorvos" NA NA NA 221.982 NA "8" 0.129303934081555 360.408204103 0.000786515024794618 TRUE +"Fluopyram" NA NA NA 129.966 NA "2" 0.988179415765439 17795.909718935 0.0154226372206749 TRUE +"Fluopyram" NA NA NA 144.998 NA "2" 0.928241190042729 3449.545446807 0.00298951213186528 TRUE +"Fluopyram" NA NA NA 149.953 NA "2" 0.988115406284376 12058.53886978 0.0104504053648994 TRUE +"Fluopyram" NA NA NA 151.993 NA "2" 0.714803770971941 843.962879701 0.000731411516855211 TRUE +"Fluopyram" NA NA NA 169.972 NA "2" 0.996118661695746 54335.19384732 0.0470890219301705 TRUE +"Fluopyram" NA NA NA 172.063 NA "2" 0.93623116209915 4358.1586747 0.00377695219022824 TRUE +"Fluopyram" NA NA NA 172.99 NA "2" 0.996725515129425 33891.795142293 0.0293719663390324 TRUE +"Fluopyram" NA NA NA 190.021 NA "2" 0.994751234429169 52936.742621562 0.0458770689439894 TRUE +"Fluopyram" NA NA NA 207.984 NA "2" 0.998926992897114 741312.313808205 0.642450487985915 TRUE +"Fluopyram" NA NA NA 208.978 NA "2" 0.479662731083597 434.75375842 0.000376774753431255 TRUE +"Fluopyram" NA NA NA 223.061 NA "2" 0.919762443227137 180.747808449 0.000156643179369186 TRUE +"Fluopyram" NA NA NA 233.132 NA "2" 0.447788622500763 228.889230719 0.000198364434572427 TRUE +"Fluopyram" NA NA NA 239.159 NA "2" 0.490523688542752 454.236178877 0.000393658987372342 TRUE +"Fluopyram" NA NA NA 251.124 NA "2" 0.399282659683872 207.703212752 0.000180003795840478 TRUE +"Fluopyram" NA NA NA 253.207 NA "2" 0.291997563579388 381.209336282 0.000330371045451865 TRUE +"Fluopyram" NA NA NA 277.084 NA "2" 0.472534154830253 407.468348983 0.000353128141495666 TRUE +"Fluopyram" NA NA NA 293.082 NA "2" 0.439013773646497 230.165272235 0.000199470302476379 TRUE +"Fluopyram" NA NA NA 295.154 NA "2" 0.556087836877115 396.002507198 0.000343191390799996 TRUE +"Fluopyram" NA NA NA 297.093 NA "2" 0.269891270141561 261.36091041 0.000226505672853008 TRUE +"Fluopyram" NA NA NA 305.245 NA "2" 0.13304535194746 151.392195691 0.000131202447588246 TRUE +"Fluopyram" NA NA NA 307.132 NA "2" 0.658489317811748 176.850197312 0.000153265355838801 TRUE +"Fluopyram" NA NA NA 309.193 NA "2" 0.620367265623824 877.951049335 0.0007608670051297 TRUE +"Fluopyram" NA NA NA 312.079 NA "2" -0.101202655215579 313.370437142 0.000271579179938356 FALSE +"Fluopyram" NA NA NA 315.092 NA "2" -0.0918425876545814 1665.552336677 0.00144343334318478 FALSE +"Fluopyram" NA NA NA 317.175 NA "2" 0.747044352703202 276.576972023 0.000239692511957673 TRUE +"Fluopyram" NA NA NA 319.208 NA "2" 0.411135022271651 205.162689204 0.000177802077937308 TRUE +"Fluopyram" NA NA NA 321.075 NA "2" 0.668663039963109 172.5105753 0.000149504468251542 TRUE +"Fluopyram" NA NA NA 322.207 NA "2" 0.457450301072192 363.92931174 0.000315395494671673 TRUE +"Fluopyram" NA NA NA 323.148 NA "2" 0.525525654158042 541.443225855 0.000469236053668481 TRUE +"Fluopyram" NA NA NA 325.172 NA "2" -0.375139543472427 284.063552627 0.000246180677974607 FALSE +"Fluopyram" NA NA NA 335.143 NA "2" 0.85099649332553 354.179540117 0.000306945958059 TRUE +"Fluopyram" NA NA NA 337.149 NA "2" -0.0800505936255548 6092.33305747 0.00527985610496276 FALSE +"Fluopyram" NA NA NA 339.165 NA "2" 0.0817418256376614 1257.39245224 0.001089705889791 TRUE +"Fluopyram" NA NA NA 351.264 NA "2" 0.0922108519959764 325.871292118 0.000282412913885544 TRUE +"Fluopyram" NA NA NA 353.206 NA "2" 0.73819712073071 219.68107702 0.000190384285413725 TRUE +"Fluopyram" NA NA NA 355.042 NA "2" 0.558938657015514 404.386810763 0.0003504575589405 TRUE +"Fluopyram" NA NA NA 357.092 NA "2" 0.962259996620823 6087.032030074 0.00527526202555257 TRUE +"Fluopyram" NA NA NA 361.224 NA "2" 0.552153478272702 857.635546693 0.000743260789310912 TRUE +"Fluopyram" NA NA NA 365.223 NA "2" -0.00936270431495669 3128.58431621 0.00271135455760717 FALSE +"Fluopyram" NA NA NA 377.099 NA "2" 0.95522089194523 6353.409628619 0.00550611535819805 TRUE +"Fluopyram" NA NA NA 379.135 NA "2" 0.976200924337964 23757.38885012 0.0205890901523317 TRUE +"Fluopyram" NA NA NA 380.163 NA "2" 0.802086185702225 299.634428489 0.000259675013101082 TRUE +"Fluopyram" NA NA NA 383.011 NA "2" 0.514484227137365 296.36061955 0.000256837801157807 TRUE +"Fluopyram" NA NA NA 397.143 NA "2" 1 1153882.4044359 1 TRUE +"Fluopyram" NA NA NA 397.852 NA "2" 0.629183355208795 786.96763037 0.000682017185932154 TRUE +"Hydroxy-tebuconazole" NA NA NA 104.943 NA "3" 0.933250800122397 148.864868642 0.000349259198550838 TRUE +"Hydroxy-tebuconazole" NA NA NA 111.016 NA "3" -0.136986211620653 819.476129504 0.00192261329911496 FALSE +"Hydroxy-tebuconazole" NA NA NA 124.953 NA "3" 0.937808762193969 1183.686924417 0.00277710617910255 TRUE +"Hydroxy-tebuconazole" NA NA NA 128.989 NA "3" 0.93947878913899 361.506768723 0.000848148830994743 TRUE +"Hydroxy-tebuconazole" NA NA NA 130.031 NA "3" 0.688489556152789 331.007312771 0.000776592555567199 TRUE +"Hydroxy-tebuconazole" NA NA NA 138.998 NA "3" 0.773254709339752 1538.894389073 0.00361047590264274 TRUE +"Hydroxy-tebuconazole" NA NA NA 142.055 NA "3" 0.570848007480712 609.52418229 0.00143003469754783 TRUE +"Hydroxy-tebuconazole" NA NA NA 143.052 NA "3" 0.806393964441417 697.26483626 0.00163588736624957 TRUE +"Hydroxy-tebuconazole" NA NA NA 144.028 NA "3" 0.617078750669289 821.504440261 0.00192737201885766 TRUE +"Hydroxy-tebuconazole" NA NA NA 150.967 NA "3" 0.969913176100367 8918.60934376 0.020924388541131 TRUE +"Hydroxy-tebuconazole" NA NA NA 163.01 NA "3" 0.943479253411026 4190.003754782 0.00983037412836093 TRUE +"Hydroxy-tebuconazole" NA NA NA 165.016 NA "3" 0.974027692942281 11141.070391724 0.0261386138415883 TRUE +"Hydroxy-tebuconazole" NA NA NA 177.025 NA "3" 0.976181868104272 5276.840125508 0.0123802544544473 TRUE +"Hydroxy-tebuconazole" NA NA NA 179.05 NA "3" 0.985734009124796 18898.49200271 0.0443386826650093 TRUE +"Hydroxy-tebuconazole" NA NA NA 181.003 NA "3" 0.815011717512525 2102.659529777 0.00493315305951243 TRUE +"Hydroxy-tebuconazole" NA NA NA 183.071 NA "3" 0.629817289150805 328.86962314 0.000771577216662296 TRUE +"Hydroxy-tebuconazole" NA NA NA 191.055 NA "3" 0.627994719460226 789.382863066 0.00185201000490732 TRUE +"Hydroxy-tebuconazole" NA NA NA 193.087 NA "3" 0.834581905027916 786.770006146 0.00184587985262806 TRUE +"Hydroxy-tebuconazole" NA NA NA 207.094 NA "3" 0.912806973260801 1817.33848199 0.00426374729985384 TRUE +"Hydroxy-tebuconazole" NA NA NA 213.136 NA "3" 0.533276651096227 209.824030864 0.000492278490719679 TRUE +"Hydroxy-tebuconazole" NA NA NA 219.028 NA "3" 0.973387546070147 5785.704654759 0.0135741265834354 TRUE +"Hydroxy-tebuconazole" NA NA NA 225.246 NA "3" 0.158710766132164 598.46658039 0.00140409191324474 TRUE +"Hydroxy-tebuconazole" NA NA NA 233.996 NA "3" 0.533892369953371 498.037124195 0.00116846942083577 TRUE +"Hydroxy-tebuconazole" NA NA NA 236.081 NA "3" 0.757916887845443 401.455109619 0.000941873600660352 TRUE +"Hydroxy-tebuconazole" NA NA NA 237.098 NA "3" 0.819617372910582 1804.698136231 0.00423409116224753 TRUE +"Hydroxy-tebuconazole" NA NA NA 241.966 NA "3" 0.0281666681525705 492.2943644595 0.00115499604944205 TRUE +"Hydroxy-tebuconazole" NA NA NA 249.215 NA "3" 0.148844380563395 668.821608301 0.00156915530856678 TRUE +"Hydroxy-tebuconazole" NA NA NA 251.196 NA "3" -0.0957358039667109 294.37336396 0.000690643844375629 FALSE +"Hydroxy-tebuconazole" NA NA NA 252.021 NA "3" 0.571270701114537 262.84086132 0.000616663887245291 TRUE +"Hydroxy-tebuconazole" NA NA NA 260.974 NA "3" 0.307249106849353 301.249457372 0.000706776185714076 TRUE +"Hydroxy-tebuconazole" NA NA NA 262.007 NA "3" -0.0664296147654578 356.3203392 0.000835980693306733 FALSE +"Hydroxy-tebuconazole" NA NA NA 264.108 NA "3" -0.234448577231542 1060.76663015 0.00248871682402531 FALSE +"Hydroxy-tebuconazole" NA NA NA 266.097 NA "3" 0.442854013871549 224.958957681 0.000527787287781417 TRUE +"Hydroxy-tebuconazole" NA NA NA 268.218 NA "3" 0.333877814717464 167.482578998 0.00039293912556858 TRUE +"Hydroxy-tebuconazole" NA NA NA 276.183 NA "3" 0.814390714374443 472.387895585 0.00110829250260451 TRUE +"Hydroxy-tebuconazole" NA NA NA 278.186 NA "3" 0.275231308762053 379.986748698 0.000891505621983662 TRUE +"Hydroxy-tebuconazole" NA NA NA 280.045 NA "3" 0.650641022624376 416.402436187 0.000976942259540319 TRUE +"Hydroxy-tebuconazole" NA NA NA 282.042 NA "3" 0.782140125615591 155.801819332 0.000365534320145864 TRUE +"Hydroxy-tebuconazole" NA NA NA 288.14 NA "3" 0.702501554923525 901.789572159 0.00211573292011017 TRUE +"Hydroxy-tebuconazole" NA NA NA 292.107 NA "3" -0.282700274468723 1574.001168335 0.00369284164615631 FALSE +"Hydroxy-tebuconazole" NA NA NA 296.201 NA "3" -0.00403563274731662 354.472442154 0.000831645251055126 TRUE +"Hydroxy-tebuconazole" NA NA NA 306.19 NA "3" 0.939487898745732 6832.34144213 0.0160296926875516 TRUE +"Hydroxy-tebuconazole" NA NA NA 307.097 NA "3" 0.647420935806109 170.978830823 0.000401141854133558 TRUE +"Hydroxy-tebuconazole" NA NA NA 324.177 NA "3" 1 426230.3448547 1 TRUE +"Hydroxy-tebuconazole" NA NA NA 325.033 NA "3" 0.526687588803207 740.769098256 0.0017379548575044 TRUE +"Isoproturon" NA NA NA 71.89 NA "2" 0.993086605464471 59907.1442268 0.115787147683237 TRUE +"Isoproturon" NA NA NA 119.978 NA "2" 0.927282017838371 790.062006494 0.00152701363761405 TRUE +"Isoproturon" NA NA NA 133.985 NA "2" 0.71269989274101 432.2311039 0.000835406315999436 TRUE +"Isoproturon" NA NA NA 137.024 NA "2" 0.213034502535958 770.65881154 0.00148951158959186 TRUE +"Isoproturon" NA NA NA 146.925 NA "2" -0.543816345969317 1151.6802063 0.00222594095999428 FALSE +"Isoproturon" NA NA NA 149.063 NA "2" 0.500520723996853 390.29506684 0.000754353310068573 TRUE +"Isoproturon" NA NA NA 161.063 NA "2" 0.400505614578046 614.84665681 0.00118836144792821 TRUE +"Isoproturon" NA NA NA 162.055 NA "2" 0.804730923860733 2048.22309885 0.00395875840011529 TRUE +"Isoproturon" NA NA NA 165.029 NA "2" 0.985177338187729 41795.7801207 0.0807819205510825 TRUE +"Isoproturon" NA NA NA 173.91 NA "2" -0.672244697055266 2538.22496785 0.00490582271945875 FALSE +"Isoproturon" NA NA NA 174.904 NA "2" -0.891117335203028 41310.6113296 0.0798441974933163 FALSE +"Isoproturon" NA NA NA 179.091 NA "2" 0.106337033555785 305.46005153 0.000590386147667693 TRUE +"Isoproturon" NA NA NA 189.09 NA "2" -0.557815616548336 2256.78026215 0.00436185287873026 FALSE +"Isoproturon" NA NA NA 192.871 NA "2" -0.457037805653279 900.73918538 0.00174092793819098 FALSE +"Isoproturon" NA NA NA 207.103 NA "2" 1 517390.275393 1 TRUE +"Malathion dicarboxilic acid" NA NA NA 98.901 NA "5" -0.0145062980310714 146.313006405 0.00728513388971739 FALSE +"Malathion dicarboxilic acid" NA NA NA 101.001 NA "5" -0.0828141093237674 435.762945656 0.0216972604232751 FALSE +"Malathion dicarboxilic acid" NA NA NA 104.913 NA "5" 0.587019603923614 89.451040273 0.00445389525494049 TRUE +"Malathion dicarboxilic acid" NA NA NA 110.87 NA "5" -0.390287162095832 129.625732421 0.00645425064690212 FALSE +"Malathion dicarboxilic acid" NA NA NA 112.962 NA "5" 0.436063164175773 214.697242755 0.0106900828412605 TRUE +"Malathion dicarboxilic acid" NA NA NA 114.854 NA "5" -0.487491202047035 169.733005041 0.00845124912412097 FALSE +"Malathion dicarboxilic acid" NA NA NA 124.899 NA "5" 0.211743045350572 976.859200016 0.0486392169662613 TRUE +"Malathion dicarboxilic acid" NA NA NA 126.97 NA "5" -0.193115673489529 251.457530026 0.0125204301300888 FALSE +"Malathion dicarboxilic acid" NA NA NA 132.921 NA "5" -0.0235937319440911 106.381536014 0.00529688885696561 FALSE +"Malathion dicarboxilic acid" NA NA NA 134.959 NA "5" 0.0943867349562522 265.367501262 0.0132130274961485 TRUE +"Malathion dicarboxilic acid" NA NA NA 142.949 NA "5" 0.324562260639024 2027.15360119 0.100934877647263 TRUE +"Malathion dicarboxilic acid" NA NA NA 144.918 NA "5" 0.0513679474641989 340.208190446 0.0169394524702548 TRUE +"Malathion dicarboxilic acid" NA NA NA 154.962 NA "5" -0.0935008127275434 89.39838505 0.00445127347606401 FALSE +"Malathion dicarboxilic acid" NA NA NA 156.946 NA "5" -0.124840593853139 283.279369826 0.014104885054885 FALSE +"Malathion dicarboxilic acid" NA NA NA 158.921 NA "5" 0.615282973488168 11570.4075283 0.576107142306516 TRUE +"Malathion dicarboxilic acid" NA NA NA 170.98 NA "5" -0.157617624578159 343.725625045 0.0171145905706306 FALSE +"Malathion dicarboxilic acid" NA NA NA 173.045 NA "5" 0.13521369536174 276.705667733 0.0137775710239911 TRUE +"Malathion dicarboxilic acid" NA NA NA 173.932 NA "5" 0.0546754802243834 145.849533325 0.00726205690206577 TRUE +"Malathion dicarboxilic acid" NA NA NA 174.978 NA "5" -0.0449871685056207 1172.409335654 0.0583759379542223 FALSE +"Malathion dicarboxilic acid" NA NA NA 177.077 NA "5" 0.124276700228139 180.05658699 0.00896527503724966 TRUE +"Malathion dicarboxilic acid" NA NA NA 183.054 NA "5" 0.118394234041897 92.657263754 0.00461353770856342 TRUE +"Malathion dicarboxilic acid" NA NA NA 184.956 NA "5" -0.074153926813293 212.018755439 0.0105567171262197 FALSE +"Malathion dicarboxilic acid" NA NA NA 187.004 NA "5" 0.108830633613764 941.066299451 0.0468570372453718 TRUE +"Malathion dicarboxilic acid" NA NA NA 189.021 NA "5" 0.508419430479885 146.580297463 0.00729844269385517 TRUE +"Malathion dicarboxilic acid" NA NA NA 189.911 NA "5" 0.87690485484064 148.989129555 0.0074183818895511 TRUE +"Malathion dicarboxilic acid" NA NA NA 192.981 NA "5" -0.0384696232288205 1596.369196382 0.0794855058946147 FALSE +"Malathion dicarboxilic acid" NA NA NA 197.022 NA "5" -0.0619440037636622 179.884572989 0.00895671021407378 FALSE +"Malathion dicarboxilic acid" NA NA NA 198.997 NA "5" -0.028668865104496 276.667024113 0.0137756469028716 FALSE +"Malathion dicarboxilic acid" NA NA NA 201.02 NA "5" 0.237137284012593 239.864170096 0.0119431801548682 TRUE +"Malathion dicarboxilic acid" NA NA NA 202.991 NA "5" -0.0966182688129124 1407.858670707 0.0700992971568763 FALSE +"Malathion dicarboxilic acid" NA NA NA 205.027 NA "5" 0.133069171499041 130.40357304 0.00649298044402344 TRUE +"Malathion dicarboxilic acid" NA NA NA 213.08 NA "5" -0.457317913367628 282.143243319 0.0140483156908721 FALSE +"Malathion dicarboxilic acid" NA NA NA 215.035 NA "5" 0.104159055038702 4632.372268515 0.23065244185969 TRUE +"Malathion dicarboxilic acid" NA NA NA 215.963 NA "5" 0.149064407342261 152.968408575 0.00761651588431708 TRUE +"Malathion dicarboxilic acid" NA NA NA 217.11 NA "5" -0.065462150775907 149.235903278 0.00743066910622917 FALSE +"Malathion dicarboxilic acid" NA NA NA 219.11 NA "5" 0.135712941972458 275.246332175 0.0137049086189782 TRUE +"Malathion dicarboxilic acid" NA NA NA 229.034 NA "5" 0.1770967268039 508.844859597 0.0253361134621037 TRUE +"Malathion dicarboxilic acid" NA NA NA 231.032 NA "5" -0.102884748154224 548.515546309 0.027311373702427 FALSE 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0.513584871583348 164.780854231 0.000849292469942643 TRUE +"Methamidophos" NA NA NA 109.875 NA "10" 0.284212959905891 434.336410282 0.0022386013496283 TRUE +"Methamidophos" NA NA NA 111.944 NA "10" 0.703154152581651 915.166019881 0.00471683201946947 TRUE +"Methamidophos" NA NA NA 114.009 NA "10" -0.0808744594898649 205.122636803 0.00105721694225077 FALSE +"Methamidophos" NA NA NA 123.965 NA "10" -0.178837358040908 522.942952646 0.00269528589328229 FALSE +"Methamidophos" NA NA NA 124.905 NA "10" 0.944616104231969 4800.928386691 0.0247443329904978 TRUE +"Methamidophos" NA NA NA 141.916 NA "10" 1 194021.3295923 1 TRUE +"Methamidophos" NA NA NA 142.955 NA "10" 0.462998313752461 215.166582594 0.0011089841670817 TRUE +"Metolachlor" NA NA NA 176.128 NA "2" 0.760582065871439 995.27586705 0.00140948787866654 TRUE +"Metolachlor" NA NA NA 196.04 NA "2" 0.191220558744757 165.330739505 0.000234137771263337 TRUE +"Metolachlor" NA NA NA 212.064 NA "2" 0.931185345473568 3303.57566825 0.00467845148748308 TRUE +"Metolachlor" NA NA NA 220.094 NA "2" 0.643787158940323 134.73387814 0.000190807166506454 TRUE +"Metolachlor" NA NA NA 222.125 NA "2" 0.424376972972785 149.329081531 0.000211476573800797 TRUE +"Metolachlor" NA NA NA 224.025 NA "2" 0.280374162629315 1240.410666011 0.0017566424106045 TRUE +"Metolachlor" NA NA NA 238.138 NA "2" 0.391062783784674 278.464510935 0.000394355339856714 TRUE +"Metolachlor" NA NA NA 240.107 NA "2" 0.591264299722738 309.572997085 0.000438410496425569 TRUE +"Metolachlor" NA NA NA 241.023 NA "2" 0.595274120987579 198.540365455 0.000281168515985718 TRUE +"Metolachlor" NA NA NA 243.012 NA "2" 0.396358480157969 350.776814924 0.000496762440566436 TRUE +"Metolachlor" NA NA NA 248.131 NA "2" 0.678240672160261 330.1702237165 0.000467579837542316 TRUE +"Metolachlor" NA NA NA 252.088 NA "2" 1 706125.8788487 1 TRUE +"Metolachlor" NA NA NA 253.149 NA "2" 0.617816316710038 610.27153687 0.000864253180842224 TRUE +"Metolachlor" NA NA NA 256.233 NA "2" 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0.000894694806181419 TRUE +"Prochloraz" NA NA NA 244.082 NA "1" 0.717875977812794 894.255809314 0.00310519160247456 TRUE +"Prochloraz" NA NA NA 245.134 NA "1" -0.306469344418807 179.53681564 0.000623419167595921 FALSE +"Prochloraz" NA NA NA 265.97 NA "1" 0.959110121105955 6848.746319913 0.0237814161659027 TRUE +"Prochloraz" NA NA NA 280.082 NA "1" 0.945296169467766 2133.000283721 0.00740657706676483 TRUE +"Prochloraz" NA NA NA 291.007 NA "1" -0.00151994503068215 389.368725297 0.00135203426521318 TRUE +"Prochloraz" NA NA NA 294.043 NA "1" 0.133059143955174 1008.16582397 0.00350072990064777 TRUE +"Prochloraz" NA NA NA 303.009 NA "1" 0.495070256706509 206.674549112 0.000717651557489022 TRUE +"Prochloraz" NA NA NA 308.012 NA "1" 1 287987.3205252 1 TRUE +"Prochloraz" NA NA NA 310.113 NA "1" 0.322378179260344 261.194522859 0.000906965356608971 TRUE +"Prochloraz" NA NA NA 315.053 NA "1" -0.154138467883504 338.202372563 0.00117436549618304 FALSE +"Prochloraz" NA NA NA 316.099 NA "1" 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0.035795246780033 TRUE +"Prochloraz" NA NA NA 377.023 NA "1" -0.0453165711816044 369.333282477 0.00128246369251066 FALSE +"Prochloraz" NA NA NA 135.973 NA "7" 0.114630923350083 143.928166396 0.000949178809656671 TRUE +"Prochloraz" NA NA NA 202.005 NA "7" 0.258425894565265 394.165222649 0.00259944447435434 TRUE +"Prochloraz" NA NA NA 233.023 NA "7" -0.273261446171226 190.591785906 0.00125691648137069 FALSE +"Prochloraz" NA NA NA 234.035 NA "7" -0.291827718735545 278.200731283 0.00183468076872653 FALSE +"Prochloraz" NA NA NA 238.026 NA "7" -0.028173451732356 205.77438355 0.00135704281744572 FALSE +"Prochloraz" NA NA NA 244.054 NA "7" 0.485699748004766 872.686310784 0.0057551997945598 TRUE +"Prochloraz" NA NA NA 266.002 NA "7" 0.963071423354662 4327.34904575 0.0285380417125085 TRUE +"Prochloraz" NA NA NA 280.094 NA "7" 0.73706774686317 1298.919650077 0.00856612738265254 TRUE +"Prochloraz" NA NA NA 293.094 NA "7" -0.0928829745817302 200.444505207 0.00132189328620453 FALSE +"Prochloraz" NA NA NA 294.038 NA "7" -0.131949255889773 1575.694126647 0.0103914022735398 FALSE +"Prochloraz" NA NA NA 304.076 NA "7" -0.195251390549766 809.598223213 0.00533914588820071 FALSE +"Prochloraz" NA NA NA 308.049 NA "7" 1 151634.4074812 1 TRUE +"Prochloraz" NA NA NA 310.076 NA "7" -0.143486884545167 105.641312124 0.000696684307201831 FALSE +"Prochloraz" NA NA NA 315.042 NA "7" 0.245421552872291 440.677309527 0.00290618281725825 TRUE +"Prochloraz" NA NA NA 316.046 NA "7" 0.202875988168563 2305.138855487 0.0152019511519692 TRUE +"Prochloraz" NA NA NA 333.982 NA "7" 0.674615895655882 201.20180177 0.00132688751261778 TRUE +"Prochloraz" NA NA NA 344.079 NA "7" -0.113070554769094 697.322455414 0.0045987086110417 FALSE +"Prochloraz" NA NA NA 358.19 NA "7" -0.564930888257682 305.289077308 0.00201332324489645 FALSE +"Prochloraz" NA NA NA 360.155 NA "7" -0.502928639051151 135.6890707 0.000894843544772799 FALSE +"Prochloraz" NA NA NA 375.87 NA "7" -0.181127485034532 375.156909479 0.00247408827396587 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0.511848259153306 144.142693995 0.00355705015215411 TRUE +"Trichlorfon (Dylox)" NA NA NA 201.178 NA "4" 0.0484047608338802 127.383673675 0.00314348305328139 TRUE +"Trichlorfon (Dylox)" NA NA NA 211.039 NA "4" 0.522207219270133 156.726169586 0.00386757614917167 TRUE +"Trichlorfon (Dylox)" NA NA NA 212.979 NA "4" 0.251045877916677 334.711538323 0.00825977158690306 TRUE +"Trichlorfon (Dylox)" NA NA NA 215.037 NA "4" 0.123612564840088 412.352368363 0.0101757363760497 TRUE +"Trichlorfon (Dylox)" NA NA NA 220.939 NA "4" 1 40523.0985871 1 TRUE +"Trichlorfon (Dylox)" NA NA NA 225.006 NA "4" -0.418502449320938 503.974612244 0.012436724480996 FALSE +"Trichlorfon (Dylox)" NA NA NA 226.966 NA "4" 0.029974355651004 177.141063216 0.00437136027086513 TRUE +"Trichlorfon (Dylox)" NA NA NA 228.998 NA "4" 0.686355561238603 1013.548554406 0.0250116252148756 TRUE +"Trichlorfon (Dylox)" NA NA NA 239.072 NA "4" -0.223508651705819 1313.5219316555 0.0324141533459547 FALSE +"Trichlorfon (Dylox)" NA NA NA 257.008 NA "4" 0.950607639404665 25290.7478033 0.624106958379313 TRUE
--- a/test-data/smol/out-smol-base.tsv Fri Aug 05 17:25:45 2022 +0000 +++ b/test-data/smol/out-smol-base.tsv Fri Sep 30 16:18:56 2022 +0000 @@ -1,20 +1,20 @@ "compoundName" "inchikey" "elemcomposition" "fragment" "fragment_mz" "ppm" "fileid" "CorWithPrecursor" "AbsoluteIntensity" "relativeIntensity" "corValid" -"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C13H8O4" "229" 2.02930325023702 "1" NA 203723.75 0.932156767504374 NA -"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" NA "312" NA "1" NA 3981.51538085938 0.0182177900573243 NA -"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" NA "313" NA "1" NA 7264.93603515625 0.0332413834452649 NA -"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C17H12O6" "367" -8.51110969664126 "1" NA 218550.953125 1 NA -"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C20H14O7" "451" -0.624494567969591 "1" NA 135964.078125 0.622116152690652 NA -"Caffeic acid" "QAIPRVGONGVQAS-DUXPYHPUSA-N" "C9H8O4" NA "109" NA "1" NA 1663.78308105469 1 NA -"Caffeic acid" "QAIPRVGONGVQAS-DUXPYHPUSA-N" "C9H8O4" NA "141" NA "1" NA 1119.27758789062 0.672730478291135 NA -"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" NA "56" NA "1" NA 959.281677246094 0.00801122428782145 NA -"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" NA "278" NA "1" NA 49810.07421875 0.415977585963074 NA -"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" "C17H11NO3" "323" -0.610124713635454 "1" 1 119742.20703125 1 TRUE -"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA "52" NA "1" NA 1706.40014648438 0.0178528316194543 NA -"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" "C5H6" "67" -3.38002342189334 "1" NA 1413.32275390625 0.0147865746503924 NA -"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA "122" NA "1" NA 40171.04296875 0.420280593374599 NA -"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" "C7H7NO" "135" -8.52289540743972 "1" NA 95581.484375 1 NA -"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA "233" NA "1" NA 17855.763671875 0.186811952007572 NA -"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA "135" NA "1" NA 1388.24841308594 0.0111932237930481 NA -"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA "177" NA "1" NA 1346.46130371094 0.0108563010474573 NA -"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA "205" NA "1" NA 1612.63024902344 0.0130023784667138 NA -"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA "217" NA "1" NA 124025.7890625 1 NA +"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C13H8O4" 229.05 2.02930325023702 "1" NA 203723.75 0.932156767504374 NA +"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" NA 312.059 NA "1" NA 3981.51538085938 0.0182177900573243 NA +"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" NA 313.068 NA "1" NA 7264.93603515625 0.0332413834452649 NA +"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C17H12O6" 367.081 -8.51110969664126 "1" NA 218550.953125 1 NA +"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C20H14O7" 451.115 -0.624494567969591 "1" NA 135964.078125 0.622116152690652 NA +"Caffeic acid" "QAIPRVGONGVQAS-DUXPYHPUSA-N" "C9H8O4" NA 109.101 NA "1" NA 1663.78308105469 1 NA +"Caffeic acid" "QAIPRVGONGVQAS-DUXPYHPUSA-N" "C9H8O4" NA 140.951 NA "1" NA 1119.27758789062 0.672730478291135 NA +"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" NA 55.575 NA "1" NA 959.281677246094 0.00801122428782145 NA +"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" NA 278.081 NA "1" NA 49810.07421875 0.415977585963074 NA +"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" "C17H11NO3" 323.106 -0.610124713635454 "1" 1 119742.20703125 1 TRUE +"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA 51.94 NA "1" NA 1706.40014648438 0.0178528316194543 NA +"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" "C5H6" 67.054 -3.38002342189334 "1" NA 1413.32275390625 0.0147865746503924 NA +"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA 122.059 NA "1" NA 40171.04296875 0.420280593374599 NA +"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" "C7H7NO" 135.117 -8.52289540743972 "1" NA 95581.484375 1 NA +"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA 232.845 NA "1" NA 17855.763671875 0.186811952007572 NA +"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA 135.071 NA "1" NA 1388.24841308594 0.0111932237930481 NA +"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA 177.092 NA "1" NA 1346.46130371094 0.0108563010474573 NA +"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA 205.034 NA "1" NA 1612.63024902344 0.0130023784667138 NA +"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA 217.015 NA "1" NA 124025.7890625 1 NA
--- a/test-data/smol/out-smol-delta-0.05mz.tsv Fri Aug 05 17:25:45 2022 +0000 +++ b/test-data/smol/out-smol-delta-0.05mz.tsv Fri Sep 30 16:18:56 2022 +0000 @@ -1,20 +1,20 @@ "compoundName" "inchikey" "elemcomposition" "fragment" "fragment_mz" "ppm" "fileid" "CorWithPrecursor" "AbsoluteIntensity" "relativeIntensity" "corValid" -"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C13H8O4" "229" 2.02930325023702 "1" NA 203723.75 0.932156767504374 NA -"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" NA "312" NA "1" NA 3981.51538085938 0.0182177900573243 NA -"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" NA "313" NA "1" NA 7264.93603515625 0.0332413834452649 NA -"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C17H12O6" "367" -8.51110969664126 "1" NA 218550.953125 1 NA -"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C20H14O7" "451" -0.624494567969591 "1" NA 135964.078125 0.622116152690652 NA -"Caffeic acid" "QAIPRVGONGVQAS-DUXPYHPUSA-N" "C9H8O4" NA "109" NA "1" NA 1663.78308105469 1 NA -"Caffeic acid" "QAIPRVGONGVQAS-DUXPYHPUSA-N" "C9H8O4" NA "141" NA "1" NA 1119.27758789062 0.672730478291135 NA -"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" NA "56" NA "1" NA 959.281677246094 0.00801122428782145 NA -"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" NA "278" NA "1" NA 49810.07421875 0.415977585963074 NA -"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" "C17H11NO3" "323" -0.610124713635454 "1" 1 119742.20703125 1 TRUE -"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA "52" NA "1" NA 1706.40014648438 0.0178528316194543 NA -"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" "C5H6" "67" -3.38002342189334 "1" NA 1413.32275390625 0.0147865746503924 NA -"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA "122" NA "1" NA 40171.04296875 0.420280593374599 NA -"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" "C7H7NO" "135" -8.52289540743972 "1" NA 95581.484375 1 NA -"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA "233" NA "1" NA 17855.763671875 0.186811952007572 NA -"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA "135" NA "1" NA 1388.24841308594 0.0111932237930481 NA -"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA "177" NA "1" NA 1346.46130371094 0.0108563010474573 NA -"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA "205" NA "1" NA 1612.63024902344 0.0130023784667138 NA -"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" "C12H8O4" "217" NA "1" NA 124025.7890625 1 NA +"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C13H8O4" 229.05 2.02930325023702 "1" NA 203723.75 0.932156767504374 NA +"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" NA 312.059 NA "1" NA 3981.51538085938 0.0182177900573243 NA +"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" NA 313.068 NA "1" NA 7264.93603515625 0.0332413834452649 NA +"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C17H12O6" 367.081 -8.51110969664126 "1" NA 218550.953125 1 NA +"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C20H14O7" 451.115 -0.624494567969591 "1" NA 135964.078125 0.622116152690652 NA +"Caffeic acid" "QAIPRVGONGVQAS-DUXPYHPUSA-N" "C9H8O4" NA 109.101 NA "1" NA 1663.78308105469 1 NA +"Caffeic acid" "QAIPRVGONGVQAS-DUXPYHPUSA-N" "C9H8O4" NA 140.951 NA "1" NA 1119.27758789062 0.672730478291135 NA +"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" NA 55.575 NA "1" NA 959.281677246094 0.00801122428782145 NA +"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" NA 278.081 NA "1" NA 49810.07421875 0.415977585963074 NA +"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" "C17H11NO3" 323.106 -0.610124713635454 "1" 1 119742.20703125 1 TRUE +"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA 51.94 NA "1" NA 1706.40014648438 0.0178528316194543 NA +"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" "C5H6" 67.054 -3.38002342189334 "1" NA 1413.32275390625 0.0147865746503924 NA +"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA 122.059 NA "1" NA 40171.04296875 0.420280593374599 NA +"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" "C7H7NO" 135.117 -8.52289540743972 "1" NA 95581.484375 1 NA +"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA 232.845 NA "1" NA 17855.763671875 0.186811952007572 NA +"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA 135.071 NA "1" NA 1388.24841308594 0.0111932237930481 NA +"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA 177.092 NA "1" NA 1346.46130371094 0.0108563010474573 NA +"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA 205.034 NA "1" NA 1612.63024902344 0.0130023784667138 NA +"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" "C12H8O4" 217.015 NA "1" NA 124025.7890625 1 NA
--- a/test-data/smol/out-smol-delta-8.542.tsv Fri Aug 05 17:25:45 2022 +0000 +++ b/test-data/smol/out-smol-delta-8.542.tsv Fri Sep 30 16:18:56 2022 +0000 @@ -1,20 +1,20 @@ "compoundName" "inchikey" "elemcomposition" "fragment" "fragment_mz" "ppm" "fileid" "CorWithPrecursor" "AbsoluteIntensity" "relativeIntensity" "corValid" -"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C13H8O4" "229" 2.02930325023702 "1" NA 203723.75 0.932156767504374 NA -"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" NA "312" NA "1" NA 3981.51538085938 0.0182177900573243 NA -"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" NA "313" NA "1" NA 7264.93603515625 0.0332413834452649 NA -"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C17H12O6" "367" -8.51110969664126 "1" NA 218550.953125 1 NA -"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C20H14O7" "451" -0.624494567969591 "1" NA 135964.078125 0.622116152690652 NA -"Caffeic acid" "QAIPRVGONGVQAS-DUXPYHPUSA-N" "C9H8O4" NA "109" NA "1" NA 1663.78308105469 1 NA -"Caffeic acid" "QAIPRVGONGVQAS-DUXPYHPUSA-N" "C9H8O4" NA "141" NA "1" NA 1119.27758789062 0.672730478291135 NA -"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" NA "56" NA "1" NA 959.281677246094 0.00801122428782145 NA -"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" NA "278" NA "1" NA 49810.07421875 0.415977585963074 NA -"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" "C17H11NO3" "323" -0.610124713635454 "1" 1 119742.20703125 1 TRUE -"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA "52" NA "1" NA 1706.40014648438 0.0178528316194543 NA -"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" "C5H6" "67" -3.38002342189334 "1" NA 1413.32275390625 0.0147865746503924 NA -"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA "122" NA "1" NA 40171.04296875 0.420280593374599 NA -"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" "C7H7NO" "135" -8.52289540743972 "1" NA 95581.484375 1 NA -"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA "233" NA "1" NA 17855.763671875 0.186811952007572 NA -"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA "135" NA "1" NA 1388.24841308594 0.0111932237930481 NA -"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA "177" NA "1" NA 1346.46130371094 0.0108563010474573 NA -"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA "205" NA "1" NA 1612.63024902344 0.0130023784667138 NA -"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA "217" NA "1" NA 124025.7890625 1 NA +"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C13H8O4" 229.05 2.02930325023702 "1" NA 203723.75 0.932156767504374 NA +"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" NA 312.059 NA "1" NA 3981.51538085938 0.0182177900573243 NA +"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" NA 313.068 NA "1" NA 7264.93603515625 0.0332413834452649 NA +"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C17H12O6" 367.081 -8.51110969664126 "1" NA 218550.953125 1 NA +"Orientin" "PLAPMLGJVGLZOV-VPRICQMDSA-N" "C21H20O11" "C20H14O7" 451.115 -0.624494567969591 "1" NA 135964.078125 0.622116152690652 NA +"Caffeic acid" "QAIPRVGONGVQAS-DUXPYHPUSA-N" "C9H8O4" NA 109.101 NA "1" NA 1663.78308105469 1 NA +"Caffeic acid" "QAIPRVGONGVQAS-DUXPYHPUSA-N" "C9H8O4" NA 140.951 NA "1" NA 1119.27758789062 0.672730478291135 NA +"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" NA 55.575 NA "1" NA 959.281677246094 0.00801122428782145 NA +"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" NA 278.081 NA "1" NA 49810.07421875 0.415977585963074 NA +"Berberine" "YBHILYKTIRIUTE-UHFFFAOYSA-N" "C20H18NO4+" "C17H11NO3" 323.106 -0.610124713635454 "1" 1 119742.20703125 1 TRUE +"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA 51.94 NA "1" NA 1706.40014648438 0.0178528316194543 NA +"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" "C5H6" 67.054 -3.38002342189334 "1" NA 1413.32275390625 0.0147865746503924 NA +"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA 122.059 NA "1" NA 40171.04296875 0.420280593374599 NA +"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" "C7H7NO" 135.117 -8.52289540743972 "1" NA 95581.484375 1 NA +"Theobromine " "YAPQBXQYLJRXSA-UHFFFAOYSA-N" "C7H8N4O2" NA 232.845 NA "1" NA 17855.763671875 0.186811952007572 NA +"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA 135.071 NA "1" NA 1388.24841308594 0.0111932237930481 NA +"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA 177.092 NA "1" NA 1346.46130371094 0.0108563010474573 NA +"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA 205.034 NA "1" NA 1612.63024902344 0.0130023784667138 NA +"Bergapten " "BGEBZHIAGXMEMV-UHFFFAOYSA-N" "C12H8O4" NA 217.015 NA "1" NA 124025.7890625 1 NA