| Next changeset 1:61ebae7e09f5 (2019-12-05) |
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Commit message:
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty" |
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added:
averageFragSpectra.R combineAnnotations.R createDatabase.R createMSP.R dbconfig.R dimsPredictPuritySingle.R filterFragSpectra.R flagRemove.R frag4feature.R frag4feature.xml macros.xml purityA.R purityX.R spectralMatching.R test-data/LCMSMS_1.mzML test-data/LCMSMS_2.mzML test-data/LCMS_1.mzML test-data/LCMS_2.mzML test-data/PR100037.sqlite test-data/PR100037.txt test-data/averageFragSpectra_output_all.RData test-data/averageFragSpectra_output_all.tsv test-data/averageFragSpectra_output_all_only.RData test-data/averageFragSpectra_output_all_only.tsv test-data/averageFragSpectra_output_inter.RData test-data/averageFragSpectra_output_inter.tsv test-data/averageFragSpectra_output_intra.RData test-data/averageFragSpectra_output_intra.tsv test-data/combineAnnotations_combined_annotations.sqlite test-data/combineAnnotations_combined_annotations.tsv test-data/combineAnnotations_input_beams.tsv test-data/combineAnnotations_input_metfrag.tsv test-data/combineAnnotations_input_probmetab.tsv test-data/combineAnnotations_input_sirus_csifingerid.tsv test-data/combinedAnnotation_input_spectralMatching.sqlite test-data/createDatabase_output.sqlite test-data/createDatabase_output_eic.sqlite test-data/createMSP_input_metadata.tsv test-data/createMSP_output_av_all.msp test-data/createMSP_output_av_all_and_all_xcms.msp test-data/createMSP_output_av_all_metadata.msp test-data/createMSP_output_av_inter.msp test-data/createMSP_output_av_intra.msp test-data/createMSP_output_max.msp test-data/createMSP_output_scans_all.msp test-data/dimsPredictPuritySingle_full_scan.mzML test-data/dimsPredictPuritySingle_input_dimspy_peakmatrix.tsv test-data/dimsPredictPuritySingle_output.tsv test-data/filterFragSpectra_output.RData test-data/filterFragSpectra_output_frag.tsv test-data/filterFragSpectra_output_prec.tsv test-data/flagRemove_input.RData test-data/flagRemove_output.tsv test-data/frag4feature_output.RData test-data/frag4feature_output.tsv test-data/metab_compound_subset.sqlite test-data/purityA_output.RData test-data/purityA_output.tsv test-data/purityX_output.Rdata test-data/purityX_output.tsv test-data/spectralMatching_db_with_spectral_matching.sqlite test-data/spectralMatching_db_with_spectral_matching_instrumentTypes.sqlite test-data/spectralMatching_input_massbank_test.sqlite test-data/spectralMatching_matched_results.tsv test-data/spectralMatching_matched_results_instrumentTypes.tsv test-data/spectralMatching_xcms_matched_results.tsv test-data/spectralMatching_xcms_matched_results_instrumentTypes.tsv test-data/xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData |
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| diff -r 000000000000 -r ab65999a5430 averageFragSpectra.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/averageFragSpectra.R Wed Nov 27 14:23:10 2019 -0500 |
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| @@ -0,0 +1,165 @@ +library(optparse) +library(msPurity) +library(xcms) +print(sessionInfo()) + + +get_av_spectra <- function(x){ + + if (length(x$av_intra)>0){ + av_intra_df <- plyr::ldply(x$av_intra) + + if (nrow(av_intra_df)==0){ + av_intra_df <- NULL + }else{ + av_intra_df$method <- 'intra' + } + + }else{ + av_intra_df <- NULL + } + + if ((is.null(x$av_inter)) || (nrow(x$av_inter)==0)){ + av_inter_df <- NULL + }else{ + av_inter_df <- x$av_inter + av_inter_df$method <- 'inter' + } + + if ((is.null(x$av_all)) || (nrow(x$av_all)==0)){ + av_all_df <- NULL + }else{ + av_all_df <- x$av_all + av_all_df$method <- 'all' + } + + combined <- plyr::rbind.fill(av_intra_df, av_inter_df, av_all_df) + + return(combined) +} + + +option_list <- list( + make_option("--out_rdata", type="character"), + make_option("--out_peaklist", type="character"), + make_option("--pa", type="character"), + + make_option("--av_level", type="character"), + + make_option("--minfrac", default=0.5), + make_option("--minnum", default=1), + make_option("--ppm", default=5.0), + + make_option("--snr", default=0), + + make_option("--ra", default=0), + + make_option("--av", default="median", type="character"), + make_option("--sumi", action="store_true"), + + make_option("--rmp", action="store_true"), + make_option("--cores", default=1) +) + +opt <- parse_args(OptionParser(option_list=option_list)) +print(opt) + + +loadRData <- function(rdata_path, name){ +#loads an RData file, and returns the named xset object if it is there + load(rdata_path) + return(get(ls()[ls() %in% name])) +} + +# Requires +pa <- loadRData(opt$pa, 'pa') + +pa@cores <- opt$cores + +if(is.null(opt$rmp)){ + rmp = FALSE +}else{ + rmp = TRUE +} + +if(is.null(opt$sumi)){ + + sumi = FALSE +}else{ + sumi = TRUE + +} + + +if(opt$av_level=="intra"){ + + pa <- msPurity::averageIntraFragSpectra(pa, + minfrac=opt$minfrac, + minnum=opt$minnum, + ppm=opt$ppm, + snr=opt$snr, + ra=opt$ra, + av=opt$av, + sumi=sumi, + rmp=rmp, + cores=opt$cores) + +} else if(opt$av_level=="inter"){ + + pa <- msPurity::averageInterFragSpectra(pa, + minfrac=opt$minfrac, + minnum=opt$minnum, + ppm=opt$ppm, + snr=opt$snr, + ra=opt$ra, + av=opt$av, + sumi=sumi, + rmp=rmp, + cores=opt$cores) +} else if(opt$av_level=="all"){ + + pa <- msPurity::averageAllFragSpectra(pa, + minfrac=opt$minfrac, + minnum=opt$minnum, + ppm=opt$ppm, + snr=opt$snr, + ra=opt$ra, + av=opt$av, + sumi=sumi, + rmp=rmp, + cores=opt$cores) + +} + +print(pa) +save(pa, file=opt$out_rdata) + + +if (length(pa)>0){ + + av_spectra <- plyr::ldply(pa@av_spectra, get_av_spectra) + + if (nrow(av_spectra)==0){ + message('No average spectra available') + } else{ + colnames(av_spectra)[1] <- 'grpid' + av_spectra$grpid <- names(pa@av_spectra)[av_spectra$grpid] + + if((length(pa@av_intra_params)>0) || (length(pa@av_inter_params)>0) ){ + # Add some extra info (only required if av_intra or av_inter performed) + colnames(av_spectra)[2] <- 'fileid' + av_spectra$avid <- 1:nrow(av_spectra) + + filenames <- sapply(av_spectra$fileid, function(x) names(pa@fileList)[as.integer(x)]) + # filenames_galaxy <- sapply(av_spectra$fileid, function(x) basename(pa@fileList[as.integer(x)])) + + av_spectra = as.data.frame(append(av_spectra, list(filename = filenames), after=2)) + } + + + print(head(av_spectra)) + write.table(av_spectra, opt$out_peaklist, row.names=FALSE, sep='\t') + + } +} + |
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| diff -r 000000000000 -r ab65999a5430 combineAnnotations.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/combineAnnotations.R Wed Nov 27 14:23:10 2019 -0500 |
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| @@ -0,0 +1,103 @@ +library(optparse) +library(msPurity) +print(sessionInfo()) + +# Get the parameter +option_list <- list( + make_option(c("-s","--sm_resultPth"),type="character"), + make_option(c("-m","--metfrag_resultPth"),type="character"), + make_option(c("-c","--sirius_csi_resultPth"),type="character"), + make_option(c("-p","--probmetab_resultPth"),type="character"), + make_option(c("-l","--ms1_lookup_resultPth"),type="character"), + + make_option("--ms1_lookup_checkAdducts", action="store_true"), + make_option("--ms1_lookup_keepAdducts", type="character", default=NA), + make_option("--ms1_lookup_dbSource", type="character", default="hmdb"), + + make_option("--sm_weight", type="numeric"), + make_option("--metfrag_weight", type="numeric"), + make_option("--sirius_csi_weight", type="numeric"), + make_option("--probmetab_weight", type="numeric"), + make_option("--ms1_lookup_weight", type="numeric"), + make_option("--biosim_weight", type="numeric"), + + make_option("--create_new_database", action="store_true"), + make_option("--outdir", type="character", default="."), + + make_option("--compoundDbType", type="character", default="sqlite"), + make_option("--compoundDbPth", type="character", default=NA), + make_option("--compoundDbHost", type="character", default=NA) +) +opt <- parse_args(OptionParser(option_list=option_list)) + +print(opt) + +if (!is.null(opt$create_new_database)){ + sm_resultPth <- file.path(opt$outdir, 'combined_annotations.sqlite') + file.copy(opt$sm_resultPth, sm_resultPth) +}else{ + sm_resultPth <- opt$sm_resultPth +} + +if (is.null(opt$ms1_lookup_checkAdducts)){ + opt$ms1_lookup_checkAdducts <- FALSE +} +if (!is.null(opt$ms1_lookup_keepAdducts)){ + opt$ms1_lookup_keepAdducts <- gsub("__ob__", "[", opt$ms1_lookup_keepAdducts) + opt$ms1_lookup_keepAdducts <- gsub("__cb__", "]", opt$ms1_lookup_keepAdducts) + ms1_lookup_keepAdducts <- strsplit(opt$ms1_lookup_keepAdducts, ",")[[1]] +} + +weights <-list('sm'=opt$sm_weight, + 'metfrag'=opt$metfrag_weight, + 'sirius_csifingerid'= opt$sirius_csi_weight, + 'probmetab'=opt$probmetab_weight, + 'ms1_lookup'=opt$ms1_lookup_weight, + 'biosim'=opt$biosim_weight + ) +print(weights) +if (round(!sum(unlist(weights),0)==1)){ + + stop(paste0('The weights should sum to 1 not ', sum(unlist(weights)))) +} + +if (opt$compoundDbType=='local_config'){ + # load in compound config + # Soure local function taken from workflow4metabolomics + source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } + source_local("dbconfig.R") +}else{ + compoundDbPth = opt$compoundDbPth + compoundDbType = opt$compoundDbType + compoundDbName = NA + compoundDbHost = NA + compoundDbPort = NA + compoundDbUser = NA + compoundDbPass = NA +} + + + +summary_output <- msPurity::combineAnnotations( + sm_resultPth = sm_resultPth, + compoundDbPth = compoundDbPth, + metfrag_resultPth = opt$metfrag_resultPth, + sirius_csi_resultPth = opt$sirius_csi_resultPth, + probmetab_resultPth = opt$probmetab_resultPth, + ms1_lookup_resultPth = opt$ms1_lookup_resultPth, + ms1_lookup_keepAdducts = ms1_lookup_keepAdducts, + ms1_lookup_checkAdducts = opt$ms1_lookup_checkAdducts, + + compoundDbType = compoundDbType, + compoundDbName = compoundDbName, + compoundDbHost = compoundDbHost, + compoundDbPort = compoundDbPort, + compoundDbUser = compoundDbUser, + compoundDbPass = compoundDbPass, + weights = weights) + +write.table(summary_output, file.path(opt$outdir, 'combined_annotations.tsv'), sep = '\t', row.names = FALSE) + + +closeAllConnections() + |
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| diff -r 000000000000 -r ab65999a5430 createDatabase.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/createDatabase.R Wed Nov 27 14:23:10 2019 -0500 |
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| @@ -0,0 +1,167 @@ +library(msPurity) +library(optparse) +library(xcms) +library(CAMERA) +print(sessionInfo()) +print('CREATING DATABASE') + +xset_pa_filename_fix <- function(opt, pa, xset){ + + if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){ + # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables + # needs to be done due to Galaxy moving the files around and screwing up any links to files + + filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]]) + filepaths <- filepaths[filepaths != ""] + new_names <- basename(filepaths) + + galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]]) + galaxy_names <- galaxy_names[galaxy_names != ""] + + nsave <- names(pa@fileList) + old_filenames <- basename(pa@fileList) + pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)] + names(pa@fileList) <- nsave + + pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)]) + pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)]) + } + + + if(!all(basename(pa@fileList)==basename(xset@filepaths))){ + if(!all(names(pa@fileList)==basename(xset@filepaths))){ + print('FILELISTS DO NOT MATCH') + message('FILELISTS DO NOT MATCH') + quit(status = 1) + }else{ + xset@filepaths <- unname(pa@fileList) + } + } + + print(xset@phenoData) + print(xset@filepaths) + + return(list(pa, xset)) +} + + + + +option_list <- list( + make_option(c("-o", "--outDir"), type="character"), + make_option("--pa", type="character"), + make_option("--xset_xa", type="character"), + make_option("--xcms_camera_option", type="character"), + make_option("--eic", action="store_true"), + make_option("--cores", default=4), + make_option("--mzML_files", type="character"), + make_option("--galaxy_names", type="character"), + make_option("--grpPeaklist", type="character") +) + + +# store options +opt<- parse_args(OptionParser(option_list=option_list)) +print(opt) + +loadRData <- function(rdata_path, name){ +#loads an RData file, and returns the named xset object if it is there + load(rdata_path) + return(get(ls()[ls() %in% name])) +} + +getxcmsSetObject <- function(xobject) { + # XCMS 1.x + if (class(xobject) == "xcmsSet") + return (xobject) + # XCMS 3.x + if (class(xobject) == "XCMSnExp") { + # Get the legacy xcmsSet object + suppressWarnings(xset <- as(xobject, 'xcmsSet')) + sampclass(xset) <- xset@phenoData$sample_group + return (xset) + } +} + + +print(paste('pa', opt$pa)) +print(opt$xset) + +print(opt$xcms_camera_option) +# Requires +pa <- loadRData(opt$pa, 'pa') + + +print(pa@fileList) + + + +if (opt$xcms_camera_option=='xcms'){ + + xset <- loadRData(opt$xset, c('xset','xdata')) + xset <- getxcmsSetObject(xset) + fix <- xset_pa_filename_fix(opt, pa, xset) + pa <- fix[[1]] + xset <- fix[[2]] + xa <- NULL +}else{ + + xa <- loadRData(opt$xset, 'xa') + fix <- xset_pa_filename_fix(opt, pa, xa@xcmsSet) + pa <- fix[[1]] + xa@xcmsSet <- fix[[2]] + xset <- NULL +} + + + +if(is.null(opt$grp_peaklist)){ + grpPeaklist = NA +}else{ + grpPeaklist = opt$grp_peaklist +} + + + +dbPth <- msPurity::createDatabase(pa, + xset=xset, + xsa=xa, + outDir=opt$outDir, + grpPeaklist=grpPeaklist, + dbName='createDatabase_output.sqlite' +) + + + + + +if (!is.null(opt$eic)){ + + if (is.null(xset)){ + xset <- xa@xcmsSet + } + # previous check should have matched filelists together + xset@filepaths <- unname(pa@fileList) + + convert2Raw <- function(x, xset){ + sid <- unique(x$sample) + # for each file get list of peaks + x$rt_raw <- xset@rt$raw[[sid]][match(x$rt, xset@rt$corrected[[sid]])] + x$rtmin_raw <- xset@rt$raw[[sid]][match(x$rtmin, xset@rt$corrected[[sid]])] + x$rtmax_raw <- xset@rt$raw[[sid]][match(x$rtmax, xset@rt$corrected[[sid]])] + return(x) + + } + + xset@peaks <- as.matrix(plyr::ddply(data.frame(xset@peaks), ~ sample, convert2Raw, xset=xset)) + + # Saves the EICS into the previously created database + px <- msPurity::purityX(xset, + saveEIC = TRUE, + cores=1, + sqlitePth=dbPth, + rtrawColumns = TRUE) + +} + +closeAllConnections() |
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| diff -r 000000000000 -r ab65999a5430 createMSP.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/createMSP.R Wed Nov 27 14:23:10 2019 -0500 |
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| @@ -0,0 +1,102 @@ +library(optparse) +library(msPurity) +print(sessionInfo()) + +# Get the parameter +option_list <- list( + make_option("--rdata_input",type="character"), + make_option("--method",type="character"), + make_option("--metadata",type="character"), + make_option("--metadata_cols",type="character"), + make_option("--metadata_cols_filter",type="character"), + make_option("--adduct_split", action="store_true"), + make_option("--xcms_groupids",type="character"), + make_option("--filter",action="store_true"), + make_option("--intensity_ra",type="character"), + make_option("--include_adducts",type="character"), + make_option("--msp_schema",type="character"), + make_option("--out_dir",type="character", default=".") +) +opt <- parse_args(OptionParser(option_list=option_list)) + +print(opt) + +load(opt$rdata_input) + +if (is.null(opt$metadata)){ + metadata <- NULL +}else{ + metadata <- read.table(opt$metadata, header = TRUE, sep='\t', stringsAsFactors = FALSE, check.names = FALSE) + + if(!opt$metadata_cols_filter==''){ + metadata_cols_filter <- strsplit(opt$metadata_cols_filter, ',')[[1]] + + metadata <- metadata[,metadata_cols_filter, drop=FALSE] + print(metadata) + + if (!"grpid" %in% colnames(metadata)){ + metadata$grpid <- 1:nrow(metadata) + } + + print(metadata) + + } + +} + + + +if (is.null(opt$metadata_cols) || opt$metadata_cols==''){ + metadata_cols <- NULL +}else{ + metadata_cols <- opt$metadata_cols + +} + + +if(is.null(opt$adduct_split)){ + adduct_split <- FALSE +}else{ + adduct_split <- TRUE +} + +if (is.null(opt$xcms_groupids)){ + xcms_groupids <- NULL +}else{ + xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ',')[[1]]) +} + +if (opt$include_adducts=='None'){ + include_adducts <- '' +}else{ + include_adducts <- opt$include_adducts + include_adducts <- gsub("__ob__", "[", include_adducts) + include_adducts <- gsub("__cb__", "]", include_adducts) + include_adducts <- trimws(include_adducts) + + include_adducts <- gsub(",", " ", include_adducts) + +} + + +if(is.null(opt$filter)){ + filter <- FALSE +}else{ + filter <- TRUE +} + + + +msPurity::createMSP(pa, + msp_file_pth = file.path(opt$out_dir, 'lcmsms_spectra.msp'), + metadata = metadata, + metadata_cols = metadata_cols, + method = opt$method, + adduct_split = adduct_split, + xcms_groupids = xcms_groupids, + filter = filter, + intensity_ra=opt$intensity_ra, + include_adducts=include_adducts, + msp_schema=opt$msp_schema) + +print('msp created') |
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| diff -r 000000000000 -r ab65999a5430 dbconfig.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dbconfig.R Wed Nov 27 14:23:10 2019 -0500 |
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| @@ -0,0 +1,22 @@ +compoundDbType <- 'mysql' +compoundDbPth <- NA +compoundDbName <- 'metab_compound' +compoundDbPort <- '3306' +compoundDbUser <- 'metab_compound' +compoundDbPass <- 'metab_compound' + +q_dbPth <- NA +q_dbType <- NA +q_dbHost <- NA +q_dbPort <- NA +q_dbUser <- NA +q_dbName <- NA +q_dbPass <- NA + +l_dbPth <- NA +l_dbType <- NA +l_dbHost <- NA +l_dbPort <- NA +l_dbUser <- NA +l_dbName <- NA +l_dbPass <- NA |
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| diff -r 000000000000 -r ab65999a5430 dimsPredictPuritySingle.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dimsPredictPuritySingle.R Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| @@ -0,0 +1,163 @@ +library(msPurity) +library(optparse) +print(sessionInfo()) + +option_list <- list( + make_option(c("--mzML_file"), type="character"), + make_option(c("--mzML_files"), type="character"), + make_option(c("--mzML_filename"), type="character", default=''), + make_option(c("--mzML_galaxy_names"), type="character", default=''), + make_option(c("--peaks_file"), type="character"), + make_option(c("-o", "--out_dir"), type="character"), + make_option("--minoffset", default=0.5), + make_option("--maxoffset", default=0.5), + make_option("--ilim", default=0.05), + make_option("--ppm", default=4), + make_option("--dimspy", action="store_true"), + make_option("--sim", action="store_true"), + make_option("--remove_nas", action="store_true"), + make_option("--iwNorm", default="none", type="character"), + make_option("--file_num_dimspy", default=1), + make_option("--exclude_isotopes", action="store_true"), + make_option("--isotope_matrix", type="character") +) + +# store options +opt<- parse_args(OptionParser(option_list=option_list)) + +print(sessionInfo()) +print(opt) + +print(opt$mzML_files) +print(opt$mzML_galaxy_names) + +str_to_vec <- function(x){ + print(x) + x <- trimws(strsplit(x, ',')[[1]]) + return(x[x != ""]) +} + +find_mzml_file <- function(mzML_files, galaxy_names, mzML_filename){ + mzML_filename <- trimws(mzML_filename) + mzML_files <- str_to_vec(mzML_files) + galaxy_names <- str_to_vec(galaxy_names) + if (mzML_filename %in% galaxy_names){ + return(mzML_files[galaxy_names==mzML_filename]) + }else{ + stop(paste("mzML file not found - ", mzML_filename)) + } +} + + +if (is.null(opt$dimspy)){ + df <- read.table(opt$peaks_file, header = TRUE, sep='\t') + if (file.exists(opt$mzML_file)){ + mzML_file <- opt$mzML_file + }else if (!is.null(opt$mzML_files)){ + mzML_file <- find_mzml_file(opt$mzML_files, opt$mzML_galaxy_names, + opt$mzML_filename) + }else{ + mzML_file <- file.path(opt$mzML_file, filename) + } +}else{ + indf <- read.table(opt$peaks_file, + header = TRUE, sep='\t', stringsAsFactors = FALSE) + + filename <- colnames(indf)[8:ncol(indf)][opt$file_num_dimspy] + print(filename) + # check if the data file is mzML or RAW (can only use mzML currently) so + # we expect an mzML file of the same name in the same folder + indf$i <- indf[,colnames(indf)==filename] + indf[,colnames(indf)==filename] <- as.numeric(indf[,colnames(indf)==filename]) + + filename = sub("raw", "mzML", filename, ignore.case = TRUE) + print(filename) + + + if (file.exists(opt$mzML_file)){ + mzML_file <- opt$mzML_file + }else if (!is.null(opt$mzML_files)){ + mzML_file <- find_mzml_file(opt$mzML_files, opt$mzML_galaxy_names, filename) + }else{ + mzML_file <- file.path(opt$mzML_file, filename) + } + + # Update the dimspy output with the correct information + df <- indf[4:nrow(indf),] + if ('blank_flag' %in% colnames(df)){ + df <- df[df$blank_flag==1,] + } + colnames(df)[colnames(df)=='m.z'] <- 'mz' + + if ('nan' %in% df$mz){ + df[df$mz=='nan',]$mz <- NA + } + df$mz <- as.numeric(df$mz) +} + +if (!is.null(opt$remove_nas)){ + df <- df[!is.na(df$mz),] +} + +if (is.null(opt$isotope_matrix)){ + im <- NULL +}else{ + im <- read.table(opt$isotope_matrix, + header = TRUE, sep='\t', stringsAsFactors = FALSE) +} + +if (is.null(opt$exclude_isotopes)){ + isotopes <- FALSE +}else{ + isotopes <- TRUE +} + +if (is.null(opt$sim)){ + sim=FALSE +}else{ + sim=TRUE +} + +minOffset = as.numeric(opt$minoffset) +maxOffset = as.numeric(opt$maxoffset) + +if (opt$iwNorm=='none'){ + iwNorm = FALSE + iwNormFun = NULL +}else if (opt$iwNorm=='gauss'){ + iwNorm = TRUE + iwNormFun = msPurity::iwNormGauss(minOff=-minOffset, maxOff=maxOffset) +}else if (opt$iwNorm=='rcosine'){ + iwNorm = TRUE + iwNormFun = msPurity::iwNormRcosine(minOff=-minOffset, maxOff=maxOffset) +}else if (opt$iwNorm=='QE5'){ + iwNorm = TRUE + iwNormFun = msPurity::iwNormQE.5() +} + +print('FIRST ROWS OF PEAK FILE') +print(head(df)) +print(mzML_file) +predicted <- msPurity::dimsPredictPuritySingle(df$mz, + filepth=mzML_file, + minOffset=minOffset, + maxOffset=maxOffset, + ppm=opt$ppm, + mzML=TRUE, + sim = sim, + ilim = opt$ilim, + isotopes = isotopes, + im = im, + iwNorm = iwNorm, + iwNormFun = iwNormFun + ) +predicted <- cbind(df, predicted) + +print(head(predicted)) +print(file.path(opt$out_dir, 'dimsPredictPuritySingle_output.tsv')) + +write.table(predicted, + file.path(opt$out_dir, 'dimsPredictPuritySingle_output.tsv'), + row.names=FALSE, sep='\t') + + |
| b |
| diff -r 000000000000 -r ab65999a5430 filterFragSpectra.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filterFragSpectra.R Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| @@ -0,0 +1,100 @@ +library(optparse) +library(msPurity) +library(xcms) +print(sessionInfo()) + + +option_list <- list( + make_option("--out_rdata", type="character"), + make_option("--out_peaklist_prec", type="character"), + make_option("--out_peaklist_frag", type="character"), + make_option("--pa", type="character"), + + make_option("--ilim", default=0.0), + make_option("--plim", default=0.0), + + make_option("--ra", default=0.0), + make_option("--snr", default=0.0), + + make_option("--rmp", action="store_true"), + make_option("--snmeth", default="median", type="character") +) + +opt <- parse_args(OptionParser(option_list=option_list)) +print(opt) + + +loadRData <- function(rdata_path, name){ + #loads an RData file, and returns the named xset object if it is there + load(rdata_path) + return(get(ls()[ls() %in% name])) +} + +# Requires +pa <- loadRData(opt$pa, 'pa') + +if(is.null(opt$rmp)){ + opt$rmp = FALSE +}else{ + opt$rmp = TRUE +} + +pa <- filterFragSpectra(pa, + ilim=opt$ilim, + plim=opt$plim, + ra=opt$ra, + snr=opt$snr, + rmp=opt$rmp, + snmeth=opt$snmeth) + +print(pa) +save(pa, file=opt$out_rdata) + +# get the msms data for grpid from the purityA object +msmsgrp <- function(grpid, pa){ + msms <- pa@grped_ms2[grpid] + + grpinfo <- pa@grped_df[pa@grped_df$grpid==grpid,] + + grpinfo$subsetid <- 1:nrow(grpinfo) + result <- plyr::ddply(grpinfo, ~subsetid, setid, msms=msms) + return(result) +} + +# Set the relevant details +setid <- function(grpinfo_i, msms){ + msms_i <- msms[[1]][[grpinfo_i$subsetid]] + n <- nrow(msms_i) + msms_i <- data.frame(msms_i) + colnames(msms_i)[1:2] <- c('mz', 'i') + m <- cbind('grpid'=rep(grpinfo_i$grpid,n), 'pid'=rep(grpinfo_i$pid,n), 'fileid'=rep(grpinfo_i$fileid,n), msms_i) + return(m) +} + + + +if (length(pa)>0){ + + if (length(pa@grped_ms2)==0){ + message('No spectra available') + } else{ + + # get group ids + grpids <- unique(as.character(pa@grped_df$grpid)) + + # loop through all the group ids + df_fragments = plyr::adply(grpids, 1, msmsgrp, pa=pa) + df_fragments = merge(df_fragments, pa@puritydf[,c("pid", "acquisitionNum", "precursorScanNum")], by="pid") + df_fragments = df_fragments[order(df_fragments$grpid, df_fragments$pid, df_fragments$mz),] + #select and reorder columns + df_fragments = df_fragments[,c("grpid", "pid", "precursorScanNum", "acquisitionNum", "fileid", "mz", "i", "snr", "ra", "purity_pass_flag", "intensity_pass_flag", "ra_pass_flag", "snr_pass_flag", "pass_flag")] + + pa@grped_df$filename = sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)]) + + print(head(pa@grped_df)) + write.table(pa@grped_df, opt$out_peaklist_prec, row.names=FALSE, sep='\t') + print(head(df_fragments)) + write.table(df_fragments, opt$out_peaklist_frag, row.names=FALSE, sep='\t') + } +} + |
| b |
| diff -r 000000000000 -r ab65999a5430 flagRemove.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flagRemove.R Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| @@ -0,0 +1,204 @@ +library(msPurity) +library(optparse) +print(sessionInfo()) +option_list <- list( + make_option(c("-o", "--out_dir"), type="character", default=getwd(), + help="Output folder for resulting files [default = %default]" + ), + make_option(c("-x", "--xset_path"), type="character", default=file.path(getwd(),"xset.rds"), + help="The path to the xcmsSet object [default = %default]" + ), + make_option("--polarity", default=NA, + help="polarity (just used for naming purpose for files being saved) [positive, negative, NA] [default %default]" + ), + make_option("--rsd_i_blank", default=100, + help="RSD threshold for the blank [default = %default]" + ), + make_option("--minfrac_blank", default=0.5, + help="minimum fraction of files for features needed for the blank [default = %default]" + ), + make_option("--rsd_rt_blank", default=100, + help="RSD threshold for the RT of the blank [default = %default]" + ), + + make_option("--ithres_blank", default=0, + help="Intensity threshold for the blank [default = %default]" + ), + make_option("--s2b", default=10, + help="fold change (sample/blank) needed for sample peak to be allowed. e.g. + if s2b set to 10 and the recorded sample 'intensity' value was 100 and blank was 10. + 1000/10 = 100, so sample has fold change higher than the threshold and the peak + is not considered a blank [default = %default]" + ), + make_option("--blank_class", default='blank', type="character", + help="A string representing the class that will be used for the blank.[default = %default]" + ), + make_option("--egauss_thr", default=NA, + help="Threshold for filtering out non gaussian shaped peaks. Note this only works + if the 'verbose columns' and 'fit gauss' was used with xcms + [default = %default]" + ), + make_option("--rsd_i_sample", default=100, + help="RSD threshold for the samples [default = %default]" + ), + make_option("--minfrac_sample", default=0.8, + help="minimum fraction of files for features needed for the samples [default = %default]" + ), + make_option("--rsd_rt_sample", default=100, + help="RSD threshold for the RT of the samples [default = %default]" + ), + make_option("--ithres_sample", default=5000, + help="Intensity threshold for the sample [default = %default]" + ), + make_option("--grp_rm_ids", default=NA, + help="vector of grouped_xcms peaks to remove (corresponds to the row from xcms::group output) + [default = %default]" + ), + make_option("--remove_spectra", action="store_true", + help=" TRUE if flagged spectra is to be removed [default = %default]" + ), + make_option("--minfrac_xcms", default=0.5, + help="minfrac for xcms grouping [default = %default]" + ), + make_option("--mzwid", default=0.001, + help="mzwid for xcms grouping [default = %default]" + ), + make_option("--bw", default=5, + help="bw for xcms grouping [default = %default]" + ), + + make_option("--temp_save", action="store_true", + help="Assign True if files for each step saved (for testing purposes) [default = %default]" + ), + + make_option("--samplelist", type="character", help="Sample list to determine the blank class") + + + + + +) + + #make_option("--multilist", action="store_true" + # help="NOT CURRENTLY IMPLEMENTED: If paired blank removal is to be performed a - multilist - sample list file has to be provided" + #), + +# store options +opt<- parse_args(OptionParser(option_list=option_list)) + +opt <- replace(opt, opt == "NA", NA) + + + + +if (is.null(opt$temp_save)){ + temp_save<-FALSE +}else{ + temp_save<-TRUE +} + +if (is.null(opt$remove_spectra)){ + remove_spectra<-FALSE +}else{ + remove_spectra<-TRUE +} + + +print(opt) + +getxcmsSetObject <- function(xobject) { + # XCMS 1.x + if (class(xobject) == "xcmsSet") + return (xobject) + # XCMS 3.x + if (class(xobject) == "XCMSnExp") { + # Get the legacy xcmsSet object + suppressWarnings(xset <- as(xobject, 'xcmsSet')) + sampclass(xset) <- xset@phenoData$sample_group + return (xset) + } +} + + +loadRData <- function(rdata_path, name){ +#loads an RData file, and returns the named xset object if it is there + load(rdata_path) + return(get(ls()[ls() %in% name])) +} + +xset <- getxcmsSetObject(loadRData(opt$xset_path, c('xset','xdata'))) + +print(xset) +if (is.null(opt$samplelist)){ + blank_class <- opt$blank_class +}else{ + samplelist <- read.table(opt$samplelist, sep='\t', header=TRUE) + samplelist_blank <- unique(samplelist$sample_class[samplelist$blank=='yes']) + + chosen_blank <- samplelist_blank[samplelist_blank %in% xset@phenoData$class] + if (length(chosen_blank)>1){ + print('ERROR: only 1 blank is currently allowed to be used with this tool') + exit() + } + blank_class <- as.character(chosen_blank) + print(blank_class) +} + + +if (is.null(opt$multilist)){ + ffrm_out <- flag_remove(xset, + pol=opt$polarity, + rsd_i_blank=opt$rsd_i_blank, + minfrac_blank=opt$minfrac_blank, + rsd_rt_blank=opt$rsd_rt_blank, + ithres_blank=opt$ithres_blank, + s2b=opt$s2b, + ref.class=blank_class, + egauss_thr=opt$egauss_thr, + rsd_i_sample=opt$rsd_i_sample, + minfrac_sample=opt$minfrac_sample, + rsd_rt_sample=opt$rsd_rt_sample, + ithres_sample=opt$ithres_sample, + minfrac_xcms=opt$minfrac_xcms, + mzwid=opt$mzwid, + bw=opt$bw, + out_dir=opt$out_dir, + temp_save=temp_save, + remove_spectra=remove_spectra, + grp_rm_ids=unlist(strsplit(as.character(opt$grp_rm_ids), split=", "))[[1]]) + print('flag remove finished') + xset <- ffrm_out[[1]] + grp_peaklist <- ffrm_out[[2]] + removed_peaks <- ffrm_out[[3]] + + save.image(file=file.path(opt$out_dir, 'xset_filtered.RData')) + + # grpid needed for mspurity ID needed for deconrank... (will clean up at some up) + peak_pth <- file.path(opt$out_dir, 'peaklist_filtered.tsv') + print(peak_pth) + write.table(data.frame('grpid'=rownames(grp_peaklist), 'ID'=rownames(grp_peaklist), grp_peaklist), + peak_pth, row.names=FALSE, sep='\t') + + removed_peaks <- data.frame(removed_peaks) + write.table(data.frame('ID'=rownames(removed_peaks),removed_peaks), + file.path(opt$out_dir, 'removed_peaks.tsv'), row.names=FALSE, sep='\t') + +}else{ + + + # TODO + #xsets <- split(xset, multilist_df$multlist) + # + #mult_grps <- unique(multilist_df$multlist) + # + #for (mgrp in mult_grps){ + # xset_i <- xsets[mgrp] + # xcms::group(xset_i, + # + # } + + + +} + + |
| b |
| diff -r 000000000000 -r ab65999a5430 frag4feature.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/frag4feature.R Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| @@ -0,0 +1,160 @@ +library(optparse) +library(msPurity) +library(xcms) +print(sessionInfo()) + +xset_pa_filename_fix <- function(opt, pa, xset=NULL){ + + + if (!is.null(opt$mzML_files) && !is.null(opt$galaxy_names)){ + # NOTE: Relies on the pa@fileList having the names of files given as 'names' of the variables + # needs to be done due to Galaxy moving the files around and screwing up any links to files + + filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]]) + filepaths <- filepaths[filepaths != ""] + new_names <- basename(filepaths) + + galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]]) + galaxy_names <- galaxy_names[galaxy_names != ""] + + nsave <- names(pa@fileList) + old_filenames <- basename(pa@fileList) + + pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)] + names(pa@fileList) <- nsave + + pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)]) + pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)]) + } + print(pa@fileList) + + if(!is.null(xset)){ + + print(xset@filepaths) + + if(!all(basename(pa@fileList)==basename(xset@filepaths))){ + if(!all(names(pa@fileList)==basename(xset@filepaths))){ + print('FILELISTS DO NOT MATCH') + message('FILELISTS DO NOT MATCH') + quit(status = 1) + }else{ + xset@filepaths <- unname(pa@fileList) + } + } + } + + return(list(pa, xset)) +} + + +option_list <- list( + make_option(c("-o", "--out_dir"), type="character"), + make_option("--pa", type="character"), + make_option("--xset", type="character"), + make_option("--ppm", default=10), + make_option("--plim", default=0.0), + make_option("--convert2RawRT", action="store_true"), + make_option("--intense", action="store_true"), + make_option("--createDB", action="store_true"), + make_option("--cores", default=4), + make_option("--mzML_files", type="character"), + make_option("--galaxy_names", type="character"), + make_option("--grp_peaklist", type="character"), + make_option("--useGroup", action="store_true") +) + +# store options +opt<- parse_args(OptionParser(option_list=option_list)) +print(opt) + +loadRData <- function(rdata_path, name){ +#loads an RData file, and returns the named xset object if it is there + load(rdata_path) + return(get(ls()[ls() %in% name])) +} + +# This function retrieve a xset like object +#@author Gildas Le Corguille lecorguille@sb-roscoff.fr +getxcmsSetObject <- function(xobject) { + # XCMS 1.x + if (class(xobject) == "xcmsSet") + return (xobject) + # XCMS 3.x + if (class(xobject) == "XCMSnExp") { + # Get the legacy xcmsSet object + suppressWarnings(xset <- as(xobject, 'xcmsSet')) + sampclass(xset) <- xset@phenoData$sample_group + return (xset) + } +} + +# Requires +pa <- loadRData(opt$pa, 'pa') +xset <- loadRData(opt$xset, c('xset','xdata')) +xset <- getxcmsSetObject(xset) + +pa@cores <- opt$cores + +print(pa@fileList) +print(xset@filepaths) + +if(is.null(opt$intense)){ + intense = FALSE +}else{ + intense = TRUE +} + +if(is.null(opt$convert2RawRT)){ + convert2RawRT = FALSE +}else{ + convert2RawRT= TRUE +} + +if(is.null(opt$createDB)){ + createDB = FALSE +}else{ + createDB = TRUE +} + +if(is.null(opt$useGroup)){ + fix <- xset_pa_filename_fix(opt, pa, xset) + pa <- fix[[1]] + xset <- fix[[2]] + useGroup=FALSE +}else{ + # if are only aligning to the group not eah file we do not need to align the files between the xset and pa object + print('useGroup') + fix <- xset_pa_filename_fix(opt, pa) + pa <- fix[[1]] + useGroup=TRUE +} + + +if(is.null(opt$grp_peaklist)){ + grp_peaklist = NA +}else{ + grp_peaklist = opt$grp_peaklist +} +print(useGroup) + + + +pa <- msPurity::frag4feature(pa=pa, + xset=xset, + ppm=opt$ppm, + plim=opt$plim, + intense=intense, + convert2RawRT=convert2RawRT, + db_name='alldata.sqlite', + out_dir=opt$out_dir, + grp_peaklist=grp_peaklist, + create_db=createDB, + use_group=useGroup) + +print(pa) +save(pa, file=file.path(opt$out_dir, 'frag4feature_output.RData')) + +pa@grped_df$filename <- sapply(pa@grped_df$fileid, function(x) names(pa@fileList)[as.integer(x)]) + +print(head(pa@grped_df)) +write.table(pa@grped_df, file.path(opt$out_dir, 'frag4feature_output.tsv'), row.names=FALSE, sep='\t') |
| b |
| diff -r 000000000000 -r ab65999a5430 frag4feature.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/frag4feature.xml Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| b'@@ -0,0 +1,168 @@\n+<tool id="mspurity_frag4feature" name="msPurity.frag4feature" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">\n+ <description>\n+ Assign fragmentation spectra to XCMS features using msPurity\n+ </description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+ Rscript \'$__tool_directory__/frag4feature.R\'\n+ --out_dir=.\n+ --xset=\'$xset\'\n+ --pa=\'$pa\'\n+ --cores=\\${GALAXY_SLOTS:-4}\n+ #if $file_load_conditional.file_load_select=="yes"\n+ --mzML_files=\'\n+ #for $i in $file_load_conditional.input\n+ $i,\n+ #end for\n+ \'\n+ --galaxy_names=\'\n+ #for $i in $file_load_conditional.input\n+ $i.name,\n+ #end for\n+ \'\n+ #end if\n+ #if $useGroup\n+ --useGroup\n+ #end if\n+\n+ --ppm=$ppm\n+ --plim=$plim\n+ #if $intense\n+ --intense\n+ #end if\n+ #if $convert2RawRT\n+ --convert2RawRT\n+ #end if\n+\n+\n+ ]]></command>\n+ <inputs>\n+\n+ <param argument="--xset" type="data" label="xcmsSet object" \n+ help="grouped xcmsSet object saved as \'xset\' in an RData file"\n+ format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata"/>\n+ <param argument="--pa" type="data" label="purityA object" format="rdata"\n+ help="purityA object generated from msPurity_purityA.\n+ Contains details of fragmentation spectra and precursor ion purity results\n+ (output from purityA tool)"/>\n+ <param argument="--ppm" type="float" value="10"\n+ label="ppm error tolerance between precursor mz and XCMS feature mz"\n+ help="Fragmentation will be ignored if the precursor mz value is not within\n+ the ppm error tolerance to the XCMS feature mz"/>\n+ <param argument="--plim" type="float" label="Precursor ion purity threshold"\n+ value="0" max="1" min="0" \n+ help="Fragmentation will be ignore if the precursor ion purity is less than the\n+ threshold (further filtering on the precursor ion purity can be done at the averaging\n+ stage if required)."/>\n+ <param argument="--intense" type="boolean" checked="true" \n+ label="Should the most intense precursor be used within the isolation window?"\n+ help="If TRUE the most intense precursor will be used. If FALSE the precursor\n+ closest to the center of the isolation window will be used"/>\n+ <param argument="--convert2RawRT" type="boolean" checked="false" \n+ label="Was retention time correction used?"\n+ help="If retention time correction has been used in XCMS set this to yes"/>\n+ <param argument="--useGroup" type="boolean" checked="false" \n+ label="For matching fragmentation to a feature, use the grouped feature range"\n+ help="For special cases where the MS2 files have no MS1 data or if the MS1 data in the MS2 file is unreliable" />\n+\n+ <expand macro="fileload" />\n+\n+ </inputs>\n+ <outputs>\n+ <data name="frag4feature_output_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv"\n+ from_work_dir="frag4feature_output.tsv" />\n+ <data name="frag4feature_output_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"\n+ from_work_dir="frag4feature_output.RData" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <conditional name="file_load_conditional">\n+ <param name="file_load_select" value="yes"/>\n+ '..b'ame="xset" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/>\n+ <param name="pa" value="purityA_output.RData"/>\n+ <output name="frag4feature_output_tsv" value="frag4feature_output.tsv"/>\n+ <output name="frag4feature_output_rdata" value="frag4feature_output.RData" ftype="rdata" compare="sim_size"/>\n+ </test>\n+ </tests>\n+\n+ <help><![CDATA[\n+=============================================================\n+Link fragmentation spectra to XCMS features\n+=============================================================\n+-----------\n+Description\n+-----------\n+\n+**General**\n+\n+Tool to Assign fragmentation spectra (MS/MS) stored within a purityA class object to grouped features within an XCMS xset object.\n+\n+Please note that the xcmsSet object needs to have been grouped.\n+\n+The data inputs are:\n+\n+* A purityA object (generated from purityA) saved in an rdata file.\n+* A xcmsSet grouped object (generated from xcms_group) saved in an rdata file\n+* [optional] a dataset collection of the mzML files to resubmit\n+\n+XCMS calculates individual chromatographic peaks for each mzML file (saved in xset@peaks), these are then grouped together\n+(using xcms.group). Ideally the mzML files that contain the MS/MS spectra also contain sufficient MS1 scans for XCMS to detect\n+MS1 chromatographic features. If this is the case, to determine if a MS2 spectra is to be linked to an XCMS grouped feature,\n+the associated acquisition time of the MS/MS event has to be within the retention time window defined for the individual peaks\n+associated for each file. The precursor m/z value also has to be within the user ppm tolerance to XCMS feature.\n+\n+See below for representation of the linking (the \\*------\\* represent a many-to-many relationship) e.g. 1 or more MS/MS events can be\n+linked to 1 or more individual feature and an individual XCMS feature can be linked to 1 or more grouped XCMS features\n+\n+* \\[grouped XCMS feature - across files\\] \\*------\\* \\[individual XCMS feature - per file\\] \\*------\\* \\[MS/MS spectra\\]\n+\n+Alternatively, if the "useGroup" argument is set to TRUE, the full width of the grouped peak (determined as the minimum rtmin\n+and maximum rtmax of the all associated individual peaks) will be used. This option should be used if the mzML file with\n+MS/MS has very limited MS1 data and so individual chromatographic peaks might not be detected with the mzML files containing the\n+MS/MS data. However, it should be noted this may lead to potential inaccurate linking.\n+\n+* \\[grouped XCMS peaks\\] \\*------\\* \\[MS/MS spectra\\]\n+\n+**Example LC-MS/MS processing workflow**\n+\n+\n+* Purity assessments\n+ + (mzML files) -> purityA -> (pa)\n+* XCMS processing\n+ + (mzML files) -> xcms.xcmsSet -> xcms.merge -> xcms.group -> xcms.retcor -> xcms.group -> (xset)\n+* Fragmentation processing\n+ + (xset, pa) -> **frag4feature** -> filterFragSpectra -> averageAllFragSpectra -> createDatabase -> spectralMatching -> (sqlite spectral database)\n+\n+**Additional notes**\n+\n+* If using only a single file, then grouping still needs to be performed within XCMS before frag4feature can be used.\n+* Fragmentation spectra below a certain precursor ion purity can be be removed (see plim argument).\n+* A SQLite database can be created directly here but the functionality has been deprecated and the createDatabase function should now be used\n+* Can experience some problems when using XCMS version < 3 and obiwarp retention time correction.\n+\n+See Bioconductor documentation for more details, function msPurity::frag4feature()\n+\n+-----------\n+Outputs\n+-----------\n+* frag4feature_rdata: An updated purityA object saved as rdata file with fragmentation-feature links added\n+* frag4feature_grouped_msms: A flat file of all the XCMS peaks for each grouped feature and the corresponding fragmentation scans\n+* frag4feature_sqlite: An SQLite database of the data (including fragmentation scans)\n+\n+ ]]></help>\n+\n+<expand macro="citations" />\n+\n+</tool>\n' |
| b |
| diff -r 000000000000 -r ab65999a5430 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| b'@@ -0,0 +1,364 @@\n+<?xml version="1.0"?>\n+<macros>\n+ <token name="@TOOL_VERSION@">1.12.0</token>\n+ <token name="@GALAXY_TOOL_VERSION@">0</token>\n+\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@" >bioconductor-mspurity</requirement>\n+ <requirement type="package" version="1.42.0" >bioconductor-camera</requirement>\n+ <requirement type="package" version="3.8.0" >bioconductor-xcms</requirement>\n+ <requirement type="package" version="1.14.0" >bioconductor-mspuritydata</requirement>\n+ <requirement type="package" version="1.6.4">r-optparse</requirement>\n+ <requirement type="package" version="1.1.1">r-rpostgres</requirement>\n+ <requirement type="package" version="0.10.17">r-rmysql</requirement>\n+ <yield />\n+ </requirements>\n+ </xml>\n+\n+\n+ <xml name="offsets">\n+ <param argument="--minoffset" type="float" label="minoffset" value="0.5"\n+ help="Offset to the \'left\' for the precursor range e.g. if precursor of interest is\n+ 100.0 then the range would be from 999.5 to 100.0"/>\n+ <param argument="--maxoffset" type="float" label="maxoffset" value="0.5"\n+ help="Offset to the \'right\' for the precursor range e.g. if precursor of interest is\n+ 100.0 then the range would be from 100.0 to 100.5"/>\n+ </xml>\n+ <xml name="general_params">\n+ <param argument="--ilim" type="float" value="0.05" \n+ label="Threshold to remove peaks below x % of the relative intensity of\n+ precursor of interest"\n+ help="All peaks less than this percentage of the precursor ion of interest will be\n+ removed from the purity calculation, default is 5\\% (0.05).\n+ Essentially a noise filter to remove peaks that are thought to have either none or\n+ very limited impact on the resulting fragmentation spectra."/>\n+ <param argument="--iw_norm" type="select" label="Normalisation for isolation efficiency">\n+ <option value="gauss" >Gaussian</option>\n+ <option value="rcosine" >Raised cosine</option>\n+ <option value="QE5"> Calculated from Q-Exactive for +/- 0.5 Da windows </option>\n+ <option value="none" selected="true" >No normalisation</option>\n+ </param>\n+ <conditional name="isotopes">\n+ <param argument="--isotopes" type="select" label="Handling of isotopic peaks" >\n+ <option value="keep" >Keep isotopes in precursor ion purity calculation</option>\n+ <option value="exclude_default" selected="true" >Exclude C12/C13 isotopes in precursor ion purity calculation</option>\n+ <option value="user" >Exclude a user supplied list of isotopes in purity calculation</option>\n+ </param>\n+ <when value="keep">\n+ </when>\n+ <when value="exclude_default">\n+ </when>\n+ <when value="user">\n+ <param argument="--im" type="data" format="tabular" label="Isotope matrix" help="\n+ tabular file composing of columns:\n+ [\'isotope_id\', \'mass diff\', \'abundance of isotope\', \'ppm tol for mz\', \'abundance buffer\',\n+ \'charge\', \'relative atomic mass (int)\', \'xflag\'].\n+ The xflag indicates if the larger (mass) isotope is the most abundant or less abundant.\n+ e.g. for c12 to c13, the c13 is less abundant so we flag as 1 for Li6 to Li7, the Li7 is more abundant\n+ so we would flag as 0.\n+ Example row: For C13 isotope (single charge) the row could be [1, 1.003355, 1.07, 4, 0.1, 1, 12, 1]"/>\n+ </when>\n+ </conditional>\n+ </xml>\n+\n+\n+ <xml name="camera_xcms">\n+ <param argument="--camera_xcms" type="select" label="Use CAMERA object or XCMS ob'..b' <option value="LC-ESI-QIT" selected="true">LC-ESI-QIT</option>\n+ <option value="LC-ESI-QQ" selected="true">LC-ESI-QQ</option>\n+ <option value="LC-ESI-QTOF" selected="true">LC-ESI-QTOF</option>\n+ <option value="LC-ESI-TOF" selected="true">LC-ESI-TOF</option>\n+ <option value="LC-Q-TOF/MS" selected="true">LC-Q-TOF/MS</option>\n+ <option value="LC-QTOF" selected="true">LC-QTOF</option>\n+ <option value="Linear Ion Trap" selected="true">Linear Ion Trap</option>\n+ <option value="LIT" selected="true">LIT</option>\n+ <option value="MALDI-QIT" selected="true">MALDI-QIT</option>\n+ <option value="MALDI-TOF" selected="true">MALDI-TOF</option>\n+ <option value="MALDI-TOFTOF" selected="true">MALDI-TOFTOF</option>\n+ <option value="orbitrap" selected="true">orbitrap</option>\n+ <option value="QIT" selected="true">QIT</option>\n+ <option value="QIT-FT" selected="true">QIT-FT</option>\n+ <option value="QIT-TOF" selected="true">QIT-TOF</option>\n+ <option value="QqQ" selected="true">QqQ</option>\n+ <option value="Q-TOF" selected="true">Q-TOF</option>\n+ <option value="Quattro_QQQ" selected="true">Quattro_QQQ</option>\n+ <option value="none">None</option>\n+ </param>\n+ <param argument="--@QL_SHRT@_instrumentTypesUser" type="text" value=""\n+ help="Types of the instruments to be included in the search. Use a comma to\n+ separate the instrument types or leave empty to ignore filter."/>\n+ </when>\n+ <when value="false">\n+ </when>\n+ </conditional>\n+ <conditional name="@QL_SHRT@_instruments_cond">\n+ <param name="@QL_SHRT@_instruments_bool" type="boolean" label="Filter on instrument name?" help="" />\n+ <when value="true">\n+ <param argument="--@QL_SHRT@_instruments" type="text" value=""\n+ help="Known instrument names to filter on. Use a comma to\n+ separate the instrument types or leave empty to ignore filter."/>\n+ </when>\n+ <when value="false">\n+ </when>\n+ </conditional>\n+\n+\n+\n+ <conditional name="@QL_SHRT@_spectraTypes_cond">\n+ <param name="@QL_SHRT@_spectraTypes_bool" type="boolean" label="Filter on spectral type?"\n+ help="" />\n+ <when value="true">\n+ <param argument="--@QL_SHRT@_spectraTypes" type="select" multiple="true" label="Spectra type" >\n+ <option value="av_all" selected="true">Averaged all spectra ignoring inter-intra relationships </option>\n+ <option value="av_inter">Averaged inter spectra</option>\n+ <option value="av_intra">Averaged intra spectra </option>\n+ <option value="scans">All individual scans</option>\n+ <option value="NA">Not applicable/defined</option>\n+ </param>\n+ </when>\n+ <when value="false">\n+ </when>\n+ </conditional>\n+\n+ <param argument="--@QL_SHRT@_spectraFilter" type="boolean" checked="true"\n+ label="Ignore any peaks flagged in the spectra in previous stages?"\n+ help="" />\n+\n+ </section>\n+ </xml>\n+\n+\n+\n+\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1021/acs.analchem.6b04358</citation>\n+ <yield />\n+ </citations>\n+ </xml>\n+\n+</macros>\n' |
| b |
| diff -r 000000000000 -r ab65999a5430 purityA.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/purityA.R Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| @@ -0,0 +1,121 @@ +library(msPurity) +library(optparse) +print(sessionInfo()) + +option_list <- list( + make_option(c("-o", "--out_dir"), type="character"), + make_option("--mzML_files", type="character"), + make_option("--galaxy_names", type="character"), + make_option("--minOffset", default=0.5), + make_option("--maxOffset", default=0.5), + make_option("--ilim", default=0.05), + make_option("--iwNorm", default="none", type="character"), + make_option("--exclude_isotopes", action="store_true"), + make_option("--isotope_matrix", type="character"), + make_option("--mostIntense", action="store_true"), + make_option("--plotP", action="store_true"), + make_option("--nearest", action="store_true"), + make_option("--cores", default=4), + make_option("--ppmInterp", default=7) +) + +opt <- parse_args(OptionParser(option_list=option_list)) +print(opt) + +minOffset = as.numeric(opt$minOffset) +maxOffset = as.numeric(opt$maxOffset) + +if (opt$iwNorm=='none'){ + iwNorm = FALSE + iwNormFun = NULL +}else if (opt$iwNorm=='gauss'){ + iwNorm = TRUE + iwNormFun = msPurity::iwNormGauss(minOff=-minOffset, maxOff=maxOffset) +}else if (opt$iwNorm=='rcosine'){ + iwNorm = TRUE + iwNormFun = msPurity::iwNormRcosine(minOff=-minOffset, maxOff=maxOffset) +}else if (opt$iwNorm=='QE5'){ + iwNorm = TRUE + iwNormFun = msPurity::iwNormQE.5() +} + +filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]]) +filepaths <- filepaths[filepaths != ""] + + + +if(is.null(opt$minOffset) || is.null(opt$maxOffset)){ + offsets = NA +}else{ + offsets = as.numeric(c(opt$minOffset, opt$maxOffset)) +} + + +if(is.null(opt$mostIntense)){ + mostIntense = FALSE +}else{ + mostIntense = TRUE +} + +if(is.null(opt$nearest)){ + nearest = FALSE +}else{ + nearest = TRUE +} + +if(is.null(opt$plotP)){ + plotP = FALSE + plotdir = NULL +}else{ + plotP = TRUE + plotdir = opt$out_dir +} + + +if (is.null(opt$isotope_matrix)){ + im <- NULL +}else{ + im <- read.table(opt$isotope_matrix, + header = TRUE, sep='\t', stringsAsFactors = FALSE) +} + +if (is.null(opt$exclude_isotopes)){ + isotopes <- FALSE +}else{ + isotopes <- TRUE +} + +pa <- msPurity::purityA(filepaths, + cores = opt$cores, + mostIntense = mostIntense, + nearest = nearest, + offsets = offsets, + plotP = plotP, + plotdir = plotdir, + interpol = "linear", + iwNorm = iwNorm, + iwNormFun = iwNormFun, + ilim = opt$ilim, + mzRback = "pwiz", + isotopes = isotopes, + im = im, + ppmInterp = opt$ppmInterp) + + +if (!is.null(opt$galaxy_names)){ + galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]]) + galaxy_names <- galaxy_names[galaxy_names != ""] + names(pa@fileList) <- galaxy_names +} + +print(pa) +save(pa, file=file.path(opt$out_dir, 'purityA_output.RData')) + +pa@puritydf$filename <- sapply(pa@puritydf$fileid, function(x) names(pa@fileList)[as.integer(x)]) + +print(head(pa@puritydf)) +write.table(pa@puritydf, file.path(opt$out_dir, 'purityA_output.tsv'), row.names=FALSE, sep='\t') + +# removed_peaks <- data.frame(removed_peaks) +# write.table(data.frame('ID'=rownames(removed_peaks),removed_peaks), +# file.path(opt$out_dir, 'removed_peaks.txt'), row.names=FALSE, sep='\t') |
| b |
| diff -r 000000000000 -r ab65999a5430 purityX.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/purityX.R Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| @@ -0,0 +1,184 @@ +library(msPurity) +library(optparse) +print(sessionInfo()) + +option_list <- list( + make_option(c("--xset_path"), type="character"), + make_option(c("-o", "--out_dir"), type="character"), + make_option(c("--mzML_path"), type="character"), + make_option("--minOffset", default=0.5), + make_option("--maxOffset", default=0.5), + make_option("--ilim", default=0.05), + make_option("--iwNorm", default="none", type="character"), + make_option("--exclude_isotopes", action="store_true"), + make_option("--isotope_matrix", type="character"), + make_option("--purityType", default="purityFWHMmedian"), + make_option("--singleFile", default=0), + make_option("--cores", default=4), + make_option("--xgroups", type="character"), + make_option("--rdata_name", default='xset'), + make_option("--camera_xcms", default='xset'), + make_option("--files", type="character"), + make_option("--galaxy_files", type="character"), + make_option("--choose_class", type="character"), + make_option("--ignore_files", type="character"), + make_option("--rtraw_columns", action="store_true") +) + + +opt<- parse_args(OptionParser(option_list=option_list)) +print(opt) + + +if (!is.null(opt$xgroups)){ + xgroups = as.numeric(strsplit(opt$xgroups, ',')[[1]]) +}else{ + xgroups = NULL +} + + + +print(xgroups) + +if (!is.null(opt$remove_nas)){ + df <- df[!is.na(df$mz),] +} + +if (is.null(opt$isotope_matrix)){ + im <- NULL +}else{ + im <- read.table(opt$isotope_matrix, + header = TRUE, sep='\t', stringsAsFactors = FALSE) +} + +if (is.null(opt$exclude_isotopes)){ + isotopes <- FALSE +}else{ + isotopes <- TRUE +} + +if (is.null(opt$rtraw_columns)){ + rtraw_columns <- FALSE +}else{ + rtraw_columns <- TRUE +} + +loadRData <- function(rdata_path, xset_name){ +#loads an RData file, and returns the named xset object if it is there + load(rdata_path) + return(get(ls()[ls() == xset_name])) +} + +target_obj <- loadRData(opt$xset_path, opt$rdata_name) + +if (opt$camera_xcms=='camera'){ + xset <- target_obj@xcmsSet +}else{ + xset <- target_obj +} + +print(xset) + +minOffset = as.numeric(opt$minOffset) +maxOffset = as.numeric(opt$maxOffset) + + +if (opt$iwNorm=='none'){ + iwNorm = FALSE + iwNormFun = NULL +}else if (opt$iwNorm=='gauss'){ + iwNorm = TRUE + iwNormFun = msPurity::iwNormGauss(minOff=-minOffset, maxOff=maxOffset) +}else if (opt$iwNorm=='rcosine'){ + iwNorm = TRUE + iwNormFun = msPurity::iwNormRcosine(minOff=-minOffset, maxOff=maxOffset) +}else if (opt$iwNorm=='QE5'){ + iwNorm = TRUE + iwNormFun = msPurity::iwNormQE.5() +} + +print(xset@filepaths) + +if (!is.null(opt$files)){ + updated_filepaths <- trimws(strsplit(opt$files, ',')[[1]]) + updated_filepaths <- updated_filepaths[updated_filepaths != ""] + print(updated_filepaths) + updated_filenames = basename(updated_filepaths) + original_filenames = basename(xset@filepaths) + update_idx = match(updated_filenames, original_filenames) + + if (!is.null(opt$galaxy_files)){ + galaxy_files <- trimws(strsplit(opt$galaxy_files, ',')[[1]]) + galaxy_files <- galaxy_files[galaxy_files != ""] + xset@filepaths <- galaxy_files[update_idx] + }else{ + xset@filepaths <- updated_filepaths[update_idx] + } +} + +if (!is.null(opt$choose_class)){ + classes <- trimws(strsplit(opt$choose_class, ',')[[1]]) + + + ignore_files_class <- which(!as.character(xset@phenoData$class) %in% classes) + + print('choose class') + print(ignore_files_class) +}else{ + ignore_files_class <- NA +} + +if (!is.null(opt$ignore_files)){ + ignore_files_string <- trimws(strsplit(opt$ignore_files, ',')[[1]]) + filenames <- rownames(xset@phenoData) + ignore_files <- which(filenames %in% ignore_files_string) + + ignore_files <- unique(c(ignore_files, ignore_files_class)) + ignore_files <- ignore_files[ignore_files != ""] +}else{ + if (anyNA(ignore_files_class)){ + ignore_files <- NULL + }else{ + ignore_files <- ignore_files_class + } + +} + +print('ignore_files') +print(ignore_files) + + +ppLCMS <- msPurity::purityX(xset=xset, + offsets=c(minOffset, maxOffset), + cores=opt$cores, + xgroups=xgroups, + purityType=opt$purityType, + ilim = opt$ilim, + isotopes = isotopes, + im = im, + iwNorm = iwNorm, + iwNormFun = iwNormFun, + singleFile = opt$singleFile, + fileignore = ignore_files, + rtrawColumns=rtraw_columns) + + +dfp <- ppLCMS@predictions + +# to make compatable with deconrank +colnames(dfp)[colnames(dfp)=='grpid'] = 'peakID' +colnames(dfp)[colnames(dfp)=='median'] = 'medianPurity' +colnames(dfp)[colnames(dfp)=='mean'] = 'meanPurity' +colnames(dfp)[colnames(dfp)=='sd'] = 'sdPurity' +colnames(dfp)[colnames(dfp)=='stde'] = 'sdePurity' +colnames(dfp)[colnames(dfp)=='RSD'] = 'cvPurity' +colnames(dfp)[colnames(dfp)=='pknm'] = 'pknmPurity' +if(sum(is.na(dfp$medianPurity))>0){ + dfp[is.na(dfp$medianPurity),]$medianPurity = 0 +} + + +print(head(dfp)) +write.table(dfp, file.path(opt$out_dir, 'purityX_output.tsv'), row.names=FALSE, sep='\t') + +save.image(file.path(opt$out_dir, 'purityX_output.RData')) |
| b |
| diff -r 000000000000 -r ab65999a5430 spectralMatching.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spectralMatching.R Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| b'@@ -0,0 +1,368 @@\n+library(msPurity)\n+library(msPurityData)\n+library(optparse)\n+print(sessionInfo())\n+# load in library spectra config\n+source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }\n+source_local("dbconfig.R")\n+\n+option_list <- list(\n+ make_option(c("-o", "--outDir"), type="character"),\n+ make_option("--q_dbPth", type="character"),\n+ make_option("--l_dbPth", type="character"),\n+\n+ make_option("--q_dbType", type="character", default=NA),\n+ make_option("--l_dbType", type="character", default=NA),\n+\n+ make_option("--q_msp", type="character", default=NA),\n+ make_option("--l_msp", type="character", default=NA),\n+\n+ make_option("--q_defaultDb", action="store_true"),\n+ make_option("--l_defaultDb", action="store_true"),\n+\n+ make_option("--q_ppmPrec", type="double"),\n+ make_option("--l_ppmPrec", type="double"),\n+\n+ make_option("--q_ppmProd", type="double"),\n+ make_option("--l_ppmProd", type="double"),\n+\n+ make_option("--q_raThres", type="double", default=NA),\n+ make_option("--l_raThres", type="double", default=NA),\n+\n+ make_option("--q_polarity", type="character", default=NA),\n+ make_option("--l_polarity", type="character", default=NA),\n+\n+ make_option("--q_purity", type="double", default=NA),\n+ make_option("--l_purity", type="double", default=NA),\n+\n+ make_option("--q_xcmsGroups", type="character", default=NA),\n+ make_option("--l_xcmsGroups", type="character", default=NA),\n+\n+ make_option("--q_pids", type="character", default=NA),\n+ make_option("--l_pids", type="character", default=NA),\n+\n+ make_option("--q_rtrangeMin", type="double", default=NA),\n+ make_option("--l_rtrangeMin", type="double", default=NA),\n+\n+ make_option("--q_rtrangeMax", type="double", default=NA),\n+ make_option("--l_rtrangeMax", type="double", default=NA),\n+\n+ make_option("--q_accessions", type="character", default=NA),\n+ make_option("--l_accessions", type="character", default=NA),\n+\n+ make_option("--q_sources", type="character", default=NA),\n+ make_option("--l_sources", type="character", default=NA),\n+\n+ make_option("--q_sourcesUser", type="character", default=NA),\n+ make_option("--l_sourcesUser", type="character", default=NA),\n+\n+ make_option("--q_instrumentTypes", type="character", default=NA),\n+ make_option("--l_instrumentTypes", type="character", default=NA),\n+\n+ make_option("--q_instrumentTypesUser", type="character", default=NA),\n+ make_option("--l_instrumentTypesUser", type="character", default=NA),\n+\n+ make_option("--q_instruments", type="character", default=NA),\n+ make_option("--l_instruments", type="character", default=NA),\n+\n+ make_option("--q_spectraTypes", type="character", default=NA),\n+ make_option("--l_spectraTypes", type="character", default=NA),\n+\n+ make_option("--q_spectraFilter", action="store_true"),\n+ make_option("--l_spectraFilter", action="store_true"),\n+\n+ make_option("--usePrecursors", action="store_true"),\n+\n+ make_option("--mzW", type="double"),\n+ make_option("--raW", type="double"),\n+\n+ make_option("--rttol", type="double", default=NA),\n+\n+ make_option("--updateDb", action="store_true"),\n+ make_option("--copyDb", action="store_true"),\n+ make_option("--cores", default=1)\n+\n+\n+)\n+\n+# store options\n+opt<- parse_args(OptionParser(option_list=option_list))\n+\n+print(opt)\n+\n+# check if the sqlite databases have any spectra\n+checkSPeakMeta <- function(dbPth, nme){\n+ if(is.null(dbPth)){\n+ return(TRUE)\n+ }else if ((file.exists(dbPth)) & (file.info(dbPth)$size>0)){\n+ con <- DBI::dbConnect(RSQLite::SQLite(), dbPth)\n+ if (DBI::dbExistsTable(con, "s_peak_meta")){\n+ spm <- DBI::dbGetQuery(con, \'SELECT * FROM s_peak_meta ORDER BY ROWID ASC LIMIT 1\')\n+ return(TRUE)\n+ }else if(DBI::dbExistsTable(con, "library_spectra_meta")){\n+ spm <- DBI::dbGetQuery(con, \'SELECT * FROM library_spectra_meta ORDER BY ROWI'..b'ta")\n+ l_dbType <- \'sqlite\'\n+}else if (!opt$l_dbType==\'local_config\'){\n+ l_dbType <- opt$l_dbType\n+ l_dbPth <- opt$l_dbPth\n+}\n+\n+\n+q_polarity <- extractMultiple(opt$q_polarity)\n+l_polarity <- extractMultiple(opt$l_polarity)\n+\n+q_xcmsGroups <- extractMultiple(opt$q_xcmsGroups)\n+l_xcmsGroups <- extractMultiple(opt$l_xcmsGroups)\n+\n+q_pids <- extractMultiple(opt$q_pids)\n+l_pids <- extractMultiple(opt$l_pids)\n+\n+q_sources <- extractMultiple(opt$q_sources)\n+l_sources <- extractMultiple(opt$l_sources)\n+\n+q_sourcesUser <- extractMultiple(opt$q_sourcesUser)\n+l_sourcesUser <- extractMultiple(opt$l_sourcesUser)\n+\n+q_sources <-c(q_sources, q_sourcesUser)\n+l_sources <-c(l_sources, l_sourcesUser)\n+\n+q_instrumentTypes <- extractMultiple(opt$q_instrumentTypes)\n+l_instrumentTypes <- extractMultiple(opt$l_instrumentTypes)\n+\n+q_instrumentTypes <-c(q_instrumentTypes, q_instrumentTypes)\n+l_instrumentTypes <-c(l_instrumentTypes, l_instrumentTypes)\n+\n+\n+if(!is.null(opt$l_spectraFilter)){\n+ l_spectraFilter <- TRUE\n+}else{\n+ l_spectraFilter <- FALSE\n+}\n+\n+if(!is.null(opt$q_spectraFilter)){\n+ q_spectraFilter <- TRUE\n+}else{\n+ q_spectraFilter <- FALSE\n+}\n+\n+if(!is.null(opt$updateDb)){\n+ updateDb <- TRUE\n+}else{\n+ updateDb <- FALSE\n+}\n+\n+if(!is.null(opt$copyDb)){\n+ copyDb <- TRUE\n+}else{\n+ copyDb <- FALSE\n+}\n+\n+if(!is.null(opt$l_rtrangeMax)){\n+ l_rtrangeMax <- opt$l_rtrangeMax\n+}else{\n+ l_rtrangeMax <- NA\n+}\n+\n+if(!is.null(opt$q_rtrangeMax)){\n+ q_rtrangeMax <- opt$q_rtrangeMax\n+}else{\n+ q_rtrangeMax <- NA\n+}\n+\n+if(!is.null(opt$l_rtrangeMin)){\n+ l_rtrangeMin <- opt$l_rtrangeMin\n+}else{\n+ l_rtrangeMin <- NA\n+}\n+\n+if(!is.null(opt$q_rtrangeMin)){\n+ q_rtrangeMin <- opt$q_rtrangeMin\n+}else{\n+ q_rtrangeMin <- NA\n+}\n+\n+q_check <- checkSPeakMeta(opt$q_dbPth, \'query\')\n+l_check <- checkSPeakMeta(opt$l_dbPth, \'library\')\n+\n+if (q_check && l_check){\n+ sm <- msPurity::spectralMatching(\n+ q_purity = opt$q_purity,\n+ l_purity = opt$l_purity,\n+ \n+ q_ppmProd = opt$q_ppmProd,\n+ l_ppmProd = opt$l_ppmProd,\n+ \n+ q_ppmPrec = opt$q_ppmPrec,\n+ l_ppmPrec = opt$l_ppmPrec,\n+ \n+ q_raThres = opt$q_raThres,\n+ l_raThres = opt$l_raThres,\n+ \n+ q_pol = q_polarity,\n+ l_pol = l_polarity,\n+ \n+ q_xcmsGroups = q_xcmsGroups,\n+ l_xcmsGroups = l_xcmsGroups,\n+ \n+ q_pids = q_pids,\n+ l_pids = l_pids,\n+ \n+ q_sources = q_sources,\n+ l_sources = l_sources,\n+ \n+ q_instrumentTypes = q_instrumentTypes,\n+ l_instrumentTypes = l_instrumentTypes,\n+ \n+ q_spectraFilter= q_spectraFilter,\n+ l_spectraFilter= l_spectraFilter,\n+ \n+ l_rtrange=c(l_rtrangeMin, l_rtrangeMax),\n+ q_rtrange=c(q_rtrangeMin, q_rtrangeMax),\n+ \n+ q_accessions = opt$q_accessions,\n+ l_accessions= opt$l_accessions,\n+ \n+ raW = opt$raW,\n+ mzW = opt$mzW,\n+ rttol=opt$rttol,\n+ cores=opt$cores,\n+ \n+ copyDb=copyDb,\n+ updateDb=updateDb,\n+ outPth = "db_with_spectral_matching.sqlite",\n+ \n+ q_dbPth = q_dbPth,\n+ q_dbType = q_dbType,\n+ q_dbName = q_dbName,\n+ q_dbHost = q_dbHost,\n+ q_dbUser = q_dbUser,\n+ q_dbPass = q_dbPass,\n+ q_dbPort = q_dbPort,\n+ \n+ l_dbPth = l_dbPth,\n+ l_dbType = l_dbType,\n+ l_dbName = l_dbName,\n+ l_dbHost = l_dbHost,\n+ l_dbUser = l_dbUser,\n+ l_dbPass = l_dbPass,\n+ l_dbPort = l_dbPort\n+ \n+ )\n+ \n+ sm <- addQueryNameColumn(sm)\n+ # Get name of the query results (and merged with the data frames)\n+ write.table(sm$matchedResults, \'matched_results.tsv\', sep = \'\\t\', row.names = FALSE, col.names = TRUE)\n+ write.table(sm$xcmsMatchedResults, \'xcms_matched_results.tsv\', sep = \'\\t\', row.names = FALSE, col.names = TRUE)\n+ \n+ if(updateDb){\n+ updateDbF(q_con, l_con)\n+ }\n+}\n' |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/LCMSMS_1.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LCMSMS_1.mzML Wed Nov 27 14:23:10 2019 -0500 |
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| diff -r 000000000000 -r ab65999a5430 test-data/LCMSMS_2.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/LCMSMS_2.mzML Wed Nov 27 14:23:10 2019 -0500 |
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| @@ -0,0 +1,46 @@ +ACCESSION: PR100037 +RECORD_TITLE: Uracil; LC-ESI-QTOF; MS2; CE:Ramp 5-60 V; [M+H]+ +DATE: 2016.01.19 (Created 2009.09.10, modified 2011.05.06) +AUTHORS: Matsuda F, Suzuki M, Sawada Y, Plant Science Center, RIKEN. +LICENSE: CC BY-SA +COMMENT: Acquisition and generation of the data is financially supported in part by CREST/JST. +CH$NAME: Uracil +CH$NAME: 2,4-Dihydroxypyrimidine +CH$NAME: 2,4(1H,3H)-Pyrimidinedione +CH$NAME: 2,4-Pyrimidinediol +CH$COMPOUND_CLASS: Pyrimidines +CH$FORMULA: C4H4N2O2 +CH$EXACT_MASS: 112.02728 +CH$SMILES: O=C(C=1)NC(=O)NC1 +CH$IUPAC: InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8) +CH$LINK: CAS 66-22-8 +CH$LINK: CHEMSPIDER 1141 +CH$LINK: KAPPAVIEW KPC01082 +CH$LINK: KEGG C00106 +CH$LINK: KNAPSACK C00001513 +CH$LINK: PUBCHEM CID:1174 +CH$LINK: INCHIKEY ISAKRJDGNUQOIC-UHFFFAOYSA-N +AC$INSTRUMENT: UPLC Q-Tof Premier, Waters +AC$INSTRUMENT_TYPE: LC-ESI-QTOF +AC$MASS_SPECTROMETRY: MS_TYPE MS2 +AC$MASS_SPECTROMETRY: ION_MODE POSITIVE +AC$MASS_SPECTROMETRY: COLLISION_ENERGY Ramp 5-60 V +AC$MASS_SPECTROMETRY: DATAFORMAT Continuum +AC$MASS_SPECTROMETRY: DESOLVATION_GAS_FLOW 600.0 L/Hr +AC$MASS_SPECTROMETRY: DESOLVATION_TEMPERATURE 400 C +AC$MASS_SPECTROMETRY: FRAGMENTATION_METHOD LOW-ENERGY CID +AC$MASS_SPECTROMETRY: IONIZATION ESI +AC$MASS_SPECTROMETRY: SOURCE_TEMPERATURE 120 C +AC$CHROMATOGRAPHY: CAPILLARY_VOLTAGE 3.0 kV +AC$CHROMATOGRAPHY: SAMPLING_CONE 23.0 V +AC$CHROMATOGRAPHY: SOLVENT CH3CN(0.1%HCOOH)/ H2O(0.1%HCOOH) +MS$FOCUSED_ION: PRECURSOR_M/Z 113.03508 +MS$FOCUSED_ION: PRECURSOR_TYPE [M+H]+ +PK$SPLASH: splash10-03di-0900000000-ff54f3083ce4ccccfd95 +PK$NUM_PEAK: 3 +PK$PEAK: m/z int. rel.int. + 92.5026 9.015 78 + 112.5167 9.848 86 + 113.0339 115 999 +// + |
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|
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/averageFragSpectra_output_all_only.RData |
| b |
| Binary file test-data/averageFragSpectra_output_all_only.RData has changed |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/averageFragSpectra_output_all_only.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/averageFragSpectra_output_all_only.tsv Wed Nov 27 14:23:10 2019 -0500 |
| b |
| b'@@ -0,0 +1,1752 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|
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/averageFragSpectra_output_inter.RData |
| b |
| Binary file test-data/averageFragSpectra_output_inter.RData has changed |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/averageFragSpectra_output_inter.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/averageFragSpectra_output_inter.tsv Wed Nov 27 14:23:10 2019 -0500 |
| b |
| b'@@ -0,0 +1,5615 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|
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/averageFragSpectra_output_intra.RData |
| b |
| Binary file test-data/averageFragSpectra_output_intra.RData has changed |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/averageFragSpectra_output_intra.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/averageFragSpectra_output_intra.tsv Wed Nov 27 14:23:10 2019 -0500 |
| b |
| b'@@ -0,0 +1,3225 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|
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/combineAnnotations_combined_annotations.sqlite |
| b |
| Binary file test-data/combineAnnotations_combined_annotations.sqlite has changed |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/combineAnnotations_combined_annotations.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combineAnnotations_combined_annotations.tsv Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| b'@@ -0,0 +1,107 @@\n+"grpid"\t"grp_name"\t"mz"\t"rt"\t"inchikey"\t"inchi"\t"inchikey..7"\t"inchikey1"\t"inchikey2"\t"inchikey3"\t"name"\t"exact_mass"\t"molecular_formula"\t"pubchem_cids"\t"kegg_cids"\t"kegg_brite"\t"kegg_drugs"\t"hmdb_ids"\t"hmdb_bio_custom_flag"\t"hmdb_drug_flag"\t"biosim_max_count"\t"biosim_hmdb_ids"\t"fragmentation_acquistion_num"\t"mean_precursor_ion_purity"\t"accession"\t"sirius_score"\t"sirius_wscore"\t"metfrag_score"\t"metfrag_wscore"\t"sm_score"\t"sm_wscore"\t"probmetab_score"\t"probmetab_wscore"\t"ms1_lookup_score"\t"ms1_lookup_wscore"\t"biosim_max_score"\t"biosim_wscore"\t"wscore"\t"rank"\t"adduct_overall"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-UHFFFAOYSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)"\t"ONIBWKKTOPOVIA-UHFFFAOYSA-N"\t"ONIBWKKTOPOVIA"\t"UHFFFAOYSA"\t"N"\t"DL-Proline"\t115.063328534\t"C5H9NO2"\t"614,25246272"\t"C16435"\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\t"CCMSLIB00000577898"\t"1.0"\t0.2\t0.9\t0.18\t0.87867085623127\t0.263601256869381\t"0"\t0\t0\t0\t1\t0.25\t0.893601256869381\t1\t"[M+H]+,M+H"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-AZXPZELESA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/i4+1"\t"ONIBWKKTOPOVIA-AZXPZELESA-N"\t"ONIBWKKTOPOVIA"\t"AZXPZELESA"\t"N"\t""\t116.066683369\t"C5H9NO2"\t"10290769"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-BYPYZUCNSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1"\t"ONIBWKKTOPOVIA-BYPYZUCNSA-N"\t"ONIBWKKTOPOVIA"\t"BYPYZUCNSA"\t"N"\t"L-Pro"\t115.063328534\t"C5H9NO2"\t"145742,6971047"\t"C00148"\t"Compounds with biological roles [BR:br08001]"\t"D00035"\t"HMDB0000162"\t"True"\t"False"\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-GIZBTRSZSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1/i1+2,2+2,3+2,4+2,5+2"\t"ONIBWKKTOPOVIA-GIZBTRSZSA-N"\t"ONIBWKKTOPOVIA"\t"GIZBTRSZSA"\t"N"\t"L-PROLINE, [U-14C]"\t125.0795385\t"C5H9NO2"\t"12210869"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-GTTLGWSSSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1/i1+1D,4+1,6+1/t1?,4-"\t"ONIBWKKTOPOVIA-GTTLGWSSSA-N"\t"ONIBWKKTOPOVIA"\t"GTTLGWSSSA"\t"N"\t"SCHEMBL16945363"\t119.07334984\t"C5H9NO2"\t"118264374"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-HOSYLAQJSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/i5+1"\t"ONIBWKKTOPOVIA-HOSYLAQJSA-N"\t"ONIBWKKTOPOVIA"\t"HOSYLAQJSA"\t"N"\t"DL-Proline-1-13C"\t116.066683369\t"C5H9NO2"\t"59340910"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-IDEBNGHGSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/i1+1,2+1,3+1,4+1,5+1,6+1"\t"ONIBWKKTOPOVIA-IDEBNGHGSA-N"\t"ONIBWKKTOPOVIA"\t"IDEBNGHGSA"\t"N"\t"SCHEMBL18875607"\t121.0771376\t"C5H9NO2"\t"129148531"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-IXBOUXNVSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1/i4+1"\t"ONIBWKKTOPOVIA-IXBOUXNVSA-N"\t"ONIBWKKTOPOVIA"\t"IXBOUXNVSA"\t"N"\t""\t116.066683369\t"C5H9NO2"\t"100915807"\t""\t""\t""\t""\t""\t""\t33\t"HMDB0000162"\t"277,343,409,410"\t0.99\tNA\t"1.0"\t0.2\t0\t0\t0\t0\t"0"\t0\t0\t0\t1\t0.25\t0.45\t2\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"ONIBWKKTOPOVIA-JGTYJTGKSA-N"\t"InChI=1S/C5H9NO2/c7-5(8)4-2-1-3-6-4/h4,6H,1-3H2,(H,7,8)/t4-/m0/s1/i6+1"\t"ONIBWKKTOPOVIA-JGTYJTGKSA-N"\t"ONIBWKKTOPOVIA"\t"JGTYJTGKSA"\t"N"\t"L-Proline-15N"\t116.06'..b'116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-HJOWPTDZSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i1D2,2D2,3D,4D2/hD"\t"RWRDLPDLKQPQOW-HJOWPTDZSA-N"\t"RWRDLPDLKQPQOW"\t"HJOWPTDZSA"\t"N"\t"pyrrolidine-d8"\t79.123713262\t"C4H9N"\t"129715569"\t""\t""\t""\t""\t""\t""\t1\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t"0"\t0\t0\t0\t0.7143\t0.178575\t0.178575\t17\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RWRDLPDLKQPQOW-KLRAWXKOSA-N"\t"InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2/i1D2,2D2,3D2,4D2/hD"\t"RWRDLPDLKQPQOW-KLRAWXKOSA-N"\t"RWRDLPDLKQPQOW"\t"KLRAWXKOSA"\t"N"\t""\t80.12999001\t"C4H9N"\t"60135501"\t""\t""\t""\t""\t""\t""\t1\t"HMDB0031641"\t"277,343,409,410"\t0.99\tNA\t"0.0"\t0\t0\t0\t0\t0\t"0"\t0\t0\t0\t0.7143\t0.178575\t0.178575\t17\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"MWFMGBPGAXYFAR-UHFFFAOYSA-N"\t"InChI=1S/C4H7NO/c1-4(2,6)3-5/h6H,1-2H3"\t"MWFMGBPGAXYFAR-UHFFFAOYSA-N"\t"MWFMGBPGAXYFAR"\t"UHFFFAOYSA"\t"N"\t"ACETONE CYANOHYDRIN"\t85.05276385\t"C4H7NO"\t"6406"\t"C02659"\t""\t""\t"HMDB0060427"\t"False"\t"False"\t0\t"HMDB0031456"\t"277,343,409,410"\t0.99\tNA\t"0"\t0\t0\t0\t0\t0\t"0"\t0\t0\t0\t0.6923\t0.173075\t0.173075\t18\t"[M+H]+"\n+12\t"M116T48"\t116.070597631071\t47.7346706134597\t"RRUDCFGSUDOHDG-UHFFFAOYSA-N"\t"InChI=1S/C2H5NO2/c1-2(4)3-5/h5H,1H3,(H,3,4)"\t"RRUDCFGSUDOHDG-UHFFFAOYSA-N"\t"RRUDCFGSUDOHDG"\t"UHFFFAOYSA"\t"N"\t"acetohydroxamic acid"\t75.032028405\t"C2H5NO2"\t"1990"\t"C06808"\t"Anatomical Therapeutic Chemical (ATC) classification [BR:br08303]"\t"D00220"\t"HMDB0014691"\t"False"\t"True"\t0\t"HMDB0003338"\t"277,343,409,410"\t0.99\tNA\t"0"\t0\t0\t0\t0\t0\t"0"\t0\t0\t0\t0.5455\t0.136375\t0.136375\t19\t"[M+H]+"\n+14\t"M118T48"\t118.086386443874\t48.4842492312617\t"XYLMUPLGERFSHI-UHFFFAOYSA-N"\t"InChI=1S/C9H10/c1-8(2)9-6-4-3-5-7-9/h3-7H,1H2,2H3"\t"XYLMUPLGERFSHI-UHFFFAOYSA-N"\t"XYLMUPLGERFSHI"\t"UHFFFAOYSA"\t"N"\t"alpha-Methylstyrene"\t118.078250322\t"C9H10"\t"7407"\t"C14395"\t"Carcinogens [BR:br08008]"\t""\t"HMDB0059899"\t"False"\t"False"\t6\t"HMDB0029641"\tNA\tNA\tNA\t"0"\t0\t0\t0\t0\t0\t"0.512"\t0\t0\t0\t0.8889\t0.222225\t0.222225\t1\t""\n+17\t"M121T41"\t120.96735318119\t41.0233512693484\t"PVNIIMVLHYAWGP-UHFFFAOYSA-N"\t"InChI=1S/C6H5NO2/c8-6(9)5-2-1-3-7-4-5/h1-4H,(H,8,9)"\t"PVNIIMVLHYAWGP-UHFFFAOYSA-N"\t"PVNIIMVLHYAWGP"\t"UHFFFAOYSA"\t"N"\t"SCHEMBL16147135"\t123.032028405\t"C6H5NO2"\t"938,117629482"\t"C00253"\t"Compounds with biological roles [BR:br08001]"\t"D00049"\t"HMDB0001488"\t"True"\t"True"\t6\t"HMDB0001488"\tNA\tNA\tNA\t"0"\t0\t0\t0\t0\t0\t"0.283"\t0\t0\t0\t1\t0.25\t0.25\t1\t""\n+17\t"M121T41"\t120.96735318119\t41.0233512693484\t"SIOXPEMLGUPBBT-UHFFFAOYSA-N"\t"InChI=1S/C6H5NO2/c8-6(9)5-3-1-2-4-7-5/h1-4H,(H,8,9)"\t"SIOXPEMLGUPBBT-UHFFFAOYSA-N"\t"SIOXPEMLGUPBBT"\t"UHFFFAOYSA"\t"N"\t"picolinic acid"\t123.032028405\t"C6H5NO2"\t"1018"\t"C10164"\t"Phytochemical compounds [BR:br08003]"\t""\t"HMDB0002243"\t"True"\t"False"\t6\t"HMDB0002243"\tNA\tNA\tNA\t"0"\t0\t0\t0\t0\t0\t"0.24"\t0\t0\t0\t1\t0.25\t0.25\t1\t""\n+17\t"M121T41"\t120.96735318119\t41.0233512693484\t"TWBYWOBDOCUKOW-UHFFFAOYSA-N"\t"InChI=1S/C6H5NO2/c8-6(9)5-1-3-7-4-2-5/h1-4H,(H,8,9)"\t"TWBYWOBDOCUKOW-UHFFFAOYSA-N"\t"TWBYWOBDOCUKOW"\t"UHFFFAOYSA"\t"N"\t"ISONICOTINIC ACID"\t123.032028405\t"C6H5NO2"\t"5922"\t"C07446"\t""\t""\t"HMDB0060665"\t"False"\t"False"\t7\t"HMDB0001488"\tNA\tNA\tNA\t"0"\t0\t0\t0\t0\t0\t"0.235"\t0\t0\t0\t0.9333\t0.233325\t0.233325\t2\t""\n+17\t"M121T41"\t120.96735318119\t41.0233512693484\t"LQNUZADURLCDLV-UHFFFAOYSA-N"\t"InChI=1S/C6H5NO2/c8-7(9)6-4-2-1-3-5-6/h1-5H"\t"LQNUZADURLCDLV-UHFFFAOYSA-N"\t"LQNUZADURLCDLV"\t"UHFFFAOYSA"\t"N"\t"NITROBENZENE"\t123.032028405\t"C6H5NO2"\t"7416"\t"C06813"\t"Carcinogens [BR:br08008]"\t""\t"HMDB0041950"\t"False"\t"False"\t2\t"HMDB0001232"\tNA\tNA\tNA\t"0"\t0\t0\t0\t0\t0\t"0.242"\t0\t0\t0\t0.7667\t0.191675\t0.191675\t3\t""\n+27\t"M132T74"\t132.101827517612\t73.554846736017\t"AGPKZVBTJJNPAG-UHFFFAOYSA-N"\t"InChI=1S/C6H13NO2/c1-3-4(2)5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)"\t"AGPKZVBTJJNPAG-UHFFFAOYSA-N"\t"AGPKZVBTJJNPAG"\t"UHFFFAOYSA"\t"N"\t"2-ammonio-3-methylpentanoate"\t131.09462866\t"C6H13NO2"\t"791,57397079"\t"C16434"\t""\t""\t"HMDB0033923"\t"True"\t"False"\t18\t"HMDB0000172"\t"478,547,616,475,541,607"\t1\t"CE000616"\t"0"\t0\t0\t0\t0.940890528192141\t0.282267158457642\t"0"\t0\t0\t0\t1\t0.25\t0.532267158457642\t1\t"[M+H]+"\n' |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/combineAnnotations_input_beams.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combineAnnotations_input_beams.tsv Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| @@ -0,0 +1,7 @@ +name mz rt intensity exact_mass ppm_error adduct C H N O P S molecular_formula compound_name compound_id +M116T48 116.070798346478 48.102596282959 111060511.65675 116.070605 -1.66576609124689 [M+H]+ 5 9 1 2 0 0 C5H9NO2 L-Proline HMDB0000162 +M116T48 116.070798346478 48.102596282959 111060511.65675 116.070605 -1.66576609124689 [M+H]+ 5 9 1 2 0 0 C5H9NO2 Phosphorus HMDB0001315 +M116T48 116.070798346478 48.102596282959 111060511.65675 116.070605 -1.66576609124689 [M+H]+ 5 9 1 2 0 0 C5H9NO2 D-Proline HMDB0003411 +M116T48 116.070798346478 48.102596282959 111060511.65675 116.070605 -1.66576609124689 [M+H]+ 5 9 1 2 0 0 C5H9NO2 Acetamidopropanal HMDB0012880 +M116T48 116.070798346478 48.102596282959 111060511.65675 116.070605 -1.66576609124689 [M+H]+ 5 9 1 2 0 0 C5H9NO2 4-Amino-2-methylenebutanoic acid HMDB0030409 +M116T48 116.070798346478 48.102596282959 111060511.65675 116.070605 -1.66576609124689 [M+H]+ 5 9 1 2 0 0 C5H9NO2 Pterolactam HMDB0034208 |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/combineAnnotations_input_metfrag.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combineAnnotations_input_metfrag.tsv Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| @@ -0,0 +1,8 @@ +grpid adduct CompoundName ExplPeaks FormulasOfExplPeaks FragmenterScore FragmenterScore_Values Identifier InChI InChIKey InChIKey1 InChIKey2 InChIKey3 MaximumTreeDepth MolecularFormula MonoisotopicMass Name NoExplPeaks NumberPeaksUsed SMILES Score +12 [M+H]+ NA NA 0 NA HMDB0060427 InChI=1S/C4H7NO/c1-4(2,6)3-5/h6H,1-2H3 MWFMGBPGAXYFAR-UHFFFAOYSA-N MWFMGBPGAXYFAR UHFFFAOYSA N 2 C4H7NO 85.05276385 Acetone cyanohydrin 0 3 CC(C)(O)C#N 0 +12 [M+H]+ NA NA 0 NA HMDB0002039 InChI=1S/C4H7NO/c6-4-2-1-3-5-4/h1-3H2,(H,5,6) HNJBEVLQSNELDL-UHFFFAOYSA-N HNJBEVLQSNELDL UHFFFAOYSA N 2 C4H7NO 85.05276385 2-Pyrrolidinone 0 3 O=C1CCCN1 0 +12 [M+H]+ NA NA 0 NA HMDB0000123 InChI=1S/C2H5NO2/c3-1-2(4)5/h1,3H2,(H,4,5) DHMQDGOQFOQNFH-UHFFFAOYSA-N DHMQDGOQFOQNFH UHFFFAOYSA N 2 C2H5NO2 75.03202841 Glycine 0 2 NCC(O)=O 0 +12 [M+H]+ NA NA 0 NA HMDB0014691 InChI=1S/C2H5NO2/c1-2(4)3-5/h5H,1H3,(H,3,4) RRUDCFGSUDOHDG-UHFFFAOYSA-N RRUDCFGSUDOHDG UHFFFAOYSA N 2 C2H5NO2 75.03202841 Acetohydroxamic Acid 0 2 CC(=O)NO 0 +12 [M+H]+ NA NA 0 NA HMDB0031239 InChI=1S/C2H5NO2/c1-2-5-3-4/h2H2,1H3 QQZWEECEMNQSTG-UHFFFAOYSA-N QQZWEECEMNQSTG UHFFFAOYSA N 2 C2H5NO2 75.03202841 Ethyl nitrite 0 2 CCON=O 0 +12 [M+H]+ 61.0115776062012_88.7;62.9908828735352_67.4;63.9986190795898_999.0 61.0115776062012:[C2H6S-H]+;62.9908828735352:[CH3OS]+;63.9986190795898:[CH3OS]+H+ 273.219394706017 622.0;272.0;272.0 HMDB0002151 InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 IAZDPXIOMUYVGZ-UHFFFAOYSA-N IAZDPXIOMUYVGZ UHFFFAOYSA N 2 C2H6OS 78.0139355 Dimethyl sulfoxide 3 8 CS(C)=O 0.8 +12 [M+H]+ test ONIBWKKTOPOVIA-UHFFFAOYSA-N ONIBWKKTOPOVIA UHFFFAOYSA N TEST 0.9 |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/combineAnnotations_input_probmetab.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combineAnnotations_input_probmetab.tsv Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| @@ -0,0 +1,18 @@ +name namecustom mz mzmin mzmax rt rtmin rtmax npeaks BLANK.P.WAX.2.AMD.0.LC.MS.POSITIVE ANIMAL.P.WAX.2.AMD.0.LC.MS.POSITIVE ANIMAL.P.WAX.2.AMD.0.LC.MSMS.POSITIVE isotopes adduct pcgroup propmz mpc proba +M116T48 104.106973271895 104.106955287478 104.106991256313 359.862889 359.826504 359.899274 2 0 0 2 [2][M]+ 22 NA NA NA +M107T71 104.107030464189 104.106984676963 104.107042846235 371.788312 370.845046 376.205158 3 0 3 0 [1][M]+ 21 NA NA NA +M108T47 104.992236979634 104.992192750892 104.99227099396 459.515063 456.526458 463.963424 6 0 5 1 [M+Na]+ 82.003 3 NA NA NA +M110T48 105.089907268842 105.089885488134 105.089975689328 175.613778 173.474062 181.67533 3 0 1 2 2 NA NA NA +M111T91 105.11025140006 105.110231257297 105.110271542824 359.862889 359.826504 359.899274 2 0 0 2 [2][M+1]+ 22 NA NA NA +M112T55 105.110283962945 105.110239712615 105.110299928917 371.788312 370.845046 376.205158 3 0 3 0 [1][M+1]+ 21 NA NA NA +M113T41 110.034674397147 110.034639940416 110.034699261062 442.404701 436.574584 444.17666 4 0 4 0 9 NA NA NA +M113T84 113.070745331511 113.070718897466 113.070777260971 109.38458 108.295648 113.605798 6 0 4 2 225 NA NA NA +M115T45 113.132038869213 113.132002009919 113.132085865821 34.4908844 33.8765988 35.138902 4 0 2 2 1 NA NA NA +M116T48 112.999616555967 112.999581977151 112.999651134783 463.493504 462.327586 464.659422 2 0 0 2 431 NA NA NA +M117T48 116.000903341961 115.998346142218 116.000963108016 35.1889595 34.9201112 36.6416092 8 0 4 2 1 NA NA NA +M118T48 119.085211610685 119.08252850984 119.08530671848 39.0737754 35.959209 45.9382142 16 5 5 1 1 118.077386610685 cpd:C14395;cpd:C19549 0.512;0.488 +M119T48 121.028174706077 121.028124729155 121.028217124878 35.1219624 33.876746 37.3323522 6 0 4 2 1 NA NA NA +M120T43 121.100892266604 121.100863233399 121.100910202317 36.1032512 35.959209 37.6828536 3 0 1 2 1 NA NA NA +M121T41 124.03919990525 124.039132829123 124.039264850136 203.05685 195.713784 207.195788 7 0 5 2 [3][M]+ 7 123.03192390525 cpd:C00253;cpd:C06813;cpd:C10164;cpd:C07446 0.283;0.242;0.24;0.235 +M121T71 124.897102002773 124.897045831144 124.897161445541 78.951638 77.505502 80.899414 7 0 5 2 286 NA NA NA +M122T45 125.0424696643 125.036088730982 125.042510820886 203.05685 195.713784 207.195788 9 0 5 2 [3][M+1]+ 7 NA NA NA |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/combineAnnotations_input_sirus_csifingerid.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/combineAnnotations_input_sirus_csifingerid.tsv Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| @@ -0,0 +1,3 @@ +grpid adduct inchikey2D InChI molecularFormula Rank Score Name smiles xlogp pubchemids links +12 [M+H]+ RWRDLPDLKQPQOW InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2 C4H9N 1 -136.145462142446 Azolidine C1CCNC1 31268;3613359;11062297;12196044;12196046;12196049;12196050;18440991;20463768;53660610;57608708;57608709;57608710;57750053;60135501;90927493;91312985 HMDB:(31641);Natural Products:(UNPD154562);CHEBI:(33135 52145);HSDB:(123-75-1);Plantcyc:(PYRROLIDINE);Biocyc:(PYRROLIDINE) +12 [M+H]+ ONIBWKKTOPOVIA TEST TEST 1 -100 TEST TEST TEST TEST TEST |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/combinedAnnotation_input_spectralMatching.sqlite |
| b |
| Binary file test-data/combinedAnnotation_input_spectralMatching.sqlite has changed |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/createDatabase_output.sqlite |
| b |
| Binary file test-data/createDatabase_output.sqlite has changed |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/createDatabase_output_eic.sqlite |
| b |
| Binary file test-data/createDatabase_output_eic.sqlite has changed |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/createMSP_input_metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/createMSP_input_metadata.tsv Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| @@ -0,0 +1,3 @@ +grpid isotope adduct AC$CHROMATOGRAPHY: COLUMN_NAME AC$MASS_SPECTROMETRY: ION_MODE AC$MASS_SPECTROMETRY: MS_TYPE CH$LINK: INCHIKEY CH$LINK: PUBCHEM CH$NAME +8 [M+H]+ 165.078 Acclaim RSLC C18 2.2um 2.1x100mm Thermo POSITIVE MS2 VACCAVUAMIDAGB-UHFFFAOYSA-N CID:5328 SomeCompound +12 [4][M]+ [M+NH4]+ 103.047 [M+H+NH3]+ 103.047 Acclaim RSLC C18 2.2um 2.1x100mm Thermo POSITIVE MS2 VACCAVUAMIDAGB-UHFFFAOYSA-N CID:5328 Unknown |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/createMSP_output_av_all.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/createMSP_output_av_all.msp Wed Nov 27 14:23:10 2019 -0500 |
| b |
| b"@@ -0,0 +1,2552 @@\n+RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484\n+AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903\n+XCMS groupid (grpid): 12\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 2\n+PK$PEAK: m/z int. rel.int.\n+112.050884246826\t502873.46875\t100\n+126.53768157959\t2499.31469726562\t0.5\n+\n+RECORD_TITLE: MZ:113.0354 | RT:83.4 | grpid:14 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 113.03541992282\n+AC$CHROMATOGRAPHY: RETENTION_TIME 83.441172\n+XCMS groupid (grpid): 14\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 2\n+PK$PEAK: m/z int. rel.int.\n+112.999992370605\t67035.0703125\t0.63\n+113.03479385376\t10613844.25\t100\n+\n+RECORD_TITLE: MZ:116.0706 | RT:47.7 | grpid:17 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070637437099\n+AC$CHROMATOGRAPHY: RETENTION_TIME 47.662548\n+XCMS groupid (grpid): 17\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 3\n+PK$PEAK: m/z int. rel.int.\n+116.016609191895\t4434.369140625\t2.81\n+116.070896148682\t157547.453125\t100\n+116.107261657715\t6152.61499023438\t3.91\n+\n+RECORD_TITLE: MZ:132.1018 | RT:73.5 | grpid:41 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 132.101827805179\n+AC$CHROMATOGRAPHY: RETENTION_TIME 73.529172\n+XCMS groupid (grpid): 41\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 1\n+PK$PEAK: m/z int. rel.int.\n+132.102035522461\t338114.46875\t100\n+\n+RECORD_TITLE: MZ:137.0456 | RT:127 | grpid:47 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 137.045578757527\n+AC$CHROMATOGRAPHY: RETENTION_TIME 126.956946\n+XCMS groupid (grpid): 47\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 4\n+PK$PEAK: m/z int. rel.int.\n+110.035266876221\t290341.673828125\t4.45\n+112.050743103027\t12029.1610107422\t0.18\n+119.035442352295\t200743.407226562\t3.08\n+137.045837402344\t6519742.5\t100\n+\n+RECORD_TITLE: MZ:138.0547 | RT:50.7 | grpid:48 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 138.05471057982\n+AC$CHROMATOGRAPHY: RETENTION_TIME 50.6971758\n+XCMS groupid (grpid): 48\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 2\n+PK$PEAK: m/z int. rel.int.\n+110.060352325439\t34625.283203125\t7.61\n+138.054901123047\t455046.234375\t100\n+\n+RECORD_TITLE: MZ:138.0487 | RT:127 | grpid:49 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 138.048727400006\n+AC$CHROMATOGRAPHY: RETENTION_TIME 126.956946\n+XCMS groupid (grpid): 49\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 8\n+PK$PEAK: m/z int. rel.int.\n+110.035133361816\t4197.11962890625\t0.87\n+111.032066345215\t3606.22302246094\t0.75\n+111.038753509521\t22056.884765625\t4.56\n+120.031585693359\t3442.69409179688\t0.71\n+120.038921356201\t14920.083984375\t3.08\n+131.267166137695\t2650.74243164062\t0.55\n+137.396865844727\t3584.59228515625\t0.74\n+138.050010681152\t483746.53125\t100\n+\n+RECORD_TITLE: MZ:140.0678 | RT:46.2 | grpid:51 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 140.067802644286\n+AC$CHROMATOGRAPHY: RETENTION_TIME 46.161033\n+XCMS groupid (grpid): 51\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 4\n+PK$PEAK: m/z int. rel.int.\n+108.959754943848\t2408.8056640625\t0.05\n+114.089179992676\t568595.515625\t10.75\n+140.06812286377\t5286829.375\t100\n+143.032638549805\t2735.88037109375\t0.05\n+\n+RECORD_TITLE: MZ:146.1174 | RT:46.2 | grpid:62 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 146.117395027245\n+AC$CHROMATOGRAPHY: RETENTION_TIME"..b"ethod 'av_all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 7\n+PK$PEAK: m/z int. rel.int.\n+103.690208435059\t5716.66162109375\t0.05\n+112.050846099854\t11784687\t100\n+174.621200561523\t5244.80419921875\t0.04\n+200.266555786133\t5990.37744140625\t0.05\n+244.092681884766\t114135.3828125\t0.97\n+294.906677246094\t6473.75732421875\t0.05\n+448.8837890625\t6051.86181640625\t0.05\n+\n+RECORD_TITLE: MZ:494.1968 | RT:49.9 | grpid:830 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 494.196757645669\n+AC$CHROMATOGRAPHY: RETENTION_TIME 49.9356528\n+XCMS groupid (grpid): 830\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 43\n+PK$PEAK: m/z int. rel.int.\n+101.02392578125\t4665.49853515625\t0.46\n+102.055374145508\t147275.96875\t14.46\n+102.392883300781\t3496.21337890625\t0.34\n+108.04434967041\t4591.63720703125\t0.45\n+108.044906616211\t7338.142578125\t0.72\n+109.028678894043\t35977.96484375\t3.53\n+110.060516357422\t4515.4990234375\t0.44\n+112.050483703613\t5202.08544921875\t0.51\n+114.055294036865\t8047.6591796875\t0.79\n+116.070938110352\t148026.921875\t14.53\n+126.055130004883\t383223.53125\t37.62\n+127.039051055908\t19638.7255859375\t1.93\n+130.049903869629\t124625.0859375\t12.23\n+131.064346313477\t4367.2939453125\t0.43\n+133.538024902344\t3557.1923828125\t0.35\n+134.355972290039\t4310.93603515625\t0.42\n+136.169921875\t4170.79638671875\t0.41\n+138.054985046387\t1018626.90625\t100\n+140.379119873047\t4150.32763671875\t0.41\n+144.054061889648\t6955.7412109375\t0.68\n+144.065574645996\t275421.6875\t27.04\n+148.060394287109\t523997.53125\t51.44\n+150.054046630859\t3918.6318359375\t0.38\n+168.051147460938\t6748.05224609375\t0.66\n+168.065574645996\t174448.5546875\t17.13\n+186.076110839844\t123347.046875\t12.11\n+197.289779663086\t4408.47607421875\t0.43\n+219.097625732422\t8514.79125976562\t0.84\n+230.102722167969\t7866.95288085938\t0.77\n+239.558517456055\t4159.935546875\t0.41\n+258.096481323242\t12516.89453125\t1.23\n+285.323272705078\t4496.87939453125\t0.44\n+291.116821289062\t6737.97021484375\t0.66\n+291.118927001953\t8675.626953125\t0.85\n+301.107269287109\t5462.4970703125\t0.54\n+301.139266967773\t89015.59375\t8.74\n+302.220367431641\t3734.84155273438\t0.37\n+319.864624023438\t4290.947265625\t0.42\n+329.133895874023\t12967.8857421875\t1.27\n+332.25048828125\t4750.3056640625\t0.47\n+342.581665039062\t3982.03881835938\t0.39\n+376.824645996094\t3809.353515625\t0.37\n+426.685913085938\t4104.65283203125\t0.4\n+\n+RECORD_TITLE: MZ:498.1693 | RT:81.2 | grpid:840 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 498.169308539313\n+AC$CHROMATOGRAPHY: RETENTION_TIME 81.162672\n+XCMS groupid (grpid): 840\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 15\n+PK$PEAK: m/z int. rel.int.\n+110.071098327637\t19380.7294921875\t1.67\n+113.020816802979\t9337.1875\t0.81\n+136.075546264648\t26832.8837890625\t2.32\n+138.054496765137\t22557.607421875\t1.95\n+208.058097839355\t58436.056640625\t5.05\n+226.068435668945\t146951.8125\t12.7\n+236.147369384766\t6149.79077148438\t0.53\n+279.0947265625\t24795.88671875\t2.14\n+298.089447021484\t615103.03125\t53.15\n+323.121139526367\t466568.765625\t40.32\n+351.116027832031\t196796\t17.01\n+369.126586914062\t886075.9375\t76.57\n+452.164505004883\t53825.01953125\t4.65\n+480.157821655273\t18973.7768554688\t1.64\n+498.169281005859\t1157278.375\t100\n+\n+RECORD_TITLE: MZ:499.2505 | RT:129.3 | grpid:843 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 499.250501059464\n+AC$CHROMATOGRAPHY: RETENTION_TIME 129.271086\n+XCMS groupid (grpid): 843\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 9\n+PK$PEAK: m/z int. rel.int.\n+110.034912109375\t5403.05908203125\t0.28\n+118.086486816406\t5748.27075195312\t0.3\n+119.035583496094\t4770.26611328125\t0.25\n+137.045799255371\t1940576.6875\t100\n+143.80290222168\t3752.88916015625\t0.19\n+185.164245605469\t6015.66552734375\t0.31\n+188.177719116211\t3627.47534179688\t0.19\n+231.170310974121\t77430.171875\t3.99\n+473.909973144531\t4030.2705078125\t0.21\n+\n" |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/createMSP_output_av_all_and_all_xcms.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/createMSP_output_av_all_and_all_xcms.msp Wed Nov 27 14:23:10 2019 -0500 |
| b |
| @@ -0,0 +1,10 @@ +RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:NA +MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484 +AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903 +XCMS groupid (grpid): 12 +COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.0 +PK$NUM_PEAK: 2 +PK$PEAK: m/z int. rel.int. +112.050884246826 502873.46875 100 +126.53768157959 2499.31469726562 0.5 + |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/createMSP_output_av_all_metadata.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/createMSP_output_av_all_metadata.msp Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| @@ -0,0 +1,36 @@ +RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+NH4]+ +MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484 +AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903 +isotope [4][M]+ +MS$FOCUSED_ION: PRECURSOR_TYPE [M+NH4]+ +AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo +AC$MASS_SPECTROMETRY: ION_MODE POSITIVE +AC$MASS_SPECTROMETRY: MS_TYPE MS2 +CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N +CH$LINK: PUBCHEM CID:5328 +CH$NAME Unknown +XCMS groupid (grpid): 12 +COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.0 +PK$NUM_PEAK: 2 +PK$PEAK: m/z int. rel.int. +112.050884246826 502873.46875 100 +126.53768157959 2499.31469726562 0.5 + +RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+H+NH3]+ +MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484 +AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903 +isotope [4][M]+ +MS$FOCUSED_ION: PRECURSOR_TYPE [M+H+NH3]+ +AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo +AC$MASS_SPECTROMETRY: ION_MODE POSITIVE +AC$MASS_SPECTROMETRY: MS_TYPE MS2 +CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N +CH$LINK: PUBCHEM CID:5328 +CH$NAME Unknown +XCMS groupid (grpid): 12 +COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.0 +PK$NUM_PEAK: 2 +PK$PEAK: m/z int. rel.int. +112.050884246826 502873.46875 100 +126.53768157959 2499.31469726562 0.5 + |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/createMSP_output_av_inter.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/createMSP_output_av_inter.msp Wed Nov 27 14:23:10 2019 -0500 |
| b |
| b"@@ -0,0 +1,3182 @@\n+RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484\n+AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903\n+XCMS groupid (grpid): 12\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_inter' msPurity version:1.12.0 \n+PK$NUM_PEAK: 2\n+PK$PEAK: m/z int. rel.int.\n+112.050884246826\t502873.46875\t100\n+126.53768157959\t2499.31469726562\t0.5\n+\n+RECORD_TITLE: MZ:113.0354 | RT:83.4 | grpid:14 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 113.03541992282\n+AC$CHROMATOGRAPHY: RETENTION_TIME 83.441172\n+XCMS groupid (grpid): 14\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_inter' msPurity version:1.12.0 \n+PK$NUM_PEAK: 2\n+PK$PEAK: m/z int. rel.int.\n+112.999992370605\t67035.0703125\t0.63\n+113.03479385376\t10613844.25\t100\n+\n+RECORD_TITLE: MZ:116.0706 | RT:47.7 | grpid:17 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070637437099\n+AC$CHROMATOGRAPHY: RETENTION_TIME 47.662548\n+XCMS groupid (grpid): 17\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_inter' msPurity version:1.12.0 \n+PK$NUM_PEAK: 3\n+PK$PEAK: m/z int. rel.int.\n+116.016647338867\t4672.2880859375\t2.97\n+116.070896148682\t157547.453125\t100\n+116.107257843018\t6525.58282470703\t4.14\n+\n+RECORD_TITLE: MZ:132.1018 | RT:73.5 | grpid:41 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 132.101827805179\n+AC$CHROMATOGRAPHY: RETENTION_TIME 73.529172\n+XCMS groupid (grpid): 41\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_inter' msPurity version:1.12.0 \n+PK$NUM_PEAK: 1\n+PK$PEAK: m/z int. rel.int.\n+132.102035522461\t338114.46875\t100\n+\n+RECORD_TITLE: MZ:137.0456 | RT:127 | grpid:47 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 137.045578757527\n+AC$CHROMATOGRAPHY: RETENTION_TIME 126.956946\n+XCMS groupid (grpid): 47\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_inter' msPurity version:1.12.0 \n+PK$NUM_PEAK: 17\n+PK$PEAK: m/z int. rel.int.\n+104.860054016113\t30638.400390625\t0.26\n+109.06566619873\t2550.77392578125\t0.02\n+110.028198242188\t67928.296875\t0.58\n+110.035272598267\t511818.559082031\t4.38\n+110.559509277344\t33952.66015625\t0.29\n+112.050750732422\t24920.3304443359\t0.21\n+119.020355224609\t16488.48828125\t0.14\n+119.035472869873\t376451.501953125\t3.22\n+127.993309020996\t1960.09631347656\t0.02\n+128.04508972168\t18434.0234375\t0.16\n+128.045852661133\t75962.28125\t0.65\n+136.124038696289\t2269.25805664062\t0.02\n+137.045829772949\t11689172.5\t100\n+138.029312133789\t2125.6455078125\t0.02\n+138.030548095703\t43127.65234375\t0.37\n+154.112442016602\t2006.76232910156\t0.02\n+159.283874511719\t2343.61376953125\t0.02\n+\n+RECORD_TITLE: MZ:138.0547 | RT:50.7 | grpid:48 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 138.05471057982\n+AC$CHROMATOGRAPHY: RETENTION_TIME 50.6971758\n+XCMS groupid (grpid): 48\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_inter' msPurity version:1.12.0 \n+PK$NUM_PEAK: 3\n+PK$PEAK: m/z int. rel.int.\n+110.060352325439\t34625.283203125\t7.61\n+110.072189331055\t8668.18530273438\t1.9\n+138.054901123047\t455046.234375\t100\n+\n+RECORD_TITLE: MZ:138.0487 | RT:127 | grpid:49 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 138.048727400006\n+AC$CHROMATOGRAPHY: RETENTION_TIME 126.956946\n+XCMS groupid (grpid): 49\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_inter' msPurity version:1.12.0 \n+PK$NUM_PEAK: 8\n+PK$PEAK: m/z int. rel.int.\n+110.035133361816\t4197.11962890625\t0.87\n+111.032066345215\t3606.22302246094\t0.75\n+111.038753509521\t22056.884765625\t4.56\n+120.031585693359\t3442.69409179688\t0.71\n+120.038921356201\t14920.083984375\t3.08\n+131.267166137695\t2650.74243164062\t0.55\n+137.396865844727\t3584.59228515625\t0.74\n+138.050010681152\t483746.53125\t100\n+\n+RECORD_TITLE: MZ:140.0678 | RT:46.2 | grpid:51 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 140"..b"69629\t124625.0859375\t12.23\n+131.064346313477\t4367.2939453125\t0.43\n+133.538024902344\t3557.1923828125\t0.35\n+134.355972290039\t4310.93603515625\t0.42\n+136.169921875\t4170.79638671875\t0.41\n+138.054985046387\t1018626.90625\t100\n+140.379119873047\t4150.32763671875\t0.41\n+144.054061889648\t6955.7412109375\t0.68\n+144.065574645996\t275421.6875\t27.04\n+148.060394287109\t523997.53125\t51.44\n+150.054046630859\t3918.6318359375\t0.38\n+168.051147460938\t6748.05224609375\t0.66\n+168.065574645996\t174448.5546875\t17.13\n+186.076110839844\t123347.046875\t12.11\n+197.289779663086\t4408.47607421875\t0.43\n+219.097625732422\t8514.79125976562\t0.84\n+230.102722167969\t7866.95288085938\t0.77\n+239.558517456055\t4159.935546875\t0.41\n+258.096481323242\t12516.89453125\t1.23\n+285.323272705078\t4496.87939453125\t0.44\n+291.116821289062\t6737.97021484375\t0.66\n+291.118927001953\t8675.626953125\t0.85\n+301.107269287109\t5462.4970703125\t0.54\n+301.139266967773\t89015.59375\t8.74\n+302.220367431641\t3734.84155273438\t0.37\n+319.864624023438\t4290.947265625\t0.42\n+329.133895874023\t12967.8857421875\t1.27\n+332.25048828125\t4750.3056640625\t0.47\n+342.581665039062\t3982.03881835938\t0.39\n+376.824645996094\t3809.353515625\t0.37\n+426.685913085938\t4104.65283203125\t0.4\n+\n+RECORD_TITLE: MZ:498.1693 | RT:81.2 | grpid:840 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 498.169308539313\n+AC$CHROMATOGRAPHY: RETENTION_TIME 81.162672\n+XCMS groupid (grpid): 840\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_inter' msPurity version:1.12.0 \n+PK$NUM_PEAK: 45\n+PK$PEAK: m/z int. rel.int.\n+101.778099060059\t3795.03295898438\t0.42\n+106.049766540527\t6611.89404296875\t0.74\n+109.610725402832\t3484.1552734375\t0.39\n+110.071098327637\t19380.7294921875\t2.16\n+113.020816802979\t9337.1875\t1.04\n+126.054611206055\t5812.5556640625\t0.65\n+127.031745910645\t4190.18701171875\t0.47\n+136.075546264648\t26832.8837890625\t2.99\n+137.078796386719\t9176.759765625\t1.02\n+138.054496765137\t22557.607421875\t2.51\n+148.036193847656\t6227.35693359375\t0.69\n+159.81298828125\t3442.19995117188\t0.38\n+167.347625732422\t4180.2548828125\t0.47\n+170.04133605957\t5330.70458984375\t0.59\n+180.837631225586\t3948.50952148438\t0.44\n+184.057907104492\t8015.86474609375\t0.89\n+186.075622558594\t4476.88330078125\t0.5\n+188.469665527344\t3955.94091796875\t0.44\n+195.686859130859\t3936.31909179688\t0.44\n+200.988327026367\t3759.4541015625\t0.42\n+208.058097839355\t58436.056640625\t6.5\n+210.997604370117\t4414.2978515625\t0.49\n+214.955703735352\t4026.87036132812\t0.45\n+226.046966552734\t7511.52294921875\t0.84\n+226.068435668945\t146951.8125\t16.35\n+236.147369384766\t6149.79077148438\t0.68\n+241.538787841797\t4289.0048828125\t0.48\n+244.78190612793\t4454.5654296875\t0.5\n+276.721008300781\t3612.77392578125\t0.4\n+279.0947265625\t24795.88671875\t2.76\n+296.157531738281\t4649.9521484375\t0.52\n+297.103424072266\t4021.5634765625\t0.45\n+298.089447021484\t615103.03125\t68.43\n+308.5830078125\t4018.92358398438\t0.45\n+311.841857910156\t3540.38208007812\t0.39\n+313.098754882812\t4193.3427734375\t0.47\n+323.121139526367\t466568.765625\t51.91\n+351.116027832031\t196796\t21.89\n+368.141418457031\t7687.5947265625\t0.86\n+368.143646240234\t8117.44580078125\t0.9\n+369.124267578125\t5257.81591796875\t0.58\n+369.126586914062\t886075.9375\t98.58\n+452.164505004883\t53825.01953125\t5.99\n+480.157821655273\t18973.7768554688\t2.11\n+498.169242858887\t898832.592529297\t100\n+\n+RECORD_TITLE: MZ:499.2505 | RT:129.3 | grpid:843 | file:NA | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 499.250501059464\n+AC$CHROMATOGRAPHY: RETENTION_TIME 129.271086\n+XCMS groupid (grpid): 843\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_inter' msPurity version:1.12.0 \n+PK$NUM_PEAK: 9\n+PK$PEAK: m/z int. rel.int.\n+110.034912109375\t5403.05908203125\t0.28\n+118.086486816406\t5748.27075195312\t0.3\n+119.035583496094\t4770.26611328125\t0.25\n+137.045799255371\t1940576.6875\t100\n+143.80290222168\t3752.88916015625\t0.19\n+185.164245605469\t6015.66552734375\t0.31\n+188.177719116211\t3627.47534179688\t0.19\n+231.170310974121\t77430.171875\t3.99\n+473.909973144531\t4030.2705078125\t0.21\n+\n" |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/createMSP_output_av_intra.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/createMSP_output_av_intra.msp Wed Nov 27 14:23:10 2019 -0500 |
| b |
| b"@@ -0,0 +1,4664 @@\n+RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:1 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484\n+AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903\n+XCMS groupid (grpid): 12\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.12.0 \n+PK$NUM_PEAK: 1\n+PK$PEAK: m/z int. rel.int.\n+112.050888061523\t440629.6875\t100\n+\n+RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484\n+AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903\n+XCMS groupid (grpid): 12\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.12.0 \n+PK$NUM_PEAK: 2\n+PK$PEAK: m/z int. rel.int.\n+112.050880432129\t565117.25\t100\n+126.53768157959\t2499.31469726562\t0.44\n+\n+RECORD_TITLE: MZ:113.0354 | RT:83.4 | grpid:14 | file:1 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 113.03541992282\n+AC$CHROMATOGRAPHY: RETENTION_TIME 83.441172\n+XCMS groupid (grpid): 14\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.12.0 \n+PK$NUM_PEAK: 1\n+PK$PEAK: m/z int. rel.int.\n+113.034782409668\t13262784\t100\n+\n+RECORD_TITLE: MZ:113.0354 | RT:83.4 | grpid:14 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 113.03541992282\n+AC$CHROMATOGRAPHY: RETENTION_TIME 83.441172\n+XCMS groupid (grpid): 14\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.12.0 \n+PK$NUM_PEAK: 2\n+PK$PEAK: m/z int. rel.int.\n+112.999992370605\t67035.0703125\t0.84\n+113.034805297852\t7964904.5\t100\n+\n+RECORD_TITLE: MZ:116.0706 | RT:47.7 | grpid:17 | file:1 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070637437099\n+AC$CHROMATOGRAPHY: RETENTION_TIME 47.662548\n+XCMS groupid (grpid): 17\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.12.0 \n+PK$NUM_PEAK: 3\n+PK$PEAK: m/z int. rel.int.\n+116.016784667969\t5682.14404296875\t3.8\n+116.070899963379\t149471.265625\t100\n+116.10725402832\t6152.61499023438\t4.12\n+\n+RECORD_TITLE: MZ:116.0706 | RT:47.7 | grpid:17 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070637437099\n+AC$CHROMATOGRAPHY: RETENTION_TIME 47.662548\n+XCMS groupid (grpid): 17\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.12.0 \n+PK$NUM_PEAK: 3\n+PK$PEAK: m/z int. rel.int.\n+116.016510009766\t3662.43212890625\t2.21\n+116.070892333984\t165623.640625\t100\n+116.107261657715\t6898.55065917969\t4.17\n+\n+RECORD_TITLE: MZ:132.1018 | RT:73.5 | grpid:41 | file:1 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 132.101827805179\n+AC$CHROMATOGRAPHY: RETENTION_TIME 73.529172\n+XCMS groupid (grpid): 41\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.12.0 \n+PK$NUM_PEAK: 1\n+PK$PEAK: m/z int. rel.int.\n+132.102035522461\t273406.25\t100\n+\n+RECORD_TITLE: MZ:132.1018 | RT:73.5 | grpid:41 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 132.101827805179\n+AC$CHROMATOGRAPHY: RETENTION_TIME 73.529172\n+XCMS groupid (grpid): 41\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.12.0 \n+PK$NUM_PEAK: 1\n+PK$PEAK: m/z int. rel.int.\n+132.102035522461\t402822.6875\t100\n+\n+RECORD_TITLE: MZ:137.0456 | RT:127 | grpid:47 | file:1 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 137.045578757527\n+AC$CHROMATOGRAPHY: RETENTION_TIME 126.956946\n+XCMS groupid (grpid): 47\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.12.0 \n+PK$NUM_PEAK: 12\n+PK$PEAK: m/z int. rel.int.\n+104.860054016113\t30638.400390625\t0.18\n+110.028198242188\t67928.296875\t0.4\n+110.035266876221\t733295.444335938\t4.35\n+110.559509277344\t33952.66015625\t0.2\n+112.050758361816\t37811.4998779297\t0.22\n+119.035530090332\t552159.596679688\t3.28\n+127.993309020996\t1960.09631347656\t0.01\n"..b" 840\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.12.0 \n+PK$NUM_PEAK: 27\n+PK$PEAK: m/z int. rel.int.\n+110.071174621582\t19027.2734375\t1.64\n+113.020904541016\t9368.123046875\t0.81\n+126.054611206055\t5812.5556640625\t0.5\n+127.031745910645\t4190.18701171875\t0.36\n+136.075302124023\t22934.310546875\t1.98\n+137.078796386719\t9176.759765625\t0.79\n+138.054428100586\t23509.2890625\t2.03\n+148.036193847656\t6227.35693359375\t0.54\n+170.04133605957\t5330.70458984375\t0.46\n+186.075622558594\t4476.88330078125\t0.39\n+208.057647705078\t61292.54296875\t5.3\n+210.997604370117\t4414.2978515625\t0.38\n+214.955703735352\t4026.87036132812\t0.35\n+226.068435668945\t138242.484375\t11.95\n+236.147445678711\t7551.0751953125\t0.65\n+241.538787841797\t4289.0048828125\t0.37\n+279.094696044922\t23287.87890625\t2.01\n+297.103424072266\t4021.5634765625\t0.35\n+298.089477539062\t604584.8125\t52.24\n+313.098754882812\t4193.3427734375\t0.36\n+323.121063232422\t447545.03125\t38.67\n+351.115936279297\t177400.859375\t15.33\n+368.141418457031\t7687.5947265625\t0.66\n+369.126556396484\t840579.1875\t72.63\n+452.164520263672\t46214.9140625\t3.99\n+480.158355712891\t21752.802734375\t1.88\n+498.169158935547\t1157278.375\t100\n+\n+RECORD_TITLE: MZ:498.1693 | RT:81.2 | grpid:840 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 498.169308539313\n+AC$CHROMATOGRAPHY: RETENTION_TIME 81.162672\n+XCMS groupid (grpid): 840\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.12.0 \n+PK$NUM_PEAK: 33\n+PK$PEAK: m/z int. rel.int.\n+101.778099060059\t3795.03295898438\t0.41\n+106.049766540527\t6611.89404296875\t0.71\n+109.610725402832\t3484.1552734375\t0.37\n+110.071022033691\t19734.185546875\t2.12\n+113.020729064941\t9306.251953125\t1\n+136.075790405273\t30731.45703125\t3.3\n+138.054565429688\t21605.92578125\t2.32\n+159.81298828125\t3442.19995117188\t0.37\n+167.347625732422\t4180.2548828125\t0.45\n+180.837631225586\t3948.50952148438\t0.42\n+184.057907104492\t8015.86474609375\t0.86\n+188.469665527344\t3955.94091796875\t0.42\n+195.686859130859\t3936.31909179688\t0.42\n+200.988327026367\t3759.4541015625\t0.4\n+208.058547973633\t55579.5703125\t5.97\n+226.046966552734\t7511.52294921875\t0.81\n+226.068435668945\t155661.140625\t16.71\n+236.14729309082\t4748.50634765625\t0.51\n+244.78190612793\t4454.5654296875\t0.48\n+276.721008300781\t3612.77392578125\t0.39\n+279.094757080078\t26303.89453125\t2.82\n+296.157531738281\t4649.9521484375\t0.5\n+298.089416503906\t625621.25\t67.16\n+308.5830078125\t4018.92358398438\t0.43\n+311.841857910156\t3540.38208007812\t0.38\n+323.121215820312\t485592.5\t52.13\n+351.116119384766\t216191.140625\t23.21\n+368.143646240234\t8117.44580078125\t0.87\n+369.124267578125\t5257.81591796875\t0.56\n+369.126617431641\t931572.6875\t100\n+452.164489746094\t61435.125\t6.59\n+480.157287597656\t16194.7509765625\t1.74\n+498.169326782227\t640386.810058594\t68.74\n+\n+RECORD_TITLE: MZ:499.2505 | RT:129.3 | grpid:843 | file:1 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 499.250501059464\n+AC$CHROMATOGRAPHY: RETENTION_TIME 129.271086\n+XCMS groupid (grpid): 843\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.12.0 \n+PK$NUM_PEAK: 8\n+PK$PEAK: m/z int. rel.int.\n+118.086380004883\t7052.74462890625\t0.36\n+119.035583496094\t4770.26611328125\t0.24\n+137.045806884766\t1959734\t100\n+143.80290222168\t3752.88916015625\t0.19\n+185.164245605469\t6015.66552734375\t0.31\n+188.177719116211\t3627.47534179688\t0.19\n+231.17024230957\t75057.1484375\t3.83\n+473.909973144531\t4030.2705078125\t0.21\n+\n+RECORD_TITLE: MZ:499.2505 | RT:129.3 | grpid:843 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 499.250501059464\n+AC$CHROMATOGRAPHY: RETENTION_TIME 129.271086\n+XCMS groupid (grpid): 843\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_intra' msPurity version:1.12.0 \n+PK$NUM_PEAK: 4\n+PK$PEAK: m/z int. rel.int.\n+110.034912109375\t5403.05908203125\t0.28\n+118.08659362793\t4443.796875\t0.23\n+137.045791625977\t1921419.375\t100\n+231.170379638672\t79803.1953125\t4.15\n+\n" |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/createMSP_output_max.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/createMSP_output_max.msp Wed Nov 27 14:23:10 2019 -0500 |
| b |
| b"@@ -0,0 +1,2587 @@\n+RECORD_TITLE: MZ:112.0507 | RT:67.6 | grpid:12 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050743103027\n+AC$CHROMATOGRAPHY: RETENTION_TIME 67.634034\n+XCMS groupid (grpid): 12\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.12.0 \n+PK$NUM_PEAK: 2\n+PK$PEAK: m/z int. rel.int.\n+112.050880432129\t565117.25\t100\n+126.53768157959\t2499.31469726562\t0.44\n+\n+RECORD_TITLE: MZ:113.0347 | RT:83.4 | grpid:14 | file:1 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 113.034736633301\n+AC$CHROMATOGRAPHY: RETENTION_TIME 83.441172\n+XCMS groupid (grpid): 14\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.12.0 \n+PK$NUM_PEAK: 1\n+PK$PEAK: m/z int. rel.int.\n+113.034782409668\t13262784\t100\n+\n+RECORD_TITLE: MZ:116.0708 | RT:47.8 | grpid:17 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070823669434\n+AC$CHROMATOGRAPHY: RETENTION_TIME 47.814411\n+XCMS groupid (grpid): 17\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.12.0 \n+PK$NUM_PEAK: 1\n+PK$PEAK: m/z int. rel.int.\n+116.070892333984\t1847702.625\t100\n+\n+RECORD_TITLE: MZ:132.1019 | RT:73.5 | grpid:41 | file:1 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 132.101867675781\n+AC$CHROMATOGRAPHY: RETENTION_TIME 73.529172\n+XCMS groupid (grpid): 41\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.12.0 \n+PK$NUM_PEAK: 2\n+PK$PEAK: m/z int. rel.int.\n+130.186950683594\t121726.4453125\t3.06\n+132.102035522461\t3973065.5\t100\n+\n+RECORD_TITLE: MZ:137.0456 | RT:127 | grpid:47 | file:1 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 137.045639038086\n+AC$CHROMATOGRAPHY: RETENTION_TIME 126.956946\n+XCMS groupid (grpid): 47\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.12.0 \n+PK$NUM_PEAK: 9\n+PK$PEAK: m/z int. rel.int.\n+104.860054016113\t30638.400390625\t0.09\n+110.028198242188\t67928.296875\t0.21\n+110.035293579102\t1441146.625\t4.36\n+110.559509277344\t33952.66015625\t0.1\n+112.050506591797\t73567.3125\t0.22\n+119.035423278809\t1085099.625\t3.28\n+128.045852661133\t75962.28125\t0.23\n+137.045822143555\t33090892\t100\n+138.030548095703\t43127.65234375\t0.13\n+\n+RECORD_TITLE: MZ:138.0548 | RT:50.8 | grpid:48 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 138.054809570312\n+AC$CHROMATOGRAPHY: RETENTION_TIME 50.8435338\n+XCMS groupid (grpid): 48\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.12.0 \n+PK$NUM_PEAK: 7\n+PK$PEAK: m/z int. rel.int.\n+110.060409545898\t151747.359375\t6.55\n+110.071807861328\t12626.90234375\t0.54\n+128.93376159668\t2266.6416015625\t0.1\n+136.491333007812\t2493.95458984375\t0.11\n+138.054901123047\t2317689.75\t100\n+154.049453735352\t5643.62890625\t0.24\n+159.010818481445\t2415.3876953125\t0.1\n+\n+RECORD_TITLE: MZ:138.0488 | RT:126.4 | grpid:49 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 138.048797607422\n+AC$CHROMATOGRAPHY: RETENTION_TIME 126.441198\n+XCMS groupid (grpid): 49\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.12.0 \n+PK$NUM_PEAK: 5\n+PK$PEAK: m/z int. rel.int.\n+111.032066345215\t4279.24560546875\t0.77\n+111.038848876953\t24677.09765625\t4.42\n+120.038902282715\t18950.03125\t3.39\n+137.396865844727\t3584.59228515625\t0.64\n+138.05012512207\t558628.8125\t100\n+\n+RECORD_TITLE: MZ:140.0681 | RT:46.3 | grpid:51 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 140.068084716797\n+AC$CHROMATOGRAPHY: RETENTION_TIME 46.2952926\n+XCMS groupid (grpid): 51\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.12.0 \n+PK$NUM_PEAK: 2\n+PK$PEAK: m/z int. rel.int.\n+114.089164733887\t856653.625\t10.81\n+140.068130493164\t7923872\t100\n+\n+RECORD_TITLE: MZ:146.1174 | RT:46.3 | grpid:62 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 146.117416381836\n+AC$CH"..b"\n+144.065582275391\t61227.703125\t22.68\n+145.069046020508\t33886.6875\t12.55\n+148.060440063477\t91076.7421875\t33.73\n+149.064071655273\t26683.80078125\t9.88\n+168.065292358398\t40215.578125\t14.9\n+169.069198608398\t34653.2890625\t12.84\n+186.076416015625\t39170.015625\t14.51\n+187.079940795898\t24879.5\t9.22\n+301.139862060547\t19206.294921875\t7.11\n+302.141815185547\t33403.7578125\t12.37\n+360.640808105469\t4196.35400390625\t1.55\n+480.125091552734\t3905.12133789062\t1.45\n+\n+RECORD_TITLE: MZ:487.1779 | RT:66.9 | grpid:812 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 487.177856445312\n+AC$CHROMATOGRAPHY: RETENTION_TIME 66.865908\n+XCMS groupid (grpid): 812\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.12.0 \n+PK$NUM_PEAK: 3\n+PK$PEAK: m/z int. rel.int.\n+112.050857543945\t12582074\t100\n+244.092895507812\t124155.421875\t0.99\n+294.906677246094\t6473.75732421875\t0.05\n+\n+RECORD_TITLE: MZ:494.1976 | RT:50.1 | grpid:830 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 494.197631835938\n+AC$CHROMATOGRAPHY: RETENTION_TIME 50.0837946\n+XCMS groupid (grpid): 830\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.12.0 \n+PK$NUM_PEAK: 29\n+PK$PEAK: m/z int. rel.int.\n+101.02392578125\t4665.49853515625\t0.46\n+102.05541229248\t139830.640625\t13.9\n+108.044906616211\t7338.142578125\t0.73\n+109.028587341309\t34949.8125\t3.47\n+110.060516357422\t4515.4990234375\t0.45\n+114.055053710938\t8607.400390625\t0.86\n+116.070930480957\t143212.125\t14.24\n+126.055122375488\t382392.125\t38.01\n+127.039169311523\t22511.798828125\t2.24\n+130.049911499023\t114702.28125\t11.4\n+136.169921875\t4170.79638671875\t0.41\n+138.054992675781\t1006045.75\t100\n+144.065567016602\t271017.65625\t26.94\n+148.060394287109\t530132.8125\t52.69\n+150.054046630859\t3918.6318359375\t0.39\n+168.065612792969\t182116.0625\t18.1\n+186.076141357422\t123048.53125\t12.23\n+197.289779663086\t4408.47607421875\t0.44\n+219.09797668457\t7606.20068359375\t0.76\n+230.102798461914\t9371.7431640625\t0.93\n+239.558517456055\t4159.935546875\t0.41\n+258.096801757812\t15609.2587890625\t1.55\n+291.118927001953\t8675.626953125\t0.86\n+301.139556884766\t84987.3046875\t8.45\n+302.220367431641\t3734.84155273438\t0.37\n+329.133361816406\t18578.4765625\t1.85\n+332.25048828125\t4750.3056640625\t0.47\n+342.581665039062\t3982.03881835938\t0.4\n+376.824645996094\t3809.353515625\t0.38\n+\n+RECORD_TITLE: MZ:498.1689 | RT:81.3 | grpid:840 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 498.168914794922\n+AC$CHROMATOGRAPHY: RETENTION_TIME 81.344292\n+XCMS groupid (grpid): 840\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.12.0 \n+PK$NUM_PEAK: 21\n+PK$PEAK: m/z int. rel.int.\n+106.049766540527\t6611.89404296875\t0.52\n+110.071022033691\t19734.185546875\t1.56\n+113.020729064941\t9306.251953125\t0.74\n+136.075790405273\t30731.45703125\t2.43\n+138.054565429688\t21605.92578125\t1.71\n+167.347625732422\t4180.2548828125\t0.33\n+180.837631225586\t3948.50952148438\t0.31\n+184.057907104492\t8015.86474609375\t0.63\n+208.058547973633\t55579.5703125\t4.39\n+226.046966552734\t7511.52294921875\t0.59\n+226.068435668945\t155661.140625\t12.3\n+236.14729309082\t4748.50634765625\t0.38\n+279.094757080078\t26303.89453125\t2.08\n+298.089416503906\t625621.25\t49.43\n+323.121215820312\t485592.5\t38.36\n+351.116119384766\t216191.140625\t17.08\n+368.143646240234\t8117.44580078125\t0.64\n+369.126617431641\t931572.6875\t73.6\n+452.164489746094\t61435.125\t4.85\n+480.157287597656\t16194.7509765625\t1.28\n+498.169281005859\t1265792.25\t100\n+\n+RECORD_TITLE: MZ:499.2504 | RT:129.5 | grpid:843 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 499.250396728516\n+AC$CHROMATOGRAPHY: RETENTION_TIME 129.525558\n+XCMS groupid (grpid): 843\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'max' msPurity version:1.12.0 \n+PK$NUM_PEAK: 4\n+PK$PEAK: m/z int. rel.int.\n+110.034912109375\t5403.05908203125\t0.28\n+118.08659362793\t4443.796875\t0.23\n+137.045791625977\t1921419.375\t100\n+231.170379638672\t79803.1953125\t4.15\n+\n" |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/createMSP_output_scans_all.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/createMSP_output_scans_all.msp Wed Nov 27 14:23:10 2019 -0500 |
| b |
| b"@@ -0,0 +1,8190 @@\n+RECORD_TITLE: MZ:112.0507 | RT:67.5 | grpid:12 | file:1 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050704956055\n+AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903\n+XCMS groupid (grpid): 12\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 1\n+PK$PEAK: m/z int. rel.int.\n+112.050888061523\t440629.6875\t100\n+\n+RECORD_TITLE: MZ:112.0507 | RT:67.6 | grpid:12 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050743103027\n+AC$CHROMATOGRAPHY: RETENTION_TIME 67.634034\n+XCMS groupid (grpid): 12\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 2\n+PK$PEAK: m/z int. rel.int.\n+112.050880432129\t565117.25\t100\n+126.53768157959\t2499.31469726562\t0.44\n+\n+RECORD_TITLE: MZ:113.0347 | RT:83.4 | grpid:14 | file:1 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 113.034736633301\n+AC$CHROMATOGRAPHY: RETENTION_TIME 83.441172\n+XCMS groupid (grpid): 14\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 1\n+PK$PEAK: m/z int. rel.int.\n+113.034782409668\t13262784\t100\n+\n+RECORD_TITLE: MZ:113.0347 | RT:83.6 | grpid:14 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 113.034736633301\n+AC$CHROMATOGRAPHY: RETENTION_TIME 83.64567\n+XCMS groupid (grpid): 14\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 2\n+PK$PEAK: m/z int. rel.int.\n+112.999992370605\t67035.0703125\t0.84\n+113.034805297852\t7964904.5\t100\n+\n+RECORD_TITLE: MZ:113.0347 | RT:83.6 | grpid:14 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 113.034713745117\n+AC$CHROMATOGRAPHY: RETENTION_TIME 83.64567\n+XCMS groupid (grpid): 14\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 9\n+PK$PEAK: m/z int. rel.int.\n+111.010963439941\t2912.13012695312\t1.32\n+113.000129699707\t40987.0078125\t18.63\n+113.008010864258\t31639.541015625\t14.38\n+113.034889221191\t219966.0625\t100\n+113.060173034668\t14124.5009765625\t6.42\n+113.070793151855\t3284.5654296875\t1.49\n+113.107765197754\t7978.56494140625\t3.63\n+122.0078125\t3665.08813476562\t1.67\n+133.994140625\t1813.58288574219\t0.82\n+\n+RECORD_TITLE: MZ:116.0708 | RT:47.7 | grpid:17 | file:1 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070838928223\n+AC$CHROMATOGRAPHY: RETENTION_TIME 47.662548\n+XCMS groupid (grpid): 17\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 3\n+PK$PEAK: m/z int. rel.int.\n+116.016784667969\t3725.93701171875\t3.82\n+116.070854187012\t97631.5859375\t100\n+116.107086181641\t3945.32666015625\t4.04\n+\n+RECORD_TITLE: MZ:116.0708 | RT:47.7 | grpid:17 | file:1 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070831298828\n+AC$CHROMATOGRAPHY: RETENTION_TIME 47.662548\n+XCMS groupid (grpid): 17\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 4\n+PK$PEAK: m/z int. rel.int.\n+103.129020690918\t4419.71240234375\t0.25\n+116.016410827637\t5682.14404296875\t0.32\n+116.070899963379\t1782171\t100\n+130.027648925781\t4081.13793945312\t0.23\n+\n+RECORD_TITLE: MZ:116.0708 | RT:47.7 | grpid:17 | file:1 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070770263672\n+AC$CHROMATOGRAPHY: RETENTION_TIME 47.662548\n+XCMS groupid (grpid): 17\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 3\n+PK$PEAK: m/z int. rel.int.\n+116.016830444336\t14364.7841796875\t9.61\n+116.070922851562\t149471.265625\t100\n+116.107421875\t8359.9033203125\t5.59\n+\n+RECORD_TITLE: MZ:116.0708 | RT:47.8 | grpid:17 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 116.070816040039\n+AC$CHROMATOGRAPHY: RETENTION_TIME 47.814411\n+XCMS groupid (grpid): 17\n+COMMENT: Exported from msPurity purityA object using"..b"759765625\t0.79\n+138.054428100586\t23509.2890625\t2.03\n+148.036193847656\t6227.35693359375\t0.54\n+170.04133605957\t5330.70458984375\t0.46\n+186.075622558594\t4476.88330078125\t0.39\n+208.057647705078\t61292.54296875\t5.3\n+210.997604370117\t4414.2978515625\t0.38\n+214.955703735352\t4026.87036132812\t0.35\n+226.068435668945\t138242.484375\t11.95\n+236.147445678711\t7551.0751953125\t0.65\n+241.538787841797\t4289.0048828125\t0.37\n+279.094696044922\t23287.87890625\t2.01\n+297.103424072266\t4021.5634765625\t0.35\n+298.089477539062\t604584.8125\t52.24\n+313.098754882812\t4193.3427734375\t0.36\n+323.121063232422\t447545.03125\t38.67\n+351.115936279297\t177400.859375\t15.33\n+368.141418457031\t7687.5947265625\t0.66\n+369.126556396484\t840579.1875\t72.63\n+452.164520263672\t46214.9140625\t3.99\n+480.158355712891\t21752.802734375\t1.88\n+498.169158935547\t1157278.375\t100\n+\n+RECORD_TITLE: MZ:498.1689 | RT:81.3 | grpid:840 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 498.168914794922\n+AC$CHROMATOGRAPHY: RETENTION_TIME 81.344292\n+XCMS groupid (grpid): 840\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 21\n+PK$PEAK: m/z int. rel.int.\n+106.049766540527\t6611.89404296875\t0.52\n+110.071022033691\t19734.185546875\t1.56\n+113.020729064941\t9306.251953125\t0.74\n+136.075790405273\t30731.45703125\t2.43\n+138.054565429688\t21605.92578125\t1.71\n+167.347625732422\t4180.2548828125\t0.33\n+180.837631225586\t3948.50952148438\t0.31\n+184.057907104492\t8015.86474609375\t0.63\n+208.058547973633\t55579.5703125\t4.39\n+226.046966552734\t7511.52294921875\t0.59\n+226.068435668945\t155661.140625\t12.3\n+236.14729309082\t4748.50634765625\t0.38\n+279.094757080078\t26303.89453125\t2.08\n+298.089416503906\t625621.25\t49.43\n+323.121215820312\t485592.5\t38.36\n+351.116119384766\t216191.140625\t17.08\n+368.143646240234\t8117.44580078125\t0.64\n+369.126617431641\t931572.6875\t73.6\n+452.164489746094\t61435.125\t4.85\n+480.157287597656\t16194.7509765625\t1.28\n+498.169281005859\t1265792.25\t100\n+\n+RECORD_TITLE: MZ:498.1697 | RT:81.3 | grpid:840 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 498.169708251953\n+AC$CHROMATOGRAPHY: RETENTION_TIME 81.344292\n+XCMS groupid (grpid): 840\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 13\n+PK$PEAK: m/z int. rel.int.\n+101.778099060059\t3795.03295898438\t25.33\n+109.610725402832\t3484.1552734375\t23.26\n+159.81298828125\t3442.19995117188\t22.98\n+188.469665527344\t3955.94091796875\t26.41\n+195.686859130859\t3936.31909179688\t26.27\n+200.988327026367\t3759.4541015625\t25.09\n+244.78190612793\t4454.5654296875\t29.73\n+276.721008300781\t3612.77392578125\t24.12\n+296.157531738281\t4649.9521484375\t31.04\n+308.5830078125\t4018.92358398438\t26.83\n+311.841857910156\t3540.38208007812\t23.63\n+369.124267578125\t5257.81591796875\t35.1\n+498.169372558594\t14981.3701171875\t100\n+\n+RECORD_TITLE: MZ:499.2504 | RT:129.3 | grpid:843 | file:1 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 499.250396728516\n+AC$CHROMATOGRAPHY: RETENTION_TIME 129.271086\n+XCMS groupid (grpid): 843\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 8\n+PK$PEAK: m/z int. rel.int.\n+118.086380004883\t7052.74462890625\t0.36\n+119.035583496094\t4770.26611328125\t0.24\n+137.045806884766\t1959734\t100\n+143.80290222168\t3752.88916015625\t0.19\n+185.164245605469\t6015.66552734375\t0.31\n+188.177719116211\t3627.47534179688\t0.19\n+231.17024230957\t75057.1484375\t3.83\n+473.909973144531\t4030.2705078125\t0.21\n+\n+RECORD_TITLE: MZ:499.2504 | RT:129.5 | grpid:843 | file:2 | adduct:NA\n+MS$FOCUSED_ION: PRECURSOR_M/Z 499.250396728516\n+AC$CHROMATOGRAPHY: RETENTION_TIME 129.525558\n+XCMS groupid (grpid): 843\n+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'all' msPurity version:1.12.0 \n+PK$NUM_PEAK: 4\n+PK$PEAK: m/z int. rel.int.\n+110.034912109375\t5403.05908203125\t0.28\n+118.08659362793\t4443.796875\t0.23\n+137.045791625977\t1921419.375\t100\n+231.170379638672\t79803.1953125\t4.15\n+\n" |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/dimsPredictPuritySingle_full_scan.mzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dimsPredictPuritySingle_full_scan.mzML Wed Nov 27 14:23:10 2019 -0500 |
| b |
| b'@@ -0,0 +1,4786 @@\n+<?xml version="1.0" encoding="utf-8"?>\n+<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.2_idx.xsd">\n+ <mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" id="A02_Polar_Daph_WAX1_Phenyl_LCMS_Pos_DIMS" version="1.1.0">\n+ <cvList count="2">\n+ <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="4.0.1" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+ <cv id="UO" fullName="Unit Ontology" version="12:10:2011" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>\n+ </cvList>\n+ <fileDescription>\n+ <fileContent>\n+ <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>\n+ </fileContent>\n+ <sourceFileList count="1">\n+ <sourceFile id="RAW1" name="A02_Polar_Daph_WAX1_Phenyl_LCMS_Pos_DIMS.raw" location="file:///R:\\daphnia_magna\\DIMS\\data\\P_WAX_1_PHE\\pos\\di-ms\\WAX1_pos_Subset_A">\n+ <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW format" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="d0b4c9c6fed4992d8991ec15459ffdc702a856fd"/>\n+ </sourceFile>\n+ </sourceFileList>\n+ </fileDescription>\n+ <referenceableParamGroupList count="1">\n+ <referenceableParamGroup id="CommonInstrumentParams">\n+ <cvParam cvRef="MS" accession="MS:1001910" name="LTQ Orbitrap Elite" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000529" name="instrument serial number" value="Slot R-258"/>\n+ </referenceableParamGroup>\n+ </referenceableParamGroupList>\n+ <softwareList count="2">\n+ <software id="Xcalibur" version="2.7.0 SP2">\n+ <cvParam cvRef="MS" accession="MS:1000532" name="Xcalibur" value=""/>\n+ </software>\n+ <software id="pwiz" version="3.0.10112">\n+ <cvParam cvRef="MS" accession="MS:1000615" name="ProteoWizard software" value=""/>\n+ </software>\n+ </softwareList>\n+ <instrumentConfigurationList count="2">\n+ <instrumentConfiguration id="IC1">\n+ <referenceableParamGroupRef ref="CommonInstrumentParams"/>\n+ <componentList count="3">\n+ <source order="1">\n+ <cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" value=""/>\n+ </source>\n+ <analyzer order="2">\n+ <cvParam cvRef="MS" accession="MS:1000484" name="orbitrap" value=""/>\n+ </analyzer>\n+ <detector order="3">\n+ <cvParam cvRef="MS" accession="MS:1000624" name="inductive detector" value=""/>\n+ </detector>\n+ </componentList>\n+ <softwareRef ref="Xcalibur"/>\n+ </instrumentConfiguration>\n+ <instrumentConfiguration id="IC2">\n+ <referenceableParamGroupRef ref="CommonInstrumentParams"/>\n+ <componentList count="3">\n+ <source order="1">\n+ <cvParam cvRef="MS" accession="MS:1000398" name="nanoelectrospray" value=""/>\n+ <cvParam cvRef="MS" accession="MS:1000485" name="nanospray inlet" value=""/>\n+ </source>\n+ <analyzer order="2">\n+ <cvParam cvRef="MS" accession="MS:1000083" name="radial ejection linear ion trap" value=""/>\n+ </analyzer>\n+ <detector order="3">\n+ <cvParam cvRef="MS" accession="MS:1000253" name="electron multiplier" value=""/>\n+ </detector>\n+ </componentList>\n+ <softwareRef ref="Xcalibur"/>\n+ </instrumentConfiguration>\n+ </instrume'..b'trollerType=0 controllerNumber=1 scan=70">721490</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=71">731907</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=72">742477</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=73">752715</offset>\n+ <offset idRef="controllerType=0 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<offset idRef="controllerType=0 controllerNumber=1 scan=87">898707</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=88">908404</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=89">919285</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=90">930126</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=91">941028</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=92">951884</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=93">962709</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=94">973371</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=95">983520</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=96">994502</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=97">1005172</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=98">1015326</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=99">1026139</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=100">1036303</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=101">1046473</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=102">1056428</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=103">1066780</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=104">1076983</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=105">1086862</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=106">1097117</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=107">1107388</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=108">1117335</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=109">1127770</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=110">1138027</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=111">1148371</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=112">1159110</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=113">1169611</offset>\n+ <offset idRef="controllerType=0 controllerNumber=1 scan=114">1180253</offset>\n+ </index>\n+ <index name="chromatogram">\n+ <offset idRef="TIC">1190853</offset>\n+ </index>\n+ </indexList>\n+ <indexListOffset>1193981</indexListOffset>\n+ <fileChecksum>ba1bd6e94c255fdca25732a2e8e5a4f6092528bb</fileChecksum>\n+</indexedmzML>\n' |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/dimsPredictPuritySingle_input_dimspy_peakmatrix.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dimsPredictPuritySingle_input_dimspy_peakmatrix.tsv Wed Nov 27 14:23:10 2019 -0500 |
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|
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/dimsPredictPuritySingle_output.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dimsPredictPuritySingle_output.tsv Wed Nov 27 14:23:10 2019 -0500 |
| b |
| b'@@ -0,0 +1,105 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|
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/filterFragSpectra_output.RData |
| b |
| Binary file test-data/filterFragSpectra_output.RData has changed |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/filterFragSpectra_output_frag.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filterFragSpectra_output_frag.tsv Wed Nov 27 14:23:10 2019 -0500 |
| b |
| b'@@ -0,0 +1,5607 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|
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/filterFragSpectra_output_prec.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filterFragSpectra_output_prec.tsv Wed Nov 27 14:23:10 2019 -0500 |
| b |
| b'@@ -0,0 +1,324 @@\n+"grpid"\t"mz"\t"mzmin"\t"mzmax"\t"rt"\t"rtmin"\t"rtmax"\t"into"\t"intf"\t"maxo"\t"maxf"\t"i"\t"sn"\t"sample"\t"cid"\t"filename"\t"inPurity"\t"pid"\t"precurMtchID"\t"precurMtchScan"\t"precurMtchRT"\t"precurMtchMZ"\t"precurMtchPPM"\t"retentionTime"\t"fileid"\t"seqNum"\t"purity_pass_flag"\n+"12"\t112.050766766484\t112.050651550293\t112.087196350098\t67.47903\t55.2769038\t80.361672\t36223791.266206\t133522503.549415\t7158012.5\t8555976.39592391\t1\t21.054952458659\t1\t9\t"LCMSMS_2.mzML"\t1\t384\t466\t462\t64.427298\t112.050704956055\t0.55162878935702\t64.958766\t1\t466\tTRUE\n+"12"\t112.05085569128\t112.050621032715\t112.120460510254\t67.634034\t55.4140188\t80.555406\t36139265.8017591\t133395720.51942\t7426335.5\t8522973.08164079\t1\t20.3803986860233\t2\t400\t"LCMSMS_1.mzML"\t1\t1218\t472\t468\t65.376156\t112.050743103027\t1.00479600749392\t65.928894\t2\t472\tTRUE\n+"14"\t113.03541992282\t113.034698486328\t113.059997558594\t83.441172\t72.006432\t95.851296\t88462324.9597518\t348004137.88132\t18599380\t22772249.3980656\t1\t27.431622141047\t1\t11\t"LCMSMS_2.mzML"\t1\t499\t604\t600\t81.93093\t113.034736633301\t6.04491512630164\t82.463394\t1\t604\tTRUE\n+"14"\t113.035371704924\t113.034713745117\t113.059936523438\t83.64567\t72.171048\t96.141564\t92812020.095242\t366177037.564437\t20943314\t23904502.6814248\t1\t27.9839052693883\t2\t402\t"LCMSMS_1.mzML"\t1\t1321\t596\t594\t81.344292\t113.034736633301\t5.61834418239318\t81.70764\t2\t596\tTRUE\n+"14"\t113.035371704924\t113.034713745117\t113.059936523438\t83.64567\t72.171048\t96.141564\t92812020.095242\t366177037.564437\t20943314\t23904502.6814248\t1\t27.9839052693883\t2\t402\t"LCMSMS_1.mzML"\t0.472133563046185\t1380\t667\t666\t90.601068\t113.034713745117\t5.8208310964319\t90.871572\t2\t667\tFALSE\n+"17"\t116.070637437099\t116.010871887207\t116.070877075195\t47.662548\t35.592657\t59.8657836\t124086403.896805\t465322432.631286\t26501960\t30360236.2301128\t1\t24.0791686953257\t1\t13\t"LCMSMS_2.mzML"\t0.950632241095866\t226\t277\t276\t40.9547952\t116.070838928223\t1.7359353575902\t41.2252842\t1\t277\tTRUE\n+"17"\t116.070637437099\t116.010871887207\t116.070877075195\t47.662548\t35.592657\t59.8657836\t124086403.896805\t465322432.631286\t26501960\t30360236.2301128\t1\t24.0791686953257\t1\t13\t"LCMSMS_2.mzML"\t1\t281\t343\t342\t49.182402\t116.070831298828\t1.67020474130592\t49.452918\t1\t343\tTRUE\n+"17"\t116.070637437099\t116.010871887207\t116.070877075195\t47.662548\t35.592657\t59.8657836\t124086403.896805\t465322432.631286\t26501960\t30360236.2301128\t1\t24.0791686953257\t1\t13\t"LCMSMS_2.mzML"\t1\t337\t410\t408\t57.5697876\t116.070770263672\t1.14435981103166\t57.9341562\t1\t410\tTRUE\n+"17"\t116.070557825043\t116.010902404785\t116.070907592773\t47.814411\t35.7440316\t60.003786\t130337063.119246\t491415399.75458\t27555850\t32138223.0150013\t1\t24.6441102264885\t2\t404\t"LCMSMS_1.mzML"\t0.989376188689562\t1055\t277\t276\t41.0984136\t116.070816040039\t2.22463819204545\t41.3688786\t2\t277\tTRUE\n+"17"\t116.070557825043\t116.010902404785\t116.070907592773\t47.814411\t35.7440316\t60.003786\t130337063.119246\t491415399.75458\t27555850\t32138223.0150013\t1\t24.6441102264885\t2\t404\t"LCMSMS_1.mzML"\t1\t1110\t343\t342\t49.3156656\t116.070823669434\t2.29036885341395\t49.586265\t2\t343\tTRUE\n+"17"\t116.070557825043\t116.010902404785\t116.070907592773\t47.814411\t35.7440316\t60.003786\t130337063.119246\t491415399.75458\t27555850\t32138223.0150013\t1\t24.6441102264885\t2\t404\t"LCMSMS_1.mzML"\t1\t1165\t409\t408\t57.7060356\t116.070785522461\t1.96171554657148\t57.976677\t2\t409\tTRUE\n+"41"\t132.101827805179\t132.101791381836\t132.10188293457\t73.529172\t61.39704\t85.770306\t2794252073.33772\t10870343001.7354\t432419872\t700350921.737476\t1\t30.9237895882097\t1\t27\t"LCMSMS_2.mzML"\t1\t391\t475\t474\t65.949288\t132.101821899414\t0.0447061558976329\t66.21981\t1\t475\tTRUE\n+"41"\t132.101827805179\t132.101791381836\t132.10188293457\t73.529172\t61.39704\t85.770306\t2794252073.33772\t10870343001.7354\t432419872\t700350921.737476\t1\t30.9237895882097\t1\t27\t"LCMSMS_2.mzML"\t1\t446\t541\t540\t74.297424\t132.101867675781\t0.301817188616646\t74.567904\t1\t541\tTRUE\n+"41"\t132.101827805179\t132.101791381836\t132.10188293457\t73.529172\t61.39704\t85.770306\t2794252073.33772\t10870343001.7354\t432419872\t700350921.737476\t1\t30.9237895882097\t1\t27\t"LCMSMS_2.mzML"\t1\t501\t607\t606\t82'..b'4711.0742877\t195241268.75592\t14374106\t12850193.8354307\t1\t21.2071228333724\t1\t371\t"LCMSMS_2.mzML"\t1\t465\t563\t558\t76.520544\t461.209899902344\t6.04192381657049\t77.141778\t1\t563\tTRUE\n+"757"\t461.20738152051\t461.121826171875\t461.243560791016\t77.474424\t65.376156\t89.831544\t48607882.314214\t192672537.990574\t14159047\t12716867.2850009\t1\t20.5600686941203\t2\t761\t"LCMSMS_1.mzML"\t1\t1299\t569\t564\t77.474424\t461.209899902344\t5.460410945608\t78.102018\t2\t569\tTRUE\n+"759"\t462.22122959389\t462.213439941406\t462.291839599609\t57.7060356\t44.7995376\t75.972048\t38559454.0832874\t105979165.2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|
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/flagRemove_input.RData |
| b |
| Binary file test-data/flagRemove_input.RData has changed |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/flagRemove_output.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flagRemove_output.tsv Wed Nov 27 14:23:10 2019 -0500 |
| b |
| @@ -0,0 +1,7 @@ +"grpid" "ID" "mzmed" "mzmin" "mzmax" "rtmed" "rtmin" "rtmax" "npeaks" "KO" "WT" "ko15" "ko16" "ko18" "wt19" "wt21" "wt22" "KO_median_I" "WT_median_I" "KO_RSD_I" "WT_RSD_I" "KO_coverage" "WT_coverage" "KO_RSD_RT" "WT_RSD_RT" "rsd_all_RT" "grpid.1" "KO_valid" "WT_valid" "all_sample_valid" "mzmin_full" "mzmax_full" "rtmin_full" "rtmax_full" +"1" "1" 205 205 205 2794.024 2793.436 2803.044 3 0 3 NA NA NA 1507943.06947222 1533767.074875 1354004.93486208 NA 1507943.06947222 NA 6.63321894286696 0 1 NA 0.19255594131829 0.19255594131829 1 0 1 1 205 205 2767.512 2816.3 +"2" "2" 231 231 231 2519.839 2504.508 2535.473 6 1 3 NA NA 30766.3350000011 45103.2999999989 104989.362833335 49776.3899999999 30766.3350000011 49776.3899999999 NA 49.9951594827002 0.333333333333333 1 NA 0.360049078987311 0.432545161192324 2 0 1 1 231 231 2507.963 2514.738 +"3" "3" 402.200012207031 402.200012207031 402.200012207031 3598.551 3592.212 3610.036 4 1 3 NA NA 14554.4999999997 37458.7453333329 91785.7281052629 142007.379692308 14554.4999999997 91785.7281052629 NA 57.8293736085665 0.333333333333333 1 NA 0.251337522585405 0.206331444617903 3 0 1 1 402.200012207031 402.200012207031 3563.503 3597.137 +"4" "4" 449.100006103516 449.100006103516 449.100006103516 2667.26 2664.638 2676.652 3 0 3 NA NA NA 6663.76999999991 11221.0499999998 6830.35200000006 NA 6830.35200000006 NA 31.3702198972974 0 1 NA 0.236631537850627 0.236631537850627 4 0 1 1 449.100006103516 449.100006103516 2659.233 2670.393 +"5" "5" 564.200012207031 564.200012207031 564.200012207031 3498.002 3491.993 3507.349 4 0 3 NA NA NA 149980.21 87237.7950000002 160589.344999999 NA 149980.21 NA 29.896461605479 0 1 NA 0.135256683436928 0.135256683436928 5 0 1 1 564.200012207031 564.200012207031 3473.214 3501.034 +"6" "6" 586.299987792969 586.299987792969 586.299987792969 3308.894 3308.249 3310.396 3 0 3 NA NA NA 10504.2799999998 7491.65500000026 12363.4999999997 NA 10504.2799999998 NA 24.294650028749 0 1 NA 0.0332903660058522 0.0332903660058522 6 0 1 1 586.299987792969 586.299987792969 3304.199 3312.024 |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/frag4feature_output.RData |
| b |
| Binary file test-data/frag4feature_output.RData has changed |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/frag4feature_output.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/frag4feature_output.tsv Wed Nov 27 14:23:10 2019 -0500 |
| b |
| b'@@ -0,0 +1,324 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| diff -r 000000000000 -r ab65999a5430 test-data/metab_compound_subset.sqlite |
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| Binary file test-data/metab_compound_subset.sqlite has changed |
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| diff -r 000000000000 -r ab65999a5430 test-data/purityA_output.RData |
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| Binary file test-data/purityA_output.RData has changed |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/purityA_output.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/purityA_output.tsv Wed Nov 27 14:23:10 2019 -0500 |
| b |
| b'@@ -0,0 +1,1659 @@\n+"pid"\t"fileid"\t"seqNum"\t"acquisitionNum"\t"precursorIntensity"\t"precursorMZ"\t"precursorRT"\t"precursorScanNum"\t"id"\t"filename"\t"retentionTime"\t"precursorNearest"\t"aMz"\t"aPurity"\t"apkNm"\t"iMz"\t"iPurity"\t"ipkNm"\t"inPkNm"\t"inPurity"\n+1\t"1"\t7\t7\t2307227.25\t391.283760714446\t2.7169029\t6\t7\t"LCMSMS_2.mzML"\t2.987508\t6\t391.283905029297\t1\t1\t391.283905029297\t1\t1\t1\t1\n+2\t"1"\t8\t8\t1477607.75\t149.02325426281\t2.7169029\t6\t8\t"LCMSMS_2.mzML"\t3.08067606\t6\t149.023284912109\t0.863727802953337\t2\t149.023284912109\t0.863727802953337\t2\t2\t0.858979132915935\n+3\t"1"\t9\t9\t1323571.125\t135.101532798642\t2.7169029\t6\t9\t"LCMSMS_2.mzML"\t3.17349\t6\t135.1015625\t0.754018193004879\t4\t135.1015625\t0.754018193004879\t4\t4\t0.752804381466648\n+4\t"1"\t10\t10\t1184293.75\t219.174200386646\t2.7169029\t6\t10\t"LCMSMS_2.mzML"\t3.26624796\t12\t219.174179077148\t0.732562161401867\t3\t219.174179077148\t0.732562161401867\t3\t3\t0.738959452730752\n+5\t"1"\t11\t11\t982792.625\t136.02\t2.7169029\t6\t11\t"LCMSMS_2.mzML"\t3.35911392\t12\t136.021499633789\t0.81713873333528\t4\t136.021499633789\t0.81713873333528\t4\t3\t0.823232032426933\n+6\t"1"\t13\t13\t849365.875\t235.169087811969\t3.5918919\t12\t13\t"LCMSMS_2.mzML"\t3.86249802\t12\t235.169036865234\t0.842792815315614\t2\t235.169036865234\t0.842792815315614\t2\t2\t0.843211278870246\n+7\t"1"\t14\t14\t706804.5\t158.153887744523\t3.5918919\t12\t14\t"LCMSMS_2.mzML"\t3.95523402\t12\t158.153869628906\t0.811448011426701\t2\t158.153869628906\t0.811448011426701\t2\t2\t0.81443178987688\n+8\t"1"\t15\t15\t669338.375\t171.149079510776\t3.5918919\t12\t15\t"LCMSMS_2.mzML"\t4.047975\t12\t171.149063110352\t0.766303662616746\t3\t171.149063110352\t0.766303662616746\t3\t3\t0.770556368013789\n+9\t"1"\t16\t16\t650086.625\t371.100940415758\t3.5918919\t12\t16\t"LCMSMS_2.mzML"\t4.142739\t18\t371.100860595703\t1\t1\t371.100860595703\t1\t1\t1\t1\n+10\t"1"\t17\t17\t555993.5625\t163.132748084438\t3.5918919\t12\t17\t"LCMSMS_2.mzML"\t4.23547908\t18\t163.132705688477\t0.716000538894822\t5\t163.132705688477\t0.716000538894822\t5\t5\t0.714400157383296\n+11\t"1"\t19\t19\t522140.46875\t279.16\t4.46726694\t18\t19\t"LCMSMS_2.mzML"\t4.73789808\t18\t279.158782958984\t0.778745945763546\t2\t279.158782958984\t0.778745945763546\t2\t2\t0.781940110910545\n+12\t"1"\t20\t20\t528064.375\t187.126259769718\t4.46726694\t18\t20\t"LCMSMS_2.mzML"\t4.83060906\t18\t187.126220703125\t0.664328071501583\t3\t187.126220703125\t0.664328071501583\t3\t3\t0.661519589836662\n+13\t"1"\t21\t21\t467025.8125\t199.169150732989\t4.46726694\t18\t21\t"LCMSMS_2.mzML"\t4.92348096\t18\t199.169128417969\t0.625379711668664\t6\t199.169128417969\t0.625379711668664\t6\t3\t0.671735350831275\n+14\t"1"\t22\t22\t454623.9375\t202.179972369132\t4.46726694\t18\t22\t"LCMSMS_2.mzML"\t5.0162229\t24\t202.179992675781\t0.813432936059855\t3\t202.179992675781\t0.813432936059855\t3\t3\t0.811188590738086\n+15\t"1"\t23\t23\t398638.59375\t195.087538239222\t4.46726694\t18\t23\t"LCMSMS_2.mzML"\t5.10911106\t24\t195.08757019043\t0.427238293287608\t7\t195.08757019043\t0.427238293287608\t7\t7\t0.42561698809495\n+16\t"1"\t25\t25\t469463.3125\t114.091558259035\t5.33325996\t24\t25\t"LCMSMS_2.mzML"\t5.68774008\t24\t114.09156036377\t0.922266019059352\t2\t114.09156036377\t0.922266019059352\t2\t2\t0.921739255221912\n+17\t"1"\t26\t26\t342817.1875\t200.02\t5.33325996\t24\t26\t"LCMSMS_2.mzML"\t5.78048988\t24\t200.022872924805\t0.724091075468091\t5\t200.022872924805\t0.724091075468091\t5\t5\t0.716395444423535\n+18\t"1"\t27\t27\t412834.21875\t195.02\t5.33325996\t24\t27\t"LCMSMS_2.mzML"\t5.87323902\t24\t195.08757019043\t0.427238293287608\t7\t195.08757019043\t0.427238293287608\t7\t7\t0.422616244430677\n+19\t"1"\t28\t28\t388953.65625\t329\t5.33325996\t24\t28\t"LCMSMS_2.mzML"\t5.96697396\t30\t329.004852294922\t1\t1\t329.004852294922\t1\t1\t1\t1\n+20\t"1"\t29\t29\t363111.84375\t327.01\t5.33325996\t24\t29\t"LCMSMS_2.mzML"\t6.0607398\t30\t327.007751464844\t1\t1\t327.007751464844\t1\t1\t1\t1\n+21\t"1"\t31\t31\t337509.625\t209.153442494811\t6.2918862\t30\t31\t"LCMSMS_2.mzML"\t6.5625\t30\t209.153457641602\t0.719647135421531\t3\t209.153457641602\t0.719647135421531\t3\t4\t0.708639826368797\n+22\t"1"\t32\t32\t316424\t136.94\t6.2918862\t30\t32\t"LCMSMS_2.mzML"\t6.6570792\t30\t136.940078735352\t0.544384631839566\t7\t136.940078735352\t0.544384631839566\t7\t6\t0.554115994578321\n+23\t"1"\t33\t33\t291629.4375\t151.11\t6.2918862\t30\t33\t"LCMSM'..b'304688\t966\t970\t"LCMSMS_1.mzML"\t130.920672\t972\t269.12548828125\t0.141370053054037\t3\t269.087615966797\t0.813617514939145\t3\t3\t0.829650086646885\n+1634\t"2"\t971\t971\t155505.515625\t229.05\t130.304688\t966\t971\t"LCMSMS_1.mzML"\t131.013402\t972\t229.047210693359\t0.342181004056544\t4\t229.154266357422\t0.50685217799906\t4\t5\t0.507238843865549\n+1635\t"2"\t973\t973\t845536.6875\t327.140534136341\t131.148558\t972\t973\t"LCMSMS_1.mzML"\t131.41923\t972\t327.140594482422\t0.727993884858406\t2\t327.140594482422\t0.727993884858406\t2\t3\t0.704180375416617\n+1636\t"2"\t974\t974\t5866483\t318.201775150359\t131.148558\t972\t974\t"LCMSMS_1.mzML"\t131.512914\t972\t318.201873779297\t1\t1\t318.201873779297\t1\t1\t1\t1\n+1637\t"2"\t975\t975\t845092.0625\t536.25\t131.148558\t972\t975\t"LCMSMS_1.mzML"\t131.60967\t972\tNA\t0\tNA\tNA\t0\tNA\tNA\t0\n+1638\t"2"\t976\t976\t614545.375\t345.21\t131.148558\t972\t976\t"LCMSMS_1.mzML"\t131.704404\t978\t345.212768554688\t1\t1\t345.212768554688\t1\t1\t2\t0.976986759297886\n+1639\t"2"\t977\t977\t469308.46875\t289.22\t131.148558\t972\t977\t"LCMSMS_1.mzML"\t131.798166\t978\t289.222900390625\t1\t1\t289.222900390625\t1\t1\t1\t1\n+1640\t"2"\t979\t979\t347938.1875\t324.1314685619\t131.936568\t978\t979\t"LCMSMS_1.mzML"\t132.207222\t978\t324.131439208984\t1\t1\t324.131439208984\t1\t1\t1\t1\n+1641\t"2"\t980\t980\t38274372\t137.045632108302\t131.936568\t978\t980\t"LCMSMS_1.mzML"\t132.282558\t978\t137.045623779297\t1\t1\t137.045623779297\t1\t1\t1\t1\n+1642\t"2"\t981\t981\t2197110.5\t537.168354555235\t131.936568\t978\t981\t"LCMSMS_1.mzML"\t132.379302\t978\tNA\t0\tNA\tNA\t0\tNA\tNA\t0\n+1643\t"2"\t982\t982\t6986065\t241.154271494938\t131.936568\t978\t982\t"LCMSMS_1.mzML"\t132.47304\t984\t241.154266357422\t1\t1\t241.154266357422\t1\t1\t1\t1\n+1644\t"2"\t983\t983\t202176\t409.17\t131.936568\t978\t983\t"LCMSMS_1.mzML"\t132.567798\t984\t409.170837402344\t0.871738208530276\t2\t409.170837402344\t0.871738208530276\t2\t2\t0.884648151922212\n+1645\t"2"\t985\t985\t3128515\t215.138771219374\t132.71007\t984\t985\t"LCMSMS_1.mzML"\t132.9807\t984\t215.138793945312\t1\t1\t215.138793945312\t1\t1\t1\t1\n+1646\t"2"\t986\t986\t3218578.75\t334.19670553683\t132.71007\t984\t986\t"LCMSMS_1.mzML"\t133.07541\t984\t334.196746826172\t0.926246562183373\t2\t334.196746826172\t0.926246562183373\t2\t1\t0.950831041455582\n+1647\t"2"\t987\t987\t2338164\t391.283610514295\t132.71007\t984\t987\t"LCMSMS_1.mzML"\t133.170168\t984\t391.283660888672\t1\t1\t391.283660888672\t1\t1\t1\t1\n+1648\t"2"\t988\t988\t2184468.25\t290.17\t132.71007\t984\t988\t"LCMSMS_1.mzML"\t133.263768\t990\t290.170593261719\t1\t1\t290.170593261719\t1\t1\t1\t1\n+1649\t"2"\t989\t989\t1960551.25\t356.157702076678\t132.71007\t984\t989\t"LCMSMS_1.mzML"\t133.358538\t990\t356.157745361328\t0.738759984327311\t3\t356.157745361328\t0.738759984327311\t3\t3\t0.735813941108667\n+1650\t"2"\t991\t991\t2031393.5\t304.186232352971\t133.503804\t990\t991\t"LCMSMS_1.mzML"\t133.774308\t990\t304.186279296875\t0.909007498607307\t2\t304.186279296875\t0.909007498607307\t2\t2\t0.911376543536852\n+1651\t"2"\t992\t992\t1841302.125\t340.183823206705\t133.503804\t990\t992\t"LCMSMS_1.mzML"\t133.86903\t990\t340.183868408203\t0.921859692577257\t2\t340.183868408203\t0.921859692577257\t2\t2\t0.929077630476246\n+1652\t"2"\t993\t993\t1325456.625\t389.2\t133.503804\t990\t993\t"LCMSMS_1.mzML"\t133.963806\t990\t389.202545166016\t1\t1\t389.202545166016\t1\t1\t1\t1\n+1653\t"2"\t994\t994\t1091136.25\t342.14\t133.503804\t990\t994\t"LCMSMS_1.mzML"\t134.058522\t996\t342.142120361328\t1\t1\t342.142120361328\t1\t1\t1\t1\n+1654\t"2"\t995\t995\t997170.5625\t483.314830443476\t133.503804\t990\t995\t"LCMSMS_1.mzML"\t134.1543\t996\t483.31494140625\t0.706612336062495\t3\t483.31494140625\t0.706612336062495\t3\t3\t0.711714458623578\n+1655\t"2"\t997\t997\t3670711.25\t269.16\t134.305698\t996\t997\t"LCMSMS_1.mzML"\t134.57631\t996\t269.087707519531\t0.504195818495762\t3\t269.087707519531\t0.504195818495762\t3\t3\t0.504195818495762\n+1656\t"2"\t998\t998\t96664.6484375\t575.124300805729\t134.305698\t996\t998\t"LCMSMS_1.mzML"\t134.673036\t996\tNA\t0\tNA\tNA\t0\tNA\tNA\t0\n+1657\t"2"\t999\t999\t71747.3984375\t118.08638548293\t134.305698\t996\t999\t"LCMSMS_1.mzML"\t134.765052\t996\t118.086380004883\t1\t1\t118.086380004883\t1\t1\t1\t1\n+1658\t"2"\t1000\t1000\t1000603.0625\t359.228373720717\t134.305698\t996\t1000\t"LCMSMS_1.mzML"\t134.859774\t996\t359.228363037109\t0.929710258388609\t2\t359.228363037109\t0.929710258388609\t2\t2\t0.929710258388609\n' |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/spectralMatching_db_with_spectral_matching.sqlite |
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| Binary file test-data/spectralMatching_db_with_spectral_matching.sqlite has changed |
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| diff -r 000000000000 -r ab65999a5430 test-data/spectralMatching_db_with_spectral_matching_instrumentTypes.sqlite |
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| Binary file test-data/spectralMatching_db_with_spectral_matching_instrumentTypes.sqlite has changed |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/spectralMatching_input_massbank_test.sqlite |
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| Binary file test-data/spectralMatching_input_massbank_test.sqlite has changed |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/spectralMatching_matched_results.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/spectralMatching_matched_results.tsv Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| @@ -0,0 +1,3 @@ +"pid" "grpid" "mz" "mzmin" "mzmax" "rt" "rtmin" "rtmax" "npeaks" "sample" "LCMSMS_2" "LCMSMS_1" "LCMS_2" "LCMS_1" "grp_name" "lpid" "mid" "dpc" "rdpc" "cdpc" "mcount" "allcount" "mpercent" "library_rt" "query_rt" "rtdiff" "library_precursor_mz" "query_precursor_mz" "library_precursor_ion_purity" "query_precursor_ion_purity" "library_accession" "library_precursor_type" "library_entry_name" "inchikey" "library_source_name" "library_compound_name" "query_entry_name" +1663 14 113.035283604395 113.035156497997 113.03541992282 80.50932 77.16429 83.64567 4 4 88462324.9597518 92812020.095242 77298864.2688328 77198465.9156761 "M113T81" 56653 1 0.942265461847349 0.996860823822942 0.753812369477879 1 4 0.25 NA 80.50932 NA "113.03508" 113.035283604395 NA 1 "PR100037" "[M+H]+" "Uracil" "ISAKRJDGNUQOIC-UHFFFAOYSA-N" "massbank" "Uracil" NA +1664 14 113.035283604395 113.035156497997 113.03541992282 80.50932 77.16429 83.64567 4 4 88462324.9597518 92812020.095242 77298864.2688328 77198465.9156761 "M113T81" 56653 2 0.942265461847349 0.996860823822942 0.753812369477879 1 4 0.25 NA 80.50932 NA "113.03508" 113.035283604395 NA 1 "PR100037" "[M+H]+" "Uracil" "ISAKRJDGNUQOIC-UHFFFAOYSA-N" "massbank" "Uracil" NA |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/spectralMatching_matched_results_instrumentTypes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/spectralMatching_matched_results_instrumentTypes.tsv Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| @@ -0,0 +1,3 @@ +"pid" "grpid" "mz" "mzmin" "mzmax" "rt" "rtmin" "rtmax" "npeaks" "sample" "LCMSMS_2" "LCMSMS_1" "LCMS_2" "LCMS_1" "grp_name" "lpid" "mid" "dpc" "rdpc" "cdpc" "mcount" "allcount" "mpercent" "library_rt" "query_rt" "rtdiff" "library_precursor_mz" "query_precursor_mz" "library_precursor_ion_purity" "query_precursor_ion_purity" "library_accession" "library_precursor_type" "library_entry_name" "inchikey" "library_source_name" "library_compound_name" "query_entry_name" +1663 14 113.035283604395 113.035156497997 113.03541992282 80.50932 77.16429 83.64567 4 4 88462324.9597518 92812020.095242 77298864.2688328 77198465.9156761 "M113T81" 56653 1 0.942265461847349 0.996860823822942 0.753812369477879 1 4 0.25 NA 80.50932 NA "113.03508" 113.035283604395 NA 1 "PR100037" "[M+H]+" "Uracil" "ISAKRJDGNUQOIC-UHFFFAOYSA-N" "massbank" "Uracil" NA +1664 14 113.035283604395 113.035156497997 113.03541992282 80.50932 77.16429 83.64567 4 4 88462324.9597518 92812020.095242 77298864.2688328 77198465.9156761 "M113T81" 56653 2 0.942265461847349 0.996860823822942 0.753812369477879 1 4 0.25 NA 80.50932 NA "113.03508" 113.035283604395 NA 1 "PR100037" "[M+H]+" "Uracil" "ISAKRJDGNUQOIC-UHFFFAOYSA-N" "massbank" "Uracil" NA |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/spectralMatching_xcms_matched_results.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/spectralMatching_xcms_matched_results.tsv Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| @@ -0,0 +1,3 @@ +"qpid" "lpid" "mid" "dpc" "rdpc" "cdpc" "mcount" "allcount" "mpercent" "library_rt" "query_rt" "rtdiff" "library_precursor_mz" "query_precursor_mz" "library_precursor_ion_purity" "query_precursor_ion_purity" "library_accession" "library_precursor_type" "library_entry_name" "inchikey" "library_source_name" "library_compound_name" "query_entry_name" +1663 56653 1 0.942265461847349 0.996860823822942 0.753812369477879 1 4 0.25 NA 80.50932 NA "113.03508" 113.035283604395 NA 1 "PR100037" "[M+H]+" "Uracil" "ISAKRJDGNUQOIC-UHFFFAOYSA-N" "massbank" "Uracil" NA +1664 56653 2 0.942265461847349 0.996860823822942 0.753812369477879 1 4 0.25 NA 80.50932 NA "113.03508" 113.035283604395 NA 1 "PR100037" "[M+H]+" "Uracil" "ISAKRJDGNUQOIC-UHFFFAOYSA-N" "massbank" "Uracil" NA |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/spectralMatching_xcms_matched_results_instrumentTypes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/spectralMatching_xcms_matched_results_instrumentTypes.tsv Wed Nov 27 14:23:10 2019 -0500 |
| [ |
| @@ -0,0 +1,3 @@ +"qpid" "lpid" "mid" "dpc" "rdpc" "cdpc" "mcount" "allcount" "mpercent" "library_rt" "query_rt" "rtdiff" "library_precursor_mz" "query_precursor_mz" "library_precursor_ion_purity" "query_precursor_ion_purity" "library_accession" "library_precursor_type" "library_entry_name" "inchikey" "library_source_name" "library_compound_name" "query_entry_name" +1663 56653 1 0.942265461847349 0.996860823822942 0.753812369477879 1 4 0.25 NA 80.50932 NA "113.03508" 113.035283604395 NA 1 "PR100037" "[M+H]+" "Uracil" "ISAKRJDGNUQOIC-UHFFFAOYSA-N" "massbank" "Uracil" NA +1664 56653 2 0.942265461847349 0.996860823822942 0.753812369477879 1 4 0.25 NA 80.50932 NA "113.03508" 113.035283604395 NA 1 "PR100037" "[M+H]+" "Uracil" "ISAKRJDGNUQOIC-UHFFFAOYSA-N" "massbank" "Uracil" NA |
| b |
| diff -r 000000000000 -r ab65999a5430 test-data/xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData |
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| Binary file test-data/xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData has changed |