# HG changeset patch # User workflow4metabolomics # Date 1657103919 0 # Node ID 85600121396653982cbb04903c6061cb5f414a5a # Parent c68c9486566702051f59c78a5cdf26d1a8f7c49a planemo upload commit 53543b5d911fc1f2d204f314a4d2aaf93a8c7715 diff -r c68c94865667 -r 856001213966 MS2snoop.R --- a/MS2snoop.R Wed Jun 22 13:07:01 2022 +0000 +++ b/MS2snoop.R Wed Jul 06 10:38:39 2022 +0000 @@ -15,7 +15,7 @@ #' -assign("MS2SNOOP_VERSION", "1.1.0") +assign("MS2SNOOP_VERSION", "2.0.0") lockBinding("MS2SNOOP_VERSION", globalenv()) assign("MISSING_PARAMETER_ERROR", 1) @@ -87,7 +87,9 @@ vmz, cor_abs_int, refcol, - c_name + c_name, + inchikey, + elemcomposition ) { ## du fait de la difference de nombre de colonne entre la dataframe qui ## inclue les scans en 1ere col, mzRef se decale de 1 @@ -156,6 +158,8 @@ corValid <- (round(cor_abs_int, 2) >= r_threshold) ##nolint object_name_linter cp_res <- data.frame( rep(c_name, length(vmz)), + rep(inchikey, length(vmz)), + rep(elemcomposition, length(vmz)), rep(fid, length(vmz)), vmz, cor_abs_int, @@ -166,6 +170,8 @@ colnames(cp_res) <- c( "compoundName", + "inchikey", + "elemcomposition", "fileid", "fragments_mz", "CorWithPrecursor", @@ -200,6 +206,8 @@ mzref, rtref, c_name, + inchikey, + elemcomposition, min_number_scan, mzdecimal, r_threshold = DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD, @@ -361,7 +369,9 @@ vmz = vmz, cor_abs_int = cor_abs_int, refcol = refcol, - c_name = c_name + c_name = c_name, + inchikey = inchikey, + elemcomposition = elemcomposition ) if (f == 1) { res_comp <- res_comp_by_file @@ -541,8 +551,10 @@ } stop_with_status <- function(msg, status) { + sink(stderr()) message(sprintf("Error: %s", msg)) message(sprintf("Error code: %s", status)) + sink(NULL) base::quit(status = status) } @@ -660,6 +672,15 @@ return(result) } +uniformize_columns <- function(df) { + cols <- colnames(df) + for (func in c(tolower)) { + cols <- func(cols) + } + colnames(df) <- cols + return(df) +} + main <- function(args) { if (args$version) { cat(sprintf("%s\n", MS2SNOOP_VERSION)) @@ -680,6 +701,24 @@ ## list of compounds : col1=Name of molecule, col2=m/z, col3=retention time compounds <- get_csv_or_tsv(args$compounds) + compounds <- uniformize_columns(compounds) + mandatory_columns <- c( + "compound_name", + "mz", + "rtsec", + "inchikey" + ) + presents <- mandatory_columns %in% colnames(compounds) + if (!all(presents)) { + stop_with_status( + sprintf( + "Some columns are missing: %s", + paste(mandatory_columns[which(!presents)], collapse = ", ") + ), + BAD_PARAMETER_VALUE_ERROR + ) + } + res_all <- NULL for (i in seq_len(nrow(compounds))) { ## loop execution for all compounds in the compounds file @@ -687,9 +726,11 @@ res_cor <- extract_fragments( precursors = precursors, fragments = fragments, - mzref = compounds[[2]][i], - rtref = compounds[[3]][i], - c_name = compounds[[1]][i], + mzref = compounds[["mz"]][i], + rtref = compounds[["rtsec"]][i], + c_name = compounds[["compound_name"]][i], + inchikey = compounds[["inchikey"]][i], + elemcomposition = compounds[["elemcomposition"]][i], min_number_scan = args$min_number_scan, mzdecimal = args$mzdecimal, r_threshold = args$r_threshold, @@ -717,8 +758,8 @@ ) } -unset_debug() -unset_verbose() +global_debug <- FALSE +global_verbose <- FALSE args <- optparse::parse_args(create_parser()) main(args) diff -r c68c94865667 -r 856001213966 MS2snoop.xml --- a/MS2snoop.xml Wed Jun 22 13:07:01 2022 +0000 +++ b/MS2snoop.xml Wed Jul 06 10:38:39 2022 +0000 @@ -4,8 +4,6 @@ macros.xml - 1.1.0 - 0 topic_0091 @@ -242,16 +240,18 @@ + + + + + + + + diff -r c68c94865667 -r 856001213966 README.md --- a/README.md Wed Jun 22 13:07:01 2022 +0000 +++ b/README.md Wed Jul 06 10:38:39 2022 +0000 @@ -5,7 +5,7 @@ ----------- * **@name**: MS2 Snoop - * **@version**: 1.1.0 + * **@version**: 2.0.0 * **@authors**: Jean François Martin (INRAE) * **@maintainers**: Lain Pavot (PFEM - INRAE - MetaboHUB) * **@init date**: 2022, April diff -r c68c94865667 -r 856001213966 macros.xml --- a/macros.xml Wed Jun 22 13:07:01 2022 +0000 +++ b/macros.xml Wed Jul 06 10:38:39 2022 +0000 @@ -1,5 +1,132 @@ + +.. class:: infomark + +**Authors** Jean-Francois Martin (jean-francois.martin@inrae.fr), Lain Pavot (lain.pavot@inrae.fr), Kevin Wagner (kevin.wagner@inrae.fr) + +.. class:: infomark + +--------------------------------------------------- + + + + + + + + + + +-------------- +Changelog/News +-------------- + +2.0.0 + | This version is motivated by a strengthening of the quality of the + input files. + Input files that don't match the newly defined format will not be + processed anymore. Previously, MS2Snoop expected the c_name, the + mzref and the rtref to be the 1st, the 2nd and the 3rd columns + respectively, and the header was somewhat ignored in the compound + file. + | + | Now, we'd like to add some new columns, some of them are optional. + This new + format of file implies a better definition of the columns order, + names, optioning or requirement. + The exact columns name are: + | - **compound_name** [MANDATORY] ; + | - **inchikey** [MANDATORY] ; + | - **elemcomposition** [OPTIONAL] ; + | - **mz** [MANDATORY] ; + | - **rtsec** [MANDATORY]. + | + | These names can be written indiferentially in lower and/or upper + case. The new definition being incompatible with the older one, that + was more flexible, but also more error-prone. + +1.1.0 + | new feature, xml improvement (IUC) + | chore: better labels in the xml parameter fields + | feat: add support for tab, comma and semicolon separated values + input files. + | chore: add some tests in an external macro.xml file + + +1.0.1 + | Bug fix, new parameters and some improvement in the xml. + | fix: the program crashed when there were no result on the first + iteration. Fixed in the main loop. + | chore: the xml matches better the IUC recommendations + | chore: add a --debug and a --verbose option to the tool. + +1.0.0 + | First version, published on the toolshed. + + + + 2.0.0 + 0 diff -r c68c94865667 -r 856001213966 planemo_retest.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo_retest.sh Wed Jul 06 10:38:39 2022 +0000 @@ -0,0 +1,5 @@ +#!/bin/sh + +export TEST_FLAGS=--failed + +./planemo_test.sh ; diff -r c68c94865667 -r 856001213966 test-data/compound_fragments_result.txt --- a/test-data/compound_fragments_result.txt Wed Jun 22 13:07:01 2022 +0000 +++ b/test-data/compound_fragments_result.txt Wed Jul 06 10:38:39 2022 +0000 @@ -1,1385 +1,1385 @@ -"compoundName" "fileid" "fragments_mz" "CorWithPrecursor" "AbsoluteIntensity" "relativeIntensity" "corValid" -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 84 0.601436519480403 406.383798606 0.00344160476662782 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 123 -0.167860259307508 295.871994004 0.00250569650751035 FALSE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 126 0.907929868611774 430.137959956 0.00364277527394095 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 137 0.676403388268515 430.806630151 0.00364843814371653 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 146 -0.125051837812104 538.358772757 0.00455928145962519 FALSE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 148 0.1558553290912 143.310915941 0.00121367912083162 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 149 -0.276972713799663 617.416199707 0.00522880720932724 FALSE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 150 -0.410733329402461 5080.527405 0.0430262411887723 FALSE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 151 -0.243340932574313 218.539256565 0.00185077690023418 FALSE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 154 0.991757449276389 16836.882397703 0.14258908675458 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 164 0.146040591250743 1829.10214243 0.0154903976822645 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 180 0.39213526382476 209.753137589 0.00177636854770712 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 182 1 118079.7407496 1 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 84 0.601436519480403 406.383798606 0.00344160476662782 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 123 -0.167860259307508 295.871994004 0.00250569650751035 FALSE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 126 0.907929868611774 430.137959956 0.00364277527394095 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 137 0.676403388268515 430.806630151 0.00364843814371653 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 146 -0.125051837812104 538.358772757 0.00455928145962519 FALSE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 148 0.1558553290912 143.310915941 0.00121367912083162 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 149 -0.276972713799663 617.416199707 0.00522880720932724 FALSE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 150 -0.410733329402461 5080.527405 0.0430262411887723 FALSE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 151 -0.243340932574313 218.539256565 0.00185077690023418 FALSE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 154 0.991757449276389 16836.882397703 0.14258908675458 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 164 0.146040591250743 1829.10214243 0.0154903976822645 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 180 0.39213526382476 209.753137589 0.00177636854770712 TRUE -"2-diethylamino-6-methyl pyrimidin-4-ol one" "7" 182 1 118079.7407496 1 TRUE -"5-hydroxy-thiabendazole" "1" 132 0.710501933879621 105.532976149 6.84594522892331e-05 TRUE -"5-hydroxy-thiabendazole" "1" 144 0.276479394498518 203.085251814 0.00013174180824369 TRUE -"5-hydroxy-thiabendazole" "1" 146 0.604633971720309 166.134730821 0.000107771931516144 TRUE -"5-hydroxy-thiabendazole" "1" 156 0.191791879044897 459.381193152 0.000298001496998986 TRUE -"5-hydroxy-thiabendazole" "1" 158 -0.331971393756239 13878.1056368 0.00900275482959977 FALSE -"5-hydroxy-thiabendazole" "1" 160 0.77523958114776 386.949028017 0.000251014606889261 TRUE -"5-hydroxy-thiabendazole" "1" 162 -0.476769537229124 213.45186329 0.000138466649801652 FALSE -"5-hydroxy-thiabendazole" "1" 172 0.593280623618274 794.89456843 0.000515649693282338 TRUE -"5-hydroxy-thiabendazole" "1" 173 0.89953946593837 207.738348006 0.000134760281031794 TRUE -"5-hydroxy-thiabendazole" "1" 174 0.150820546879602 1525.52666664 0.000989612193854381 TRUE -"5-hydroxy-thiabendazole" "1" 175 0.646696639290413 163.18886233 0.000105860940745588 TRUE -"5-hydroxy-thiabendazole" "1" 176 0.506660895270366 1125.51529793 0.000730124020482966 TRUE -"5-hydroxy-thiabendazole" "1" 177 -0.349150043770229 185.412219041 0.000120277276605531 FALSE -"5-hydroxy-thiabendazole" "1" 186 -0.386785516946622 13148.1585083 0.00852923667024592 FALSE -"5-hydroxy-thiabendazole" "1" 188 -0.333885650073135 540.530680192 0.000350643331229711 FALSE -"5-hydroxy-thiabendazole" "1" 190 0.710817170481525 358.462937357 0.000232535623015143 TRUE -"5-hydroxy-thiabendazole" "1" 191 0.943541098312933 285.348824959 0.000185106352354628 TRUE -"5-hydroxy-thiabendazole" "1" 200 0.285023586376285 2249.33108917 0.00145914556758363 TRUE -"5-hydroxy-thiabendazole" "1" 204 0.272327432166324 220.729373931 0.000143187585481591 TRUE -"5-hydroxy-thiabendazole" "1" 218 1 1541539.884122 1 TRUE -"5-hydroxy-thiabendazole" "1" 219 0.989745977797565 55751.12976688 0.0361658691683048 TRUE -"5-hydroxy-thiabendazole" "1" 132 0.710501933879621 105.532976149 6.84594522892331e-05 TRUE -"5-hydroxy-thiabendazole" "1" 144 0.276479394498518 203.085251814 0.00013174180824369 TRUE -"5-hydroxy-thiabendazole" "1" 146 0.604633971720309 166.134730821 0.000107771931516144 TRUE -"5-hydroxy-thiabendazole" "1" 156 0.191791879044897 459.381193152 0.000298001496998986 TRUE -"5-hydroxy-thiabendazole" "1" 158 -0.331971393756239 13878.1056368 0.00900275482959977 FALSE -"5-hydroxy-thiabendazole" "1" 160 0.77523958114776 386.949028017 0.000251014606889261 TRUE -"5-hydroxy-thiabendazole" "1" 162 -0.476769537229124 213.45186329 0.000138466649801652 FALSE -"5-hydroxy-thiabendazole" "1" 172 0.593280623618274 794.89456843 0.000515649693282338 TRUE -"5-hydroxy-thiabendazole" "1" 173 0.89953946593837 207.738348006 0.000134760281031794 TRUE -"5-hydroxy-thiabendazole" "1" 174 0.150820546879602 1525.52666664 0.000989612193854381 TRUE -"5-hydroxy-thiabendazole" "1" 175 0.646696639290413 163.18886233 0.000105860940745588 TRUE -"5-hydroxy-thiabendazole" "1" 176 0.506660895270366 1125.51529793 0.000730124020482966 TRUE -"5-hydroxy-thiabendazole" "1" 177 -0.349150043770229 185.412219041 0.000120277276605531 FALSE -"5-hydroxy-thiabendazole" "1" 186 -0.386785516946622 13148.1585083 0.00852923667024592 FALSE -"5-hydroxy-thiabendazole" "1" 188 -0.333885650073135 540.530680192 0.000350643331229711 FALSE -"5-hydroxy-thiabendazole" "1" 190 0.710817170481525 358.462937357 0.000232535623015143 TRUE -"5-hydroxy-thiabendazole" "1" 191 0.943541098312933 285.348824959 0.000185106352354628 TRUE -"5-hydroxy-thiabendazole" "1" 200 0.285023586376285 2249.33108917 0.00145914556758363 TRUE -"5-hydroxy-thiabendazole" "1" 204 0.272327432166324 220.729373931 0.000143187585481591 TRUE -"5-hydroxy-thiabendazole" "1" 218 1 1541539.884122 1 TRUE -"5-hydroxy-thiabendazole" "1" 219 0.989745977797565 55751.12976688 0.0361658691683048 TRUE -"acetamiprid-N-desmethyl" "2" 99 0.667400010170284 282.404261107 0.000748607853773036 TRUE -"acetamiprid-N-desmethyl" "2" 107 0.644182822419527 250.776102526 0.000664766739544435 TRUE -"acetamiprid-N-desmethyl" "2" 121 0.468461643454679 182.548945409 0.000483907621278365 TRUE -"acetamiprid-N-desmethyl" "2" 126 0.99471830230169 148406.8197 0.393402388283387 TRUE -"acetamiprid-N-desmethyl" "2" 127 0.685580673617811 301.425851346 0.000799031001739535 TRUE -"acetamiprid-N-desmethyl" "2" 131 0.71686560485514 235.917765632 0.00062537970037848 TRUE -"acetamiprid-N-desmethyl" "2" 132 0.825023006886452 3437.337815361 0.00911182456866446 TRUE -"acetamiprid-N-desmethyl" "2" 133 0.609229728784487 1059.475870153 0.00280849854804084 TRUE -"acetamiprid-N-desmethyl" "2" 135 -0.0630703589928776 1620.073705625 0.00429455240855075 FALSE -"acetamiprid-N-desmethyl" "2" 139 0.388512588178974 560.54565096 0.00148591552783965 TRUE -"acetamiprid-N-desmethyl" "2" 141 0.971318347491603 11361.06560494 0.0301163406874599 TRUE -"acetamiprid-N-desmethyl" "2" 146 0.677368485127156 744.749183894 0.00197420919205914 TRUE -"acetamiprid-N-desmethyl" "2" 147 0.814646347538386 171.753984928 0.00045529193337915 TRUE -"acetamiprid-N-desmethyl" "2" 149 -0.156704527239734 1569.49830252 0.00416048522477764 FALSE -"acetamiprid-N-desmethyl" "2" 151 0.451637386634768 547.910546303 0.00145242191643876 TRUE -"acetamiprid-N-desmethyl" "2" 153 0.307104196288287 353.766232977 0.00093777685707774 TRUE -"acetamiprid-N-desmethyl" "2" 156 0.486407391413412 347.237878558 0.000920471249254685 TRUE -"acetamiprid-N-desmethyl" "2" 159 0.161971228755214 544.50952719 0.00144340636685447 TRUE -"acetamiprid-N-desmethyl" "2" 163 -0.0146119879123163 804.357781409 0.00213222190786309 FALSE -"acetamiprid-N-desmethyl" "2" 165 0.907832718528441 5504.73675146 0.0145921635493123 TRUE -"acetamiprid-N-desmethyl" "2" 167 0.967321684550227 14122.07723917 0.0374353343373474 TRUE -"acetamiprid-N-desmethyl" "2" 168 0.977465016016083 20360.7667386 0.0539730874796597 TRUE -"acetamiprid-N-desmethyl" "2" 173 0.825972891702218 4449.28006372 0.0117943192014181 TRUE -"acetamiprid-N-desmethyl" "2" 174 0.438640287775404 357.580513016 0.00094788789429259 TRUE -"acetamiprid-N-desmethyl" "2" 175 -0.153796105444945 275.919033053 0.000731416566942933 FALSE -"acetamiprid-N-desmethyl" "2" 177 -0.495623187250053 34391.2702636 0.0911656747658185 FALSE -"acetamiprid-N-desmethyl" "2" 179 0.00427133435060827 165.392969587 0.000438429914287877 TRUE -"acetamiprid-N-desmethyl" "2" 180 0.855262507886083 2962.451229122 0.00785297731644369 TRUE -"acetamiprid-N-desmethyl" "2" 181 0.514902430711196 334.53332619 0.000886793543245312 TRUE -"acetamiprid-N-desmethyl" "2" 182 0.983758938668445 16217.3405395 0.0429895372243752 TRUE -"acetamiprid-N-desmethyl" "2" 191 0.248678055177222 2196.72544869 0.00582316257207377 TRUE -"acetamiprid-N-desmethyl" "2" 192 0.98871539868282 29705.473639 0.0787443885550213 TRUE -"acetamiprid-N-desmethyl" "2" 193 0.375698142428829 714.29845333 0.0018934892483728 TRUE -"acetamiprid-N-desmethyl" "2" 195 0.144605138810588 367.760202152 0.000974872597732636 TRUE -"acetamiprid-N-desmethyl" "2" 207 0.7622236383338 134.383083348 0.000356227739674342 TRUE -"acetamiprid-N-desmethyl" "2" 209 1 377239.244397 1 TRUE -"acetamiprid-N-desmethyl" "2" 210 0.765065526384015 386.747904794 0.00102520591518043 TRUE -"acetamiprid-N-desmethyl" "2" 99 0.667400010170284 282.404261107 0.000748607853773036 TRUE -"acetamiprid-N-desmethyl" "2" 107 0.644182822419527 250.776102526 0.000664766739544435 TRUE -"acetamiprid-N-desmethyl" "2" 121 0.468461643454679 182.548945409 0.000483907621278365 TRUE -"acetamiprid-N-desmethyl" "2" 126 0.99471830230169 148406.8197 0.393402388283387 TRUE -"acetamiprid-N-desmethyl" "2" 127 0.685580673617811 301.425851346 0.000799031001739535 TRUE -"acetamiprid-N-desmethyl" "2" 131 0.71686560485514 235.917765632 0.00062537970037848 TRUE -"acetamiprid-N-desmethyl" "2" 132 0.825023006886452 3437.337815361 0.00911182456866446 TRUE -"acetamiprid-N-desmethyl" "2" 133 0.609229728784487 1059.475870153 0.00280849854804084 TRUE -"acetamiprid-N-desmethyl" "2" 135 -0.0630703589928776 1620.073705625 0.00429455240855075 FALSE -"acetamiprid-N-desmethyl" "2" 139 0.388512588178974 560.54565096 0.00148591552783965 TRUE -"acetamiprid-N-desmethyl" "2" 141 0.971318347491603 11361.06560494 0.0301163406874599 TRUE -"acetamiprid-N-desmethyl" "2" 146 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0.414268218911412 122.097583527 0.00152077028399292 TRUE -"Chlorfenvinphos" "3" 271 -0.208600220564307 998.660381296 0.0124386821409954 FALSE -"Chlorfenvinphos" "3" 277 -0.0965894124411186 2095.40770716 0.0260990732318137 FALSE -"Chlorfenvinphos" "3" 281 -0.469852594334717 209.236600657 0.00260611877328836 FALSE -"Chlorfenvinphos" "3" 285 0.0829139920350994 331.69540905 0.00413138824576793 TRUE -"Chlorfenvinphos" "3" 297 0.377407626252506 235.281828857 0.00293052166433834 TRUE -"Chlorfenvinphos" "3" 299 0.0684165551844081 4636.7299574 0.0577521760089082 TRUE -"Chlorfenvinphos" "3" 301 0.755131276527433 309.120713465 0.00385021211415135 TRUE -"Chlorfenvinphos" "3" 303 0.256144790638075 675.674108275 0.00841576938581104 TRUE -"Chlorfenvinphos" "3" 313 -0.204360058382281 243.367131218 0.00303122707727542 FALSE -"Chlorfenvinphos" "3" 315 -0.382059666252692 364.384241579 0.00453853967082075 FALSE -"Chlorfenvinphos" "3" 317 0.310202941106162 455.98356629 0.00567944293057693 TRUE 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0.799420559123311 545.251562146 0.00679130863248403 TRUE -"Chlorfenvinphos" "3" 171 -0.531295080469301 99.739204413 0.0012422884535372 FALSE -"Chlorfenvinphos" "3" 173 -0.198218744905989 168.180216313 0.0020947464145984 FALSE -"Chlorfenvinphos" "3" 181 -0.128976632201229 461.190903668 0.00574430223175579 FALSE -"Chlorfenvinphos" "3" 185 -0.2544333889353 247.534089571 0.00308312807527082 FALSE -"Chlorfenvinphos" "3" 203 -0.172388876944166 163.480865011 0.00203621426672387 FALSE -"Chlorfenvinphos" "3" 205 0.752272235645639 6250.3470306075 0.0778503697961336 TRUE -"Chlorfenvinphos" "3" 213 0.264335947671665 352.834961408 0.004394689140956 TRUE -"Chlorfenvinphos" "3" 217 -0.442009813945246 491.887822143 0.00612664363506956 FALSE -"Chlorfenvinphos" "3" 227 0.458106805328464 167.324791902 0.00208409178911874 TRUE -"Chlorfenvinphos" "3" 229 -0.395326148767009 213.640604973 0.00266097226588732 FALSE -"Chlorfenvinphos" "3" 231 0.234108428261132 159.982762809 0.00199264411795024 TRUE 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0.00293052166433834 TRUE -"Chlorfenvinphos" "3" 299 0.0684165551844081 4636.7299574 0.0577521760089082 TRUE -"Chlorfenvinphos" "3" 301 0.755131276527433 309.120713465 0.00385021211415135 TRUE -"Chlorfenvinphos" "3" 303 0.256144790638075 675.674108275 0.00841576938581104 TRUE -"Chlorfenvinphos" "3" 313 -0.204360058382281 243.367131218 0.00303122707727542 FALSE -"Chlorfenvinphos" "3" 315 -0.382059666252692 364.384241579 0.00453853967082075 FALSE -"Chlorfenvinphos" "3" 317 0.310202941106162 455.98356629 0.00567944293057693 TRUE -"Chlorfenvinphos" "3" 318 0.415225959687801 228.938733097 0.00285151607502464 TRUE -"Chlorfenvinphos" "3" 323 -0.314263466258524 563.653416619 0.00702051049417945 FALSE -"Chlorfenvinphos" "3" 327 -0.140520115757785 2409.41143152 0.0300101050415808 FALSE -"Chlorfenvinphos" "3" 331 0.71483882497497 12451.37509615 0.155086453753502 TRUE -"Chlorfenvinphos" "3" 341 -0.150166105415009 1974.064373155 0.0245876974028676 FALSE -"Chlorfenvinphos" "3" 342 0.842450324350269 114.13835049 0.00142163511082737 TRUE -"Chlorfenvinphos" "3" 343 -0.147385439331454 393.598319057 0.0049024117444477 FALSE -"Chlorfenvinphos" "3" 359 1 22584.7152179 0.28130092982741 TRUE -"Chlorfenvinphos" "3" 360 -0.226912638302916 850.672736164 0.0105954416229301 FALSE -"Chlorfenvinphos" "6" 119 0.0731250401711081 66.353376868 0.000891803512611579 TRUE -"Chlorfenvinphos" "6" 127 0.967444814451871 20710.93127215 0.278359325927056 TRUE -"Chlorfenvinphos" "6" 155 0.963091521050382 74403.5832217 1 TRUE -"Chlorfenvinphos" "6" 170 0.449862694478131 251.752763748 0.00338361074624395 TRUE -"Chlorfenvinphos" "6" 177 0.170534803208042 308.496086376 0.00414625308376313 TRUE -"Chlorfenvinphos" "6" 181 -0.0163271234849685 354.258750916 0.00476131303865322 FALSE -"Chlorfenvinphos" "6" 185 0.257029822176199 620.034171576 0.00833339127940232 TRUE -"Chlorfenvinphos" "6" 187 0.089332028465713 255.646638389 0.00343594525047605 TRUE -"Chlorfenvinphos" "6" 195 -0.00564478295778355 215.919657704 0.00290200617167355 FALSE -"Chlorfenvinphos" "6" 205 0.920038935805411 4144.892359716 0.0557082358166203 TRUE -"Chlorfenvinphos" "6" 215 -0.485598529136673 111.581706056 0.00149968188660377 FALSE -"Chlorfenvinphos" "6" 217 -0.102544969577153 184.536623947 0.00248021151611929 FALSE -"Chlorfenvinphos" "6" 227 -0.218545060535632 385.765646933 0.00518477242935378 FALSE -"Chlorfenvinphos" "6" 257 -0.190658380546032 116.439049717 0.00156496561959989 FALSE -"Chlorfenvinphos" "6" 263 -0.283711355460578 130.036875959 0.00174772329944822 FALSE -"Chlorfenvinphos" "6" 269 -0.096686341821556 521.926541329 0.00701480384047927 FALSE -"Chlorfenvinphos" "6" 271 -0.29431709758827 286.086881162 0.00384506859447277 FALSE -"Chlorfenvinphos" "6" 277 -0.244117217731705 7365.76094096 0.0989973953137751 FALSE -"Chlorfenvinphos" "6" 287 -0.285814972272172 1436.521243097 0.0193071513614688 FALSE -"Chlorfenvinphos" "6" 299 0.0846894086356431 4075.071828875 0.054769833016409 TRUE -"Chlorfenvinphos" "6" 301 0.659557765349154 184.163766389 0.00247520023115349 TRUE -"Chlorfenvinphos" "6" 303 0.432503000199826 558.96223402 0.00751257143563184 TRUE -"Chlorfenvinphos" "6" 315 -0.531353518553151 228.835577496 0.00307559888364704 FALSE -"Chlorfenvinphos" "6" 317 0.102388860009693 371.096517574 0.00498761620751847 TRUE -"Chlorfenvinphos" "6" 327 -0.0392538720434494 857.215583061 0.0115211599487992 FALSE -"Chlorfenvinphos" "6" 331 0.927142862540353 10942.34945269 0.147067506414108 TRUE -"Chlorfenvinphos" "6" 341 0.27843013514813 681.509114277 0.0091596275981267 TRUE -"Chlorfenvinphos" "6" 359 1 70775.23458992 0.951234221865785 TRUE -"Chlorfenvinphos" "6" 360 0.211699399531209 336.06626725 0.0045168021847634 TRUE -"Chlormequat" "3" 104 0.258848039085982 1344.00603488 0.0035075545862099 TRUE -"Chlormequat" "3" 122 1 383174.65968 1 TRUE -"Chlormequat" "3" 104 0.258848039085982 1344.00603488 0.0035075545862099 TRUE -"Chlormequat" "3" 122 1 383174.65968 1 TRUE -"Chlormequat" "7" 104 -0.238480528781348 249.84195518 0.00659545474896182 FALSE -"Chlormequat" "7" 122 1 37880.9293202 1 TRUE -"Desisopropylatrazine" "1" 79 -0.00233999251843864 530.25218964 0.0010623465213357 TRUE -"Desisopropylatrazine" "1" 115 0.0134526232413478 19215.13916 0.0384970333785257 TRUE -"Desisopropylatrazine" "1" 130 0.263395383425939 3994.6477049 0.00800317316208218 TRUE -"Desisopropylatrazine" "1" 132 -0.0312768712385 7326.0765379 0.0146776045005323 FALSE -"Desisopropylatrazine" "1" 133 0.249785689081156 9816.328859 0.0196667604950881 TRUE -"Desisopropylatrazine" "1" 142 -0.064738762712863 4465.0982056 0.0089457085492884 FALSE -"Desisopropylatrazine" "1" 146 0.267964087777204 1514.5723649 0.00303440648544061 TRUE -"Desisopropylatrazine" "1" 156 -0.877674937275134 2233.4023818 0.00447456379700939 FALSE -"Desisopropylatrazine" "1" 159 -0.178626327953242 56937.500976 0.114072807764298 FALSE -"Desisopropylatrazine" "1" 174 1 499132.98438 1 TRUE -"Desisopropylatrazine" "1" 79 -0.00233999251843864 530.25218964 0.0010623465213357 TRUE -"Desisopropylatrazine" "1" 115 0.0134526232413478 19215.13916 0.0384970333785257 TRUE -"Desisopropylatrazine" "1" 130 0.263395383425939 3994.6477049 0.00800317316208218 TRUE -"Desisopropylatrazine" "1" 132 -0.0312768712385 7326.0765379 0.0146776045005323 FALSE -"Desisopropylatrazine" "1" 133 0.249785689081156 9816.328859 0.0196667604950881 TRUE -"Desisopropylatrazine" "1" 142 -0.064738762712863 4465.0982056 0.0089457085492884 FALSE -"Desisopropylatrazine" "1" 146 0.267964087777204 1514.5723649 0.00303440648544061 TRUE -"Desisopropylatrazine" "1" 156 -0.877674937275134 2233.4023818 0.00447456379700939 FALSE -"Desisopropylatrazine" "1" 159 -0.178626327953242 56937.500976 0.114072807764298 FALSE -"Desisopropylatrazine" "1" 174 1 499132.98438 1 TRUE -"Dichlorvos" "8" 77 0.673126587009387 741.86317154 0.00161896017936163 TRUE -"Dichlorvos" "8" 79 0.878900088282318 1378.256703748 0.00300775507655178 TRUE -"Dichlorvos" "8" 95 0.23830151975066 167.451852342 0.000365428412276191 TRUE -"Dichlorvos" "8" 99 0.0952811367061809 779.789044359 0.00170172541184249 TRUE -"Dichlorvos" "8" 105 0.421334905224525 170.538307904 0.000372163951715189 TRUE -"Dichlorvos" "8" 107 0.259129043686515 193.227040286 0.000421677333233239 TRUE -"Dichlorvos" "8" 109 0.967088540122942 63244.728942055 0.138018305315196 TRUE -"Dichlorvos" "8" 111 0.669971084873578 362.689319128 0.000791493078068717 TRUE -"Dichlorvos" "8" 117 0.427724412537125 150.021759756 0.000327390904954265 TRUE -"Dichlorvos" "8" 119 0.352320220252662 842.015996927 0.00183752263450484 TRUE -"Dichlorvos" "8" 121 0.347913703205373 778.073791986 0.00169798223466916 TRUE -"Dichlorvos" "8" 123 0.375380270767784 270.12158084 0.000589483478548166 TRUE -"Dichlorvos" "8" 127 0.948284758535013 7147.09441171 0.0155970287980156 TRUE -"Dichlorvos" "8" 133 0.111433255667834 852.743870701 0.00186093396036062 TRUE -"Dichlorvos" "8" 135 0.0748728027193132 220.929068083 0.000482131176490902 TRUE -"Dichlorvos" "8" 137 0.453769927098964 505.667025571 0.00110351181972854 TRUE -"Dichlorvos" "8" 139 0.467524552074558 137.935647968 0.000301015510597557 TRUE -"Dichlorvos" "8" 143 0.278796612798532 266.444155698 0.000581458272424074 TRUE -"Dichlorvos" "8" 145 0.994170372012309 44316.40897363 0.0967112321692371 TRUE -"Dichlorvos" "8" 146 0.346301417994264 207.562618724 0.000452961714948885 TRUE -"Dichlorvos" "8" 147 -0.183799172220307 819.102781302 0.00178751936557185 FALSE -"Dichlorvos" "8" 149 0.291827272614207 273.867382537 0.000597657902107486 TRUE -"Dichlorvos" "8" 151 -0.0612144593206886 544.88402842 0.00118909467166422 FALSE -"Dichlorvos" "8" 153 0.459453598609755 595.225358962 0.00129895402666414 TRUE -"Dichlorvos" "8" 157 -0.0788899965991259 259.340542296 0.000565956131775221 FALSE -"Dichlorvos" "8" 159 0.0596826580176188 1143.682675356 0.00249584664700842 TRUE -"Dichlorvos" "8" 161 0.106726535917086 9549.15720075 0.0208390251026838 TRUE -"Dichlorvos" "8" 163 0.0347987341572495 754.856181158 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(Dylox)" NA NA "4" 199 0.34691746641912 144.142693995 0.00355705015215411 TRUE +"Trichlorfon (Dylox)" NA NA "4" 201 0.095844899247823 127.383673675 0.00314348305328139 TRUE +"Trichlorfon (Dylox)" NA NA "4" 211 0.589929547507267 156.726169586 0.00386757614917167 TRUE +"Trichlorfon (Dylox)" NA NA "4" 213 0.214402092378455 334.711538323 0.00825977158690306 TRUE +"Trichlorfon (Dylox)" NA NA "4" 215 0.177739314274526 412.352368363 0.0101757363760497 TRUE +"Trichlorfon (Dylox)" NA NA "4" 221 0.950607639404665 40523.0985871 1 TRUE +"Trichlorfon (Dylox)" NA NA "4" 225 -0.377401610724356 503.974612244 0.012436724480996 FALSE +"Trichlorfon (Dylox)" NA NA "4" 227 0.163495046198974 177.141063216 0.00437136027086513 TRUE +"Trichlorfon (Dylox)" NA NA "4" 229 0.602334206324447 1013.548554406 0.0250116252148756 TRUE +"Trichlorfon (Dylox)" NA NA "4" 239 -0.216616311827602 1313.5219316555 0.0324141533459547 FALSE +"Trichlorfon (Dylox)" NA NA "4" 257 1 25290.7478033 0.624106958379313 TRUE +"Trichlorfon (Dylox)" NA NA "4" 79 0.0521595798449914 279.873629576 0.00690652095555926 TRUE +"Trichlorfon (Dylox)" NA NA "4" 109 0.922563790701349 9640.82224867 0.237909305675332 TRUE +"Trichlorfon (Dylox)" NA NA "4" 125 -0.441808918074544 178.089407913 0.00439476284199285 FALSE +"Trichlorfon (Dylox)" NA NA "4" 127 0.769422232032552 1076.07612804 0.0265546358881489 TRUE +"Trichlorfon (Dylox)" NA NA "4" 140 0.348604833045235 1970.98268515 0.0486384988777101 TRUE +"Trichlorfon (Dylox)" NA NA "4" 145 0.820960207936605 4235.84716059 0.104529202066952 TRUE +"Trichlorfon (Dylox)" NA NA "4" 185 0.31275352450403 348.909767164 0.00861014530796692 TRUE +"Trichlorfon (Dylox)" NA NA "4" 187 -0.260474354038597 107.324927324 0.00264848767902871 FALSE +"Trichlorfon (Dylox)" NA NA "4" 197 -0.0360245652498858 2081.96281053 0.0513771869161251 FALSE +"Trichlorfon (Dylox)" NA NA "4" 199 0.34691746641912 144.142693995 0.00355705015215411 TRUE +"Trichlorfon (Dylox)" NA NA "4" 201 0.095844899247823 127.383673675 0.00314348305328139 TRUE +"Trichlorfon (Dylox)" NA NA "4" 211 0.589929547507267 156.726169586 0.00386757614917167 TRUE +"Trichlorfon (Dylox)" NA NA "4" 213 0.214402092378455 334.711538323 0.00825977158690306 TRUE +"Trichlorfon (Dylox)" NA NA "4" 215 0.177739314274526 412.352368363 0.0101757363760497 TRUE +"Trichlorfon (Dylox)" NA NA "4" 221 0.950607639404665 40523.0985871 1 TRUE +"Trichlorfon (Dylox)" NA NA "4" 225 -0.377401610724356 503.974612244 0.012436724480996 FALSE +"Trichlorfon (Dylox)" NA NA "4" 227 0.163495046198974 177.141063216 0.00437136027086513 TRUE +"Trichlorfon (Dylox)" NA NA "4" 229 0.602334206324447 1013.548554406 0.0250116252148756 TRUE +"Trichlorfon (Dylox)" NA NA "4" 239 -0.216616311827602 1313.5219316555 0.0324141533459547 FALSE +"Trichlorfon (Dylox)" NA NA "4" 257 1 25290.7478033 0.624106958379313 TRUE diff -r c68c94865667 -r 856001213966 test-data/compounds_pos.csv --- a/test-data/compounds_pos.csv Wed Jun 22 13:07:01 2022 +0000 +++ b/test-data/compounds_pos.csv Wed Jul 06 10:38:39 2022 +0000 @@ -1,33 +1,33 @@ -Compounds,mz,rt -2-diethylamino-6-methyl pyrimidin-4-ol one,182.12879,345.0 -5-hydroxy-thiabendazole,218.03826,315.0 -acetamiprid-N-desmethyl,209.05885,526.2 -Acetochlor,270.12554,1158.6 -Avermectin B1a (Abamectin),895.49221,1663.8 -Benzophenone-3 (Oxybenzone),229.08592,1178.4 -Butocarboxim,191.0849,1267.8 -Carbendazim,192.07676,339.0 -Cefoperazone,646.1497,1755.0 -Chlorfenvinphos,358.97681,1255.8 -Chlormequat,122.0737,54.0 -Desisopropylatrazine,174.0541,399.0 -Dichlorvos,220.9532,763.2 -Dimethyldithiophosphate,158.96979,615.0 -Emamectin B1a,886.5311,1663.8 -Fluopyram,397.05369,1161.0 -Hydroxy-tebuconazole,324.14733,1098.6 -Isoproturon,207.14919,936.0 -Ivermectin B1a ,897.4971,1650.0 -Malathion dicarboxilic acid,274.98075,574.8 -Methamidophos,142.0086,139.2 -Metolachlor,284.14119,1158.0 -"N,N-diethyl-m-toluamide ou DEET",192.13829,945.0 -Nigericin,747.4654,1663.8 -Omethoate,214.02975,237.0 -Prochloraz,376.03809,1271.4 -p-Toluenesulfonamide,172.04323,393.0 -Rifaximin,786.3596,1183.2 -Spinosad A (Spinosyn A),732.4681,1212.0 -TCMTB,238.9766,1032.0 -Trichlorfon (Dylox),256.9299,444.0 -Tylosin,916.5264,909.0 +Compound_name,mz,rtsec,inchikey,elemcomposition +2-diethylamino-6-methyl pyrimidin-4-ol one,182.12879,345.0,, +5-hydroxy-thiabendazole,218.03826,315.0,, +acetamiprid-N-desmethyl,209.05885,526.2,, +Acetochlor,270.12554,1158.6,, +Avermectin B1a (Abamectin),895.49221,1663.8,, +Benzophenone-3 (Oxybenzone),229.08592,1178.4,, +Butocarboxim,191.0849,1267.8,, +Carbendazim,192.07676,339.0,, +Cefoperazone,646.1497,1755.0,, +Chlorfenvinphos,358.97681,1255.8,, +Chlormequat,122.0737,54.0,, +Desisopropylatrazine,174.0541,399.0,, +Dichlorvos,220.9532,763.2,, +Dimethyldithiophosphate,158.96979,615.0,, +Emamectin B1a,886.5311,1663.8,, +Fluopyram,397.05369,1161.0,, +Hydroxy-tebuconazole,324.14733,1098.6,, +Isoproturon,207.14919,936.0,, +Ivermectin B1a ,897.4971,1650.0,, +Malathion dicarboxilic acid,274.98075,574.8,, +Methamidophos,142.0086,139.2,, +Metolachlor,284.14119,1158.0,, +"N,N-diethyl-m-toluamide ou DEET",192.13829,945.0,, +Nigericin,747.4654,1663.8,, +Omethoate,214.02975,237.0,, +Prochloraz,376.03809,1271.4,, +p-Toluenesulfonamide,172.04323,393.0,, +Rifaximin,786.3596,1183.2,, +Spinosad A (Spinosyn A),732.4681,1212.0,, +TCMTB,238.9766,1032.0,, +Trichlorfon (Dylox),256.9299,444.0,, +Tylosin,916.5264,909.0,, diff -r c68c94865667 -r 856001213966 test-data/compounds_pos.txt --- a/test-data/compounds_pos.txt Wed Jun 22 13:07:01 2022 +0000 +++ b/test-data/compounds_pos.txt Wed Jul 06 10:38:39 2022 +0000 @@ -1,33 +1,33 @@ -Compounds mz rt -2-diethylamino-6-methyl pyrimidin-4-ol one 182.12879 345.0 -5-hydroxy-thiabendazole 218.03826 315.0 -acetamiprid-N-desmethyl 209.05885 526.2 -Acetochlor 270.12554 1158.6 -Avermectin B1a (Abamectin) 895.49221 1663.8 -Benzophenone-3 (Oxybenzone) 229.08592 1178.4 -Butocarboxim 191.0849 1267.8 -Carbendazim 192.07676 339.0 -Cefoperazone 646.1497 1755.0 -Chlorfenvinphos 358.97681 1255.8 -Chlormequat 122.0737 54.0 -Desisopropylatrazine 174.0541 399.0 -Dichlorvos 220.9532 763.2 -Dimethyldithiophosphate 158.96979 615.0 -Emamectin B1a 886.5311 1663.8 -Fluopyram 397.05369 1161.0 -Hydroxy-tebuconazole 324.14733 1098.6 -Isoproturon 207.14919 936.0 -Ivermectin B1a 897.4971 1650.0 -Malathion dicarboxilic acid 274.98075 574.8 -Methamidophos 142.0086 139.2 -Metolachlor 284.14119 1158.0 -N,N-diethyl-m-toluamide ou DEET 192.13829 945.0 -Nigericin 747.4654 1663.8 -Omethoate 214.02975 237.0 -Prochloraz 376.03809 1271.4 -p-Toluenesulfonamide 172.04323 393.0 -Rifaximin 786.3596 1183.2 -Spinosad A (Spinosyn A) 732.4681 1212.0 -TCMTB 238.9766 1032.0 -Trichlorfon (Dylox) 256.9299 444.0 -Tylosin 916.5264 909.0 +Compound_name mz rtsec inchikey elemcomposition +2-diethylamino-6-methyl pyrimidin-4-ol one 182.12879 345.0 +5-hydroxy-thiabendazole 218.03826 315.0 +acetamiprid-N-desmethyl 209.05885 526.2 +Acetochlor 270.12554 1158.6 +Avermectin B1a (Abamectin) 895.49221 1663.8 +Benzophenone-3 (Oxybenzone) 229.08592 1178.4 +Butocarboxim 191.0849 1267.8 +Carbendazim 192.07676 339.0 +Cefoperazone 646.1497 1755.0 +Chlorfenvinphos 358.97681 1255.8 +Chlormequat 122.0737 54.0 +Desisopropylatrazine 174.0541 399.0 +Dichlorvos 220.9532 763.2 +Dimethyldithiophosphate 158.96979 615.0 +Emamectin B1a 886.5311 1663.8 +Fluopyram 397.05369 1161.0 +Hydroxy-tebuconazole 324.14733 1098.6 +Isoproturon 207.14919 936.0 +Ivermectin B1a 897.4971 1650.0 +Malathion dicarboxilic acid 274.98075 574.8 +Methamidophos 142.0086 139.2 +Metolachlor 284.14119 1158.0 +N,N-diethyl-m-toluamide ou DEET 192.13829 945.0 +Nigericin 747.4654 1663.8 +Omethoate 214.02975 237.0 +Prochloraz 376.03809 1271.4 +p-Toluenesulfonamide 172.04323 393.0 +Rifaximin 786.3596 1183.2 +Spinosad A (Spinosyn A) 732.4681 1212.0 +TCMTB 238.9766 1032.0 +Trichlorfon (Dylox) 256.9299 444.0 +Tylosin 916.5264 909.0 diff -r c68c94865667 -r 856001213966 test-data/compounds_pos_old_format.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/compounds_pos_old_format.txt Wed Jul 06 10:38:39 2022 +0000 @@ -0,0 +1,33 @@ +Compounds mz rt +2-diethylamino-6-methyl pyrimidin-4-ol one 182.12879 345.0 +5-hydroxy-thiabendazole 218.03826 315.0 +acetamiprid-N-desmethyl 209.05885 526.2 +Acetochlor 270.12554 1158.6 +Avermectin B1a (Abamectin) 895.49221 1663.8 +Benzophenone-3 (Oxybenzone) 229.08592 1178.4 +Butocarboxim 191.0849 1267.8 +Carbendazim 192.07676 339.0 +Cefoperazone 646.1497 1755.0 +Chlorfenvinphos 358.97681 1255.8 +Chlormequat 122.0737 54.0 +Desisopropylatrazine 174.0541 399.0 +Dichlorvos 220.9532 763.2 +Dimethyldithiophosphate 158.96979 615.0 +Emamectin B1a 886.5311 1663.8 +Fluopyram 397.05369 1161.0 +Hydroxy-tebuconazole 324.14733 1098.6 +Isoproturon 207.14919 936.0 +Ivermectin B1a 897.4971 1650.0 +Malathion dicarboxilic acid 274.98075 574.8 +Methamidophos 142.0086 139.2 +Metolachlor 284.14119 1158.0 +N,N-diethyl-m-toluamide ou DEET 192.13829 945.0 +Nigericin 747.4654 1663.8 +Omethoate 214.02975 237.0 +Prochloraz 376.03809 1271.4 +p-Toluenesulfonamide 172.04323 393.0 +Rifaximin 786.3596 1183.2 +Spinosad A (Spinosyn A) 732.4681 1212.0 +TCMTB 238.9766 1032.0 +Trichlorfon (Dylox) 256.9299 444.0 +Tylosin 916.5264 909.0