Mercurial > repos > recetox > rename_annotated_feature
changeset 0:268fcec93d9c draft default tip
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rename_annotated_feature commit 7948bcdd36cec524d201712dc20c438973b4cc28
| author | recetox |
|---|---|
| date | Tue, 21 May 2024 07:44:25 +0000 |
| parents | |
| children | |
| files | macros.xml rename_annotated_feature.py rename_annotated_feature.xml test-data/abundance_table.tsv test-data/annotated_table.tsv test-data/multi_mode_output.tsv test-data/single_mode_output.tsv |
| diffstat | 7 files changed, 221 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue May 21 07:44:25 2024 +0000 @@ -0,0 +1,26 @@ +<macros> + <token name="@TOOL_VERSION@">1.0.0</token> + <xml name="creator"> + <creator> + <person + givenName="Wudmir" + familyName="Rojas" + url="https://github.com/wverastegui" + identifier="0000-0001-7036-9987" /> + <person + givenName="Helge" + familyName="Hecht" + url="https://github.com/hechth" + identifier="0000-0001-6744-996X" /> + <organization + url="https://www.recetox.muni.cz/" + email="GalaxyToolsDevelopmentandDeployment@space.muni.cz" + name="RECETOX MUNI"/> + </creator> + </xml> + <token name="@HELP@"><![CDATA[ + This tool uses an annotations table to rename columns in an abundance table. It accepts paths to these tables, + a renaming mode ("single" or "multiple"), and an output path for the CSV result. 'Single' mode renames based on + the highest match, 'multiple' mode renames based on all matches. + ]]></token> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rename_annotated_feature.py Tue May 21 07:44:25 2024 +0000 @@ -0,0 +1,94 @@ +import argparse +from collections import defaultdict +from typing import Tuple + +import pandas as pd + + +def parse_arguments() -> argparse.Namespace: + """Parses command-line arguments. + + Returns: + argparse.Namespace: Namespace with argument values as attributes. + """ + parser = argparse.ArgumentParser(description='Rename annotated feature.') + parser.add_argument('--annotations_table_path', type=str, required=True, help='Path to the annotations table file.') + parser.add_argument('--abundance_table_path', type=str, required=True, help='Path to the abundance table file.') + parser.add_argument('--mode', type=str, choices=['single', 'multiple'], default='single', help='Mode to use for renaming. Can be "single" or "multiple".') + parser.add_argument('--output_path', type=str, default='output.csv', help='Path to the output CSV file.') + return parser.parse_args() + + +def load_tables(annotations_table_path: str, abundance_table_path: str) -> Tuple[pd.DataFrame, pd.DataFrame]: + """Loads annotation and abundance tables from files. + + Args: + annotations_table_path (str): Path to the annotations table file. + abundance_table_path (str): Path to the abundance table file. + + Returns: + Tuple[pd.DataFrame, pd.DataFrame]: Tuple of DataFrames for annotations and abundance tables. + """ + annotations_table = pd.read_table(annotations_table_path) + abundance_table = pd.read_table(abundance_table_path) + + annotations_table.columns = annotations_table.columns.str.strip() + abundance_table.columns = abundance_table.columns.str.strip() + + return annotations_table, abundance_table + + +def rename_single(annotations_table: pd.DataFrame, abundance_table: pd.DataFrame) -> None: + """Renames columns in abundance table based on single best match in annotations table. + + Args: + annotations_table (pd.DataFrame): DataFrame of annotations. + abundance_table (pd.DataFrame): DataFrame of abundance data. + """ + scores_col = annotations_table.columns[-1] + ref_idxs = annotations_table.groupby("query")[scores_col].idxmax() + results = annotations_table.loc[ref_idxs] + + queries = results["query"] + refs = results["reference"] + + mapping = dict(zip(queries, refs)) + abundance_table.rename(columns=mapping, inplace=True) + + +def rename_multiple(annotations_table: pd.DataFrame, abundance_table: pd.DataFrame) -> None: + """Renames columns in abundance table based on multiple matches in annotations table. + + Args: + annotations_table (pd.DataFrame): DataFrame of annotations. + abundance_table (pd.DataFrame): DataFrame of abundance data. + """ + queries = annotations_table["query"] + refs = annotations_table["reference"] + + mapping = defaultdict(list) + for query, ref in zip(queries, refs): + mapping[query].append(ref) + + for query, refs in mapping.items(): + new_column_name = ', '.join(refs) + if query in abundance_table.columns: + abundance_table.rename(columns={query: new_column_name}, inplace=True) + + +def main() -> None: + """Main function to parse arguments, load tables, rename columns, and save output.""" + args = parse_arguments() + + annotations_table, abundance_table = load_tables(args.annotations_table_path, args.abundance_table_path) + + if args.mode == "single": + rename_single(annotations_table, abundance_table) + else: + rename_multiple(annotations_table, abundance_table) + + abundance_table.to_csv(args.output_path, sep="\t", index=False) + + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rename_annotated_feature.xml Tue May 21 07:44:25 2024 +0000 @@ -0,0 +1,53 @@ +<tool id="rename_annotated_feature" name="Rename Annotated Feature" version="@TOOL_VERSION@+galaxy0" profile="21.09"> + <description>Rename columns in abundance table based on annotations table</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="creator"/> + <requirements> + <requirement type="package" version="2.2.1">pandas</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python3 '${__tool_directory__}/rename_annotated_feature.py' + --annotations_table_path '$annotations_table_path' + --abundance_table_path '$abundance_table_path' + --mode '$mode' + --output_path '$output_path' + ]]></command> + <inputs> + <param name="annotations_table_path" type="data" format="tabular" label="Annotations table file" help="Path to the annotations table file."/> + <param name="abundance_table_path" type="data" format="tabular" label="Abundance table file" help="Path to the abundance table file."/> + <param name="mode" type="select" label="Mode to use for renaming" help="Can be single or multiple."> + <option value="single" selected="true">Single</option> + <option value="multiple">Multiple</option> + </param> + </inputs> + <outputs> + <data name="output_path" format="tabular" label="Renamed abundance table"/> + </outputs> + <tests> + <test> + <param name="annotations_table_path" value="annotated_table.tsv" ftype="tabular"/> + <param name="abundance_table_path" value="abundance_table.tsv" ftype="tabular"/> + <param name="mode" value="single"/> + <output name="output_path" file="single_mode_output.tsv"/> + </test> + <test> + <param name="annotations_table_path" value="annotated_table.tsv" ftype="tabular"/> + <param name="abundance_table_path" value="abundance_table.tsv" ftype="tabular" /> + <param name="mode" value="multiple"/> + <output name="output_path" file="multi_mode_output.tsv"/> + </test> + </tests> + <help> + <![CDATA[ + @HELP@ + ]]> + </help> + <!-- Update to the correct citation for this tool --> + <citations> + <citation type="doi">10.5281/zenodo.7178586</citation> + <citation type="doi">10.21105/joss.02411</citation> + <citation type="doi">10.1021/ac501530d</citation> + </citations> +</tool> \ No newline at end of file
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2460772.68362305 533022.360392473 694353.520762331 1346439.22702378 732792.803930996 277876.306394059 624532.078388532 3179015.67820813 576021.279400396 280494.819397593 134799.623752372 212768.984776508 3382421.33569654 92898512.4311801 13223985.2130325 498589.729518623 183637.56405057 68802.2298879015 404358.30488774 116068.972557888 429396.952556901 1296701.25183242 1521322.80636681 29765.8618627488 521065.668857697 425892.743778167 401604.676424981 1110376.94558137 520056.093266083 725594.814779287 85275.43391835 648833.158157628 681989.285538676 174571.160772883 69864.2971794516 1203380.76736934 274728.442550141 490534.204548014 168879.838000285 201847.854173309 438930.867349431 5235936.5032364 200827.152998417 460869.461412979 155588.44181464 145502.897006461 1494716.86778102 83883.1120468015 2192460.0568132 128780.225719568 4825351.00009989 27536510.9922369 559616.504840751 82205.6965348961 901809.673640509 375667.610860315 116639.209688359 127566.558332909 533034.745956742 1451958.91597655 2130895.51711982 1789252.34307323 486562.695964036 180134.910838113 601329.558263094 104101.938801513 324963.288542131 1612702.63173759 550651.64417898 2766138.53520165 377252.413645581 123645.758494625 387984.302285353 839980.494379911 166449.589738398 62989.0720363598 43500.3045640958 67599.1059232596 183767.071005481 263671.601883412 31282.7592109649 143605.049243715 374413.913927304 333450.092078756 958386.9421518 2024127.8869989 232757.82387132 104973.936368178 591507.310898803 260232.622896598 6809650.66711065 52108.0066840428 302097.543370192 2669673.87128252 6797924.97522905 608080481.884683 1249942.28967707 387359.772548752 619485.451267781 1093158.58654422 292582.969255941 393260.173910113 322829.328085645 311466.238896017 67980.3184126115 235917.042528019 79809.2691081252 141123.511607319 410692.406563824 172647.485631286 41542.5708173683 229199.860761181 349745.759666562 714591.181152216 690729.685633624 58760.5411542359 162951.716694776 4710155.27664862 86701.3290312996 134461.799649973 3754716.23512648 62515.9202444047 254624.404911054 305155.292227914 961022.029191935 540567.624226532 208547.918338895 682683258.60297 328018.74245691 466936.776542758 2410303.382939 100134.82557748 227294.902194971 663499.787776114 5146445.21144571 46933.9752065662 84050.309586464 1418921.21031416 138078.867821352 208099.207247074 844084.663582396 201933.132950629 262702.774765263 2488702.34271486 3068896.24914106 166383.287052717 3268682.53402307 62654.4183308775 1023499.55431711 717153.348912889 1004911.55505811 152739.523887268 32547.1285883596 32364.3820380837 378187.022615471 2822699.99759349 412526.782356598 164117.14382635 151475.868438157 22355.394099169 162139.451814641 1274172.26222152 213542.022736542 1039684.18056762 224059.120983437 390197.420071386 6446979.44757867 1821543.2671682 116615.433523564 461336.290361989 226841.404377312 2313784.34863521 77819.0589368957 128077.152216948 526344.103752229 729995.760348558 204105.86720904 904285.338382647 13901.6387172006 1333143.00364644 105427.601767016 166788.10170103 378425.0273745 92266.6638853474 80787.6483250491
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotated_table.tsv Tue May 21 07:44:25 2024 +0000 @@ -0,0 +1,36 @@ +query reference matches score +C001 Uridine_4TMS isomer 1 81 0.7870108353155918 +C004 Asparagine_3TMS 56 0.9097767959597624 +C012 Myo-inositol_6TMS 29 0.6889601235553525 +C016 Acetylglutamine_3TMS 36 0.626807029456144 +C025 Glutamic acid_3TMS spectra 1 28 0.8777837139197799 +C025 Glutamic acid_3TMS spectra 2 26 0.9028865192715256 +C032 Citric acid_4TMS 26 0.9102768232927689 +C035 Maleamic acid_3TMS 25 0.6630039541546467 +C042 Tyrosine_3TMS 15 0.7833587796868388 +C043 Xanthine_3TMS 21 0.9343825213743766 +C044 Guanine_3TMS 19 0.9879561890993698 +C045 Fructose_5TMS isomer 1 17 0.8525338249207454 +C045 Fructose_5TMS isomer 2 17 0.8720082595139022 +C048 Glycine_3TMS 15 0.8899759223441942 +C053 Isoleucine_2TMS 17 0.9618511468752681 +C053 Leucine_2TMS 12 0.9689201964961467 +C059 Asparagine_2TMS 15 0.874229139105799 +C068 Tryptophan_3TMS 9 0.9813702571055418 +C099 Lysine_3TMS 20 0.7179326994285286 +C111 Proline_2TMS 8 0.7340774949729849 +C129 Glutamic acid_2TMS 4 0.8513864715294999 +C129 gamma-Aminobutyric acid_3TMS 7 0.7661841956333684 +C160 Orotic acid_3TMS 17 0.8126095426096038 +C162 Myo-inositol_6TMS 14 0.6725414287502448 +C177 Arginine_3TMS 16 0.7941810738472939 +C206 Alanine_2TMS 9 0.6132326627080693 +C206 Sarcosine_2TMS 5 0.7334160526716176 +C254 trans-Aconitic acid_3TMS 7 0.7845936148464933 +C257 Histidine_4TMS 15 0.7486358620781661 +C320 Uric acid_4TMS 13 0.9144373802322492 +C354 Serine_3TMS 4 0.8111915304679743 +C373 6-Aminocaproic acid_3TMS 4 0.9672953388615115 +C393 Guanine_4TMS 5 0.7315123727541482 +C482 Aspartic acid_3TMS isomer 4 0.9171115408384085 +C482 Aspartic acid_3TMS isomer 4 0.8609332820067314
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multi_mode_output.tsv Tue May 21 07:44:25 2024 +0000 @@ -0,0 +1,4 @@ +Unnamed: 0 Uridine_4TMS isomer 1 C002 C003 Asparagine_3TMS C005 C006 C007 C008 C009 C010 C011 Myo-inositol_6TMS C013 C014 C015 Acetylglutamine_3TMS C017 C018 C019 C020 C021 C022 C023 C024 Glutamic acid_3TMS spectra 1, Glutamic acid_3TMS spectra 2 C026 C027 C028 C029 C030 C031 Citric acid_4TMS C033 C034 Maleamic acid_3TMS C036 C037 C038 C039 C040 C041 Tyrosine_3TMS Xanthine_3TMS Guanine_3TMS Fructose_5TMS isomer 1, Fructose_5TMS isomer 2 C046 C047 Glycine_3TMS C049 C050 C051 C052 Isoleucine_2TMS, Leucine_2TMS C054 C055 C056 C057 C058 Asparagine_2TMS C060 C061 C062 C063 C064 C065 C066 C067 Tryptophan_3TMS C069 C070 C071 C072 C073 C074 C075 C076 C077 C078 C079 C080 C081 C082 C083 C084 C085 C086 C087 C088 C089 C090 C091 C092 C093 C094 C095 C096 C097 C098 Lysine_3TMS C100 C101 C102 C103 C104 C105 C106 C107 C108 C109 C110 Proline_2TMS C112 C113 C114 C115 C116 C117 C118 C119 C120 C121 C122 C123 C124 C125 C126 C127 C128 Glutamic acid_2TMS, gamma-Aminobutyric acid_3TMS C130 C131 C132 C133 C134 C135 C136 C137 C138 C139 C140 C141 C142 C143 C144 C145 C146 C147 C148 C149 C150 C151 C152 C153 C154 C155 C156 C157 C158 C159 Orotic acid_3TMS C161 Myo-inositol_6TMS C163 C164 C165 C166 C167 C168 C169 C170 C171 C172 C173 C174 C175 C176 Arginine_3TMS C178 C179 C180 C181 C182 C183 C184 C185 C186 C187 C188 C189 C190 C191 C192 C193 C194 C195 C196 C197 C198 C199 C200 C201 C202 C203 C204 C205 Alanine_2TMS, Sarcosine_2TMS C207 C208 C209 C210 C211 C212 C213 C214 C215 C216 C217 C218 C219 C220 C221 C222 C223 C224 C225 C226 C227 C228 C229 C230 C231 C232 C233 C234 C235 C236 C237 C238 C239 C240 C241 C242 C243 C244 C245 C246 C247 C248 C249 C250 C251 C252 C253 trans-Aconitic acid_3TMS C255 C256 Histidine_4TMS C258 C259 C260 C261 C262 C263 C264 C265 C266 C267 C268 C269 C270 C271 C272 C273 C274 C275 C276 C277 C278 C279 C280 C281 C282 C283 C284 C285 C286 C287 C288 C289 C290 C291 C292 C293 C294 C295 C296 C297 C298 C299 C300 C301 C302 C303 C304 C305 C306 C307 C308 C309 C310 C311 C312 C313 C314 C315 C316 C317 C318 C319 Uric acid_4TMS C321 C322 C323 C324 C325 C326 C327 C328 C329 C330 C331 C332 C333 C334 C335 C336 C337 C338 C339 C340 C341 C342 C343 C344 C345 C346 C347 C348 C349 C350 C351 C352 C353 Serine_3TMS C355 C356 C357 C358 C359 C360 C361 C362 C363 C364 C365 C366 C367 C368 C369 C370 C371 C372 6-Aminocaproic acid_3TMS C374 C375 C376 C377 C378 C379 C380 C381 C382 C383 C384 C385 C386 C387 C388 C389 C390 C391 C392 Guanine_4TMS C394 C395 C396 C397 C398 C399 C400 C401 C402 C403 C404 C405 C406 C407 C408 C409 C410 C411 C412 C413 C414 C415 C416 C417 C418 C419 C420 C421 C422 C423 C424 C425 C426 C427 C428 C429 C430 C431 C432 C433 C434 C435 C436 C437 C438 C439 C440 C441 C442 C443 C444 C445 C446 C447 C448 C449 C450 C451 C452 C453 C454 C455 C456 C457 C458 C459 C460 C461 C462 C463 C464 C465 C466 C467 C468 C469 C470 C471 C472 C473 C474 C475 C476 C477 C478 C479 C480 C481 Aspartic acid_3TMS isomer, Aspartic acid_3TMS isomer C483 C484 C485 C486 C487 C488 C489 C490 C491 C492 C493 C494 C495 C496 C497 C498 C499 C500 C501 C502 C503 C504 C505 C506 C507 C508 C509 C510 C511 C512 C513 C514 C515 C516 C517 C518 C519 C520 C521 C522 C523 C524 C525 C526 C527 C528 C529 C530 C531 C532 C533 C534 C535 C536 C537 C538 C539 C540 C541 C542 C543 C544 C545 C546 C547 C548 C549 C550 C551 C552 C553 C554 C555 C556 C557 C558 C559 C560 C561 C562 C563 C564 C565 C566 C567 C568 C569 C570 C571 +29_qc_no_dil_milliq 14440614.0614047 100829162.950447 254866018.799615 15274982.3781313 5224836.34188986 5885730.25849524 951826.455585983 889479.276736861 1795609403.16384 2421762.67187108 5163569.54055468 238798215.712716 354389395.659526 796483.933541114 823048.878299925 23198329.5204869 292115.435176988 712515.418590804 19610929.4892356 1232587.75701825 3596492.79850348 1629639.47376732 24462390.9163424 485438.836480317 868952050.264982 81375.1586185473 99599261.6309831 959158.254779201 536304.782185507 4001011.6875862 7739617.79445237 1615156866.41566 3949722.78923788 2175945.26658084 40746732.6515362 618603.541165935 9321812.02744594 1806309.45076003 946808.521216693 1380448.93849442 4008025.45350866 774432771.67135 6185010.41280613 3977041.90828131 807444239.555129 117208.261097281 4416621.75166316 11070753.8362958 26211662.9499907 69183910.0525939 60290768.6032428 1576348.77745384 312940893.106132 13076274.7260471 2432709.41029711 225559.955293657 143921764.917415 533636.785572528 10234910.8210168 894305.68092461 352072.205688018 3044048.84816934 7269277.56727447 3913511.40312328 307875.120452888 371077.171892254 287190.462230271 41540567.0240222 13559092.3758615 406492.348681204 24808557.5598735 619094.13446721 266980.599376974 2656865.33861078 2652633.12587089 114017.206962404 164284.989815954 1192746.89473896 7651824.79355225 213604941.362295 272303.678962713 945765.455015841 2146660.56421118 237213.177102788 1153528.12133704 1010797.7193887 124737.084480499 4189366.61204168 102986538.666234 736946.506777988 304127.295255388 691072.335977527 1103791.97882047 2479973.07098931 8905173.39736247 25041688.9624318 124766.399660988 347141.68677344 642044.289099355 354238.743461047 194317.090990598 385095.809290498 127341.597037749 157303.861084333 170750.262677683 917565.301446466 1769184.65218783 166453.198335507 32742511.7781421 2038450.00024453 5717892.0841901 1404987.61805938 845139.568618001 1484031.62670076 302411.519888222 68405.8335896558 146616.523047761 4481021.17562366 46129245.2993171 353938.191426674 183453.986464873 253913.946132376 2372475.39288604 3403842.6347695 2206305.34331278 271644.825859711 1343015.60252275 1156634.49928246 1292699.04759743 343130.988071445 1785108.12921876 528828.965191606 842233.399693472 5777215.15464433 233629.063207309 171218.372521778 2107892.64296657 88120.628416599 596649.828309023 3672583.70822133 6617213.15405245 181008.115138583 2586463.86881571 185920.318958129 1241015.34911364 92227.7955224766 129802.79504124 192555.107703765 145542.62302623 1160899.31563216 112917.924001808 124007.85633309 633684.584728627 2280834.12973503 445536.016790919 124683.380919967 1570606.04419484 154953.831906835 256155.469878756 894605.176902167 1626458.96750198 285181808.698182 610253.234772327 391783.348061144 398324.505959962 328390.586957152 1838374.29468941 1283743.91041274 209311.885783803 940521.92798673 451883.662719365 7734925.17999533 384861.106784837 1484189.97511908 57114.8878988477 39988988.1680606 6479747.39105557 894880.987138881 1812684.67197649 527085.019807927 260908.733449833 888505.281443954 8846164.30225623 459345.290532086 867204.157305589 410857.517229929 80160100.051693 523488.39469134 191980.824793793 1330690.93776021 149920.873203244 158072.175838165 290862.088795427 193353.481374758 349518.966398228 118883.741228244 314215.271673589 79056291.3427869 807794.876841978 511667.260958486 147711.77271555 6414204.41935647 428033.644825501 54406.1929007828 7038434.23383763 5063741.97165563 1718815.64454285 160341727.997531 91202.3205404207 42856493.4461666 4121822.89471918 1352655.82108955 100262.368423675 473760.589138636 2855738.67974274 74540.1352325425 283974.144147633 1079790.73322084 470186.03418124 371174.561962158 1534860.936247 274393.399828041 63825735.564163 73772.2577391385 116119.044871487 412139.136220895 244747.931389062 286713.59221739 971284.016318051 756099.137390138 78333.202817093 165271.223381125 2431597.42755326 85935.807989955 179193.179701008 172855.809883764 246051.049985504 126545.58012136 426177.723240474 2769018.85026361 404802.734176745 1923748.89716192 3016143.88485513 2363523.00565838 23284927.1740917 167790.389630975 171671.864404718 793909.181841846 118189.781563813 1713640.80852142 111893418.150679 305902.081876272 1523388.37838287 22017276.8530788 4130667.64546185 26372022.3156075 1610541.08448918 190673.536242371 1764055.84738082 50304425.5172517 107590.092617611 581867.629417969 58538157.0973169 91699.1040984271 3743222.54773702 602264.045466521 1573453.05821107 41175.5168575104 87483.2620456882 100650.630521181 288897.447441482 561627.500087703 46354.5731825084 7707887.24466242 339148.793690526 336184.961195537 453582.157952033 943536.01891475 1075473.18291486 153513426.619558 355045.125851123 657067.432521505 185275.512026864 1130209.36515672 632077.098383767 56679.1852977019 440021.861428079 672029.168164225 93314.8672883753 700162.344771704 225501.155502694 112928.950453556 1904021.99277836 11711071.7927272 507050.635006828 584463.880609796 4371864.16207653 2346017.75808067 190871472.352814 6943800.33128494 752144.080942573 104496.029479091 151268.386433917 732547.303427989 46411.238985187 99769.8370011166 85383.8079864119 2432865.45207562 33742.3879554692 32130520.3912716 406313.76326123 1279524.0344208 635256.679687322 55355795.0847213 6040550.33118436 1281717.97028531 235408.917370418 687178.284350906 293361.429494415 18822059.6938834 251167.774654372 15810813.4501523 43325.1468710441 1579624.18533472 12723639.1718413 49747.8041228634 132131.624787816 351740.412541555 928533.48729402 18612.2660593575 89233.3083720041 706013.63777662 12252274.5364418 8476222.08930386 64961.4777280155 103528.375171996 201548.646113665 575552.884111883 1009434.13627759 597447.929513582 3105056.22085957 976477.781884932 469457.874228353 22962.1545852533 4746136.24003677 73960.4175520273 240537.341751784 704240.729082267 158243.634136728 333589.832455627 157921.836197013 1005166.97509011 323922.648002014 10714583.5602912 3768765.86352035 1442019.63453249 443328.936401396 6106021.40480165 177975.999539493 11196525.972035 625328.312809426 443677.323448254 2193290.16040304 534663.884635537 181390.54127271 50137.0675933401 845211.037905123 7620896.74648852 20216.7639282066 60432.7329863589 476450.541255207 2797378.73376289 2767283.91708911 140302.013859978 23829799.234559 1559442.52397802 159117416.793444 241636.23259973 937302.145246527 520945.653223278 275146.782466926 40544.235086722 4148579.43970073 97486.9208667038 164443.854994334 221480.787686943 1977377.9139714 224692.808446301 1286466.01384832 512291.442394607 366463.466814217 226208.030212206 336279.830141342 304927.717052496 273227.545158626 123111.99615553 79584.5162287934 126929.069529116 3380783.0865406 75366116.0055795 14197428.5171494 748603.842091047 102903.412752503 50856.5279264592 379824.451200794 59364.4879636598 380768.703886271 649444.831936768 1436511.9788102 30452.2209443197 400315.601502185 475633.291261145 376904.56436793 1347517.59748949 313180.639965119 279877.124145521 136217.494292502 534480.726483347 274557.607422378 112040.793282691 44183.8398343819 675011.809801576 91700.0840682597 241613.851069268 104171.24400331 100370.748910995 239898.744232248 4553200.30600612 200810.03855976 379375.516382329 53135.8731573179 83877.4066423819 1182743.80960836 67240.4270471499 916634.105671495 66171.840828263 1739872.56914696 19393272.422516 103859.947983179 55204.0233194981 2090182.62101482 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717153.348912889 1004911.55505811 152739.523887268 32547.1285883596 32364.3820380837 378187.022615471 2822699.99759349 412526.782356598 164117.14382635 151475.868438157 22355.394099169 162139.451814641 1274172.26222152 213542.022736542 1039684.18056762 224059.120983437 390197.420071386 6446979.44757867 1821543.2671682 116615.433523564 461336.290361989 226841.404377312 2313784.34863521 77819.0589368957 128077.152216948 526344.103752229 729995.760348558 204105.86720904 904285.338382647 13901.6387172006 1333143.00364644 105427.601767016 166788.10170103 378425.0273745 92266.6638853474 80787.6483250491
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/single_mode_output.tsv Tue May 21 07:44:25 2024 +0000 @@ -0,0 +1,4 @@ +Unnamed: 0 Uridine_4TMS isomer 1 C002 C003 Asparagine_3TMS C005 C006 C007 C008 C009 C010 C011 Myo-inositol_6TMS C013 C014 C015 Acetylglutamine_3TMS C017 C018 C019 C020 C021 C022 C023 C024 Glutamic acid_3TMS spectra 2 C026 C027 C028 C029 C030 C031 Citric acid_4TMS C033 C034 Maleamic acid_3TMS C036 C037 C038 C039 C040 C041 Tyrosine_3TMS Xanthine_3TMS Guanine_3TMS Fructose_5TMS isomer 2 C046 C047 Glycine_3TMS C049 C050 C051 C052 Leucine_2TMS C054 C055 C056 C057 C058 Asparagine_2TMS C060 C061 C062 C063 C064 C065 C066 C067 Tryptophan_3TMS C069 C070 C071 C072 C073 C074 C075 C076 C077 C078 C079 C080 C081 C082 C083 C084 C085 C086 C087 C088 C089 C090 C091 C092 C093 C094 C095 C096 C097 C098 Lysine_3TMS C100 C101 C102 C103 C104 C105 C106 C107 C108 C109 C110 Proline_2TMS C112 C113 C114 C115 C116 C117 C118 C119 C120 C121 C122 C123 C124 C125 C126 C127 C128 Glutamic acid_2TMS C130 C131 C132 C133 C134 C135 C136 C137 C138 C139 C140 C141 C142 C143 C144 C145 C146 C147 C148 C149 C150 C151 C152 C153 C154 C155 C156 C157 C158 C159 Orotic acid_3TMS C161 Myo-inositol_6TMS C163 C164 C165 C166 C167 C168 C169 C170 C171 C172 C173 C174 C175 C176 Arginine_3TMS C178 C179 C180 C181 C182 C183 C184 C185 C186 C187 C188 C189 C190 C191 C192 C193 C194 C195 C196 C197 C198 C199 C200 C201 C202 C203 C204 C205 Sarcosine_2TMS C207 C208 C209 C210 C211 C212 C213 C214 C215 C216 C217 C218 C219 C220 C221 C222 C223 C224 C225 C226 C227 C228 C229 C230 C231 C232 C233 C234 C235 C236 C237 C238 C239 C240 C241 C242 C243 C244 C245 C246 C247 C248 C249 C250 C251 C252 C253 trans-Aconitic acid_3TMS C255 C256 Histidine_4TMS C258 C259 C260 C261 C262 C263 C264 C265 C266 C267 C268 C269 C270 C271 C272 C273 C274 C275 C276 C277 C278 C279 C280 C281 C282 C283 C284 C285 C286 C287 C288 C289 C290 C291 C292 C293 C294 C295 C296 C297 C298 C299 C300 C301 C302 C303 C304 C305 C306 C307 C308 C309 C310 C311 C312 C313 C314 C315 C316 C317 C318 C319 Uric acid_4TMS C321 C322 C323 C324 C325 C326 C327 C328 C329 C330 C331 C332 C333 C334 C335 C336 C337 C338 C339 C340 C341 C342 C343 C344 C345 C346 C347 C348 C349 C350 C351 C352 C353 Serine_3TMS C355 C356 C357 C358 C359 C360 C361 C362 C363 C364 C365 C366 C367 C368 C369 C370 C371 C372 6-Aminocaproic acid_3TMS C374 C375 C376 C377 C378 C379 C380 C381 C382 C383 C384 C385 C386 C387 C388 C389 C390 C391 C392 Guanine_4TMS C394 C395 C396 C397 C398 C399 C400 C401 C402 C403 C404 C405 C406 C407 C408 C409 C410 C411 C412 C413 C414 C415 C416 C417 C418 C419 C420 C421 C422 C423 C424 C425 C426 C427 C428 C429 C430 C431 C432 C433 C434 C435 C436 C437 C438 C439 C440 C441 C442 C443 C444 C445 C446 C447 C448 C449 C450 C451 C452 C453 C454 C455 C456 C457 C458 C459 C460 C461 C462 C463 C464 C465 C466 C467 C468 C469 C470 C471 C472 C473 C474 C475 C476 C477 C478 C479 C480 C481 Aspartic acid_3TMS isomer C483 C484 C485 C486 C487 C488 C489 C490 C491 C492 C493 C494 C495 C496 C497 C498 C499 C500 C501 C502 C503 C504 C505 C506 C507 C508 C509 C510 C511 C512 C513 C514 C515 C516 C517 C518 C519 C520 C521 C522 C523 C524 C525 C526 C527 C528 C529 C530 C531 C532 C533 C534 C535 C536 C537 C538 C539 C540 C541 C542 C543 C544 C545 C546 C547 C548 C549 C550 C551 C552 C553 C554 C555 C556 C557 C558 C559 C560 C561 C562 C563 C564 C565 C566 C567 C568 C569 C570 C571 +29_qc_no_dil_milliq 14440614.0614047 100829162.950447 254866018.799615 15274982.3781313 5224836.34188986 5885730.25849524 951826.455585983 889479.276736861 1795609403.16384 2421762.67187108 5163569.54055468 238798215.712716 354389395.659526 796483.933541114 823048.878299925 23198329.5204869 292115.435176988 712515.418590804 19610929.4892356 1232587.75701825 3596492.79850348 1629639.47376732 24462390.9163424 485438.836480317 868952050.264982 81375.1586185473 99599261.6309831 959158.254779201 536304.782185507 4001011.6875862 7739617.79445237 1615156866.41566 3949722.78923788 2175945.26658084 40746732.6515362 618603.541165935 9321812.02744594 1806309.45076003 946808.521216693 1380448.93849442 4008025.45350866 774432771.67135 6185010.41280613 3977041.90828131 807444239.555129 117208.261097281 4416621.75166316 11070753.8362958 26211662.9499907 69183910.0525939 60290768.6032428 1576348.77745384 312940893.106132 13076274.7260471 2432709.41029711 225559.955293657 143921764.917415 533636.785572528 10234910.8210168 894305.68092461 352072.205688018 3044048.84816934 7269277.56727447 3913511.40312328 307875.120452888 371077.171892254 287190.462230271 41540567.0240222 13559092.3758615 406492.348681204 24808557.5598735 619094.13446721 266980.599376974 2656865.33861078 2652633.12587089 114017.206962404 164284.989815954 1192746.89473896 7651824.79355225 213604941.362295 272303.678962713 945765.455015841 2146660.56421118 237213.177102788 1153528.12133704 1010797.7193887 124737.084480499 4189366.61204168 102986538.666234 736946.506777988 304127.295255388 691072.335977527 1103791.97882047 2479973.07098931 8905173.39736247 25041688.9624318 124766.399660988 347141.68677344 642044.289099355 354238.743461047 194317.090990598 385095.809290498 127341.597037749 157303.861084333 170750.262677683 917565.301446466 1769184.65218783 166453.198335507 32742511.7781421 2038450.00024453 5717892.0841901 1404987.61805938 845139.568618001 1484031.62670076 302411.519888222 68405.8335896558 146616.523047761 4481021.17562366 46129245.2993171 353938.191426674 183453.986464873 253913.946132376 2372475.39288604 3403842.6347695 2206305.34331278 271644.825859711 1343015.60252275 1156634.49928246 1292699.04759743 343130.988071445 1785108.12921876 528828.965191606 842233.399693472 5777215.15464433 233629.063207309 171218.372521778 2107892.64296657 88120.628416599 596649.828309023 3672583.70822133 6617213.15405245 181008.115138583 2586463.86881571 185920.318958129 1241015.34911364 92227.7955224766 129802.79504124 192555.107703765 145542.62302623 1160899.31563216 112917.924001808 124007.85633309 633684.584728627 2280834.12973503 445536.016790919 124683.380919967 1570606.04419484 154953.831906835 256155.469878756 894605.176902167 1626458.96750198 285181808.698182 610253.234772327 391783.348061144 398324.505959962 328390.586957152 1838374.29468941 1283743.91041274 209311.885783803 940521.92798673 451883.662719365 7734925.17999533 384861.106784837 1484189.97511908 57114.8878988477 39988988.1680606 6479747.39105557 894880.987138881 1812684.67197649 527085.019807927 260908.733449833 888505.281443954 8846164.30225623 459345.290532086 867204.157305589 410857.517229929 80160100.051693 523488.39469134 191980.824793793 1330690.93776021 149920.873203244 158072.175838165 290862.088795427 193353.481374758 349518.966398228 118883.741228244 314215.271673589 79056291.3427869 807794.876841978 511667.260958486 147711.77271555 6414204.41935647 428033.644825501 54406.1929007828 7038434.23383763 5063741.97165563 1718815.64454285 160341727.997531 91202.3205404207 42856493.4461666 4121822.89471918 1352655.82108955 100262.368423675 473760.589138636 2855738.67974274 74540.1352325425 283974.144147633 1079790.73322084 470186.03418124 371174.561962158 1534860.936247 274393.399828041 63825735.564163 73772.2577391385 116119.044871487 412139.136220895 244747.931389062 286713.59221739 971284.016318051 756099.137390138 78333.202817093 165271.223381125 2431597.42755326 85935.807989955 179193.179701008 172855.809883764 246051.049985504 126545.58012136 426177.723240474 2769018.85026361 404802.734176745 1923748.89716192 3016143.88485513 2363523.00565838 23284927.1740917 167790.389630975 171671.864404718 793909.181841846 118189.781563813 1713640.80852142 111893418.150679 305902.081876272 1523388.37838287 22017276.8530788 4130667.64546185 26372022.3156075 1610541.08448918 190673.536242371 1764055.84738082 50304425.5172517 107590.092617611 581867.629417969 58538157.0973169 91699.1040984271 3743222.54773702 602264.045466521 1573453.05821107 41175.5168575104 87483.2620456882 100650.630521181 288897.447441482 561627.500087703 46354.5731825084 7707887.24466242 339148.793690526 336184.961195537 453582.157952033 943536.01891475 1075473.18291486 153513426.619558 355045.125851123 657067.432521505 185275.512026864 1130209.36515672 632077.098383767 56679.1852977019 440021.861428079 672029.168164225 93314.8672883753 700162.344771704 225501.155502694 112928.950453556 1904021.99277836 11711071.7927272 507050.635006828 584463.880609796 4371864.16207653 2346017.75808067 190871472.352814 6943800.33128494 752144.080942573 104496.029479091 151268.386433917 732547.303427989 46411.238985187 99769.8370011166 85383.8079864119 2432865.45207562 33742.3879554692 32130520.3912716 406313.76326123 1279524.0344208 635256.679687322 55355795.0847213 6040550.33118436 1281717.97028531 235408.917370418 687178.284350906 293361.429494415 18822059.6938834 251167.774654372 15810813.4501523 43325.1468710441 1579624.18533472 12723639.1718413 49747.8041228634 132131.624787816 351740.412541555 928533.48729402 18612.2660593575 89233.3083720041 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