| Next changeset 1:f680068b7863 (2022-07-22) |
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Commit message:
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122" |
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added:
macros.xml matchms_similarity.xml matchms_similarity_wrapper.py test-data/filtering/clean_metadata.msp test-data/filtering/default_filters.msp test-data/filtering/input.msp test-data/filtering/mz_range.msp test-data/filtering/normalise_intensities.msp test-data/filtering/relative_intensity.msp test-data/formatter/test2_threshold_formatting.tsv test-data/formatter/test2_topk_formatting.tsv test-data/matches_test2_out.tsv test-data/scores_test2_out.tsv test-data/similarity/fill.mgf test-data/similarity/fill.msp test-data/similarity/fill2.msp test-data/similarity/matches_test1_out.tsv test-data/similarity/matches_test3_out.tsv test-data/similarity/matches_test4_out.tsv test-data/similarity/matches_test5_out.tsv test-data/similarity/matches_test6_out.tsv test-data/similarity/recetox_gc-ei_ms_20201028.msp test-data/similarity/scores_test1_out.tsv test-data/similarity/scores_test3_out.tsv test-data/similarity/scores_test4_out.tsv test-data/similarity/scores_test5_out.tsv test-data/similarity/scores_test6_out.tsv |
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| diff -r 000000000000 -r 30e680e555d4 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Mar 22 16:07:32 2022 +0000 |
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| @@ -0,0 +1,70 @@ +<macros> + <token name="@TOOL_VERSION@">0.14.0</token> + + <xml name="creator"> + <creator> + <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_matchms@"> + <![CDATA[ + Documentation + For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst + and https://matchms.readthedocs.io/en/latest/. + + Upstream Tools + +-----------+---------------+--------+-----------+ + | Name | Output File | Format | Parameter | + +===========+===============+========+===========+ + | RAMClustR | Mass spectra | msp | references| + +-----------+---------------+--------+-----------+ + | RAMClustR | Mass spectra | msp | queries | + +-----------+---------------+--------+-----------+ + + Downstream Tools + The outputs are two tsv datasets. One containing the similarity scores and the other number of matched peaks. + ]]> + </token> + + <token name="@HELP_formatter@"> + <![CDATA[ + Usage + This tool creates user friendly tables from the data matrices produces by matchms. + The tool can be operated on two modes based on (i) thresholds or (ii) top k matches. + + Input Table Format + The tool expects two data matrices with the format as depicted below. + The tool assumes the reference compound labels as row labels and the query labels as column labels (as naturally outputted by matchms). + + +----------+------+------+-----+ + | | C001 | C002 | ... | + +==========+======+======+=====+ + | Perylene | 0.1 | 0.0 | ... | + +----------+------+------+-----+ + | Glycine | 0.5 | 0.34 | ... | + +----------+------+------+-----+ + | ... | ... | ... | ... | + +----------+------+------+-----+ + + Output Table Format + +----------+-----------+---------+--------+ + | query | reference | matches | scores | + +==========+===========+=========+========+ + | C001 | Glycine | 6 | 0.5 | + +----------+-----------+---------+--------+ + | C002 | Glycine | 3 | 0.34 | + +----------+-----------+---------+--------+ + | ... | ... | ... | ... | + +----------+-----------+---------+--------+ + ]]> + </token> +</macros> |
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| diff -r 000000000000 -r 30e680e555d4 matchms_similarity.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matchms_similarity.xml Tue Mar 22 16:07:32 2022 +0000 |
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| @@ -0,0 +1,151 @@ +<tool id="matchms" name="matchMS similarity" version="@TOOL_VERSION@+galaxy1" python_template_version="3.8"> + <description>calculate the similarity score and matched peaks</description> + + <macros> + <import>macros.xml</import> + </macros> + <expand macro="creator"/> + + <requirements> + <requirement type="package" version="1.1.4">pandas</requirement> + <requirement type="package" version="0.55.1">numba</requirement> + <requirement type="package" version="@TOOL_VERSION@">matchms</requirement> + </requirements> + + <environment_variables> + <environment_variable name="MPLCONFIGDIR">/tmp</environment_variable> + </environment_variables> + + <command detect_errors="exit_code"><![CDATA[ + sh ${matchms_python_cli} + ]]> </command> + + <configfiles> + <configfile name="matchms_python_cli"> + python3 ${__tool_directory__}/matchms_similarity_wrapper.py \ + #if $ri_filtering.is_true + -r $ri_filtering.tolerance \ + #end if + #if $symmetric.is_symmetric + -s \ + #else + --ref "$references" \ + --ref_format "$references.ext" \ + #end if + "$queries" \ + "$queries.ext" \ + "$similarity_metric" \ + "$algorithm.tolerance" \ + "$algorithm.mz_power" \ + "$algorithm.intensity_power" \ + "$similarity_scores" \ + "$similarity_matches" + </configfile> + </configfiles> + + <inputs> + <param label="Queries spectra" name="queries" type="data" format="msp,mgf" + help="Query mass spectra to match against references."/> + <conditional name="symmetric"> + <param name="is_symmetric" label="Symmetric" type="boolean" truevalue="TRUE" falsevalue="FALSE" + checked="false"/> + <when value="FALSE"> + <param label="Reference spectra" name="references" type="data" format="msp,mgf" + help="Reference mass spectra to match against as library."/> + </when> + </conditional> + <param label="Similarity metric" name="similarity_metric" type="select" display="radio" + help="Similarity metric to use for score computation."> + <option value="CosineGreedy" selected="true">CosineGreedy</option> + <option value="CosineHungarian">CosineHungarian</option> + <option value="ModifiedCosine">ModifiedCosine</option> + </param> + + <section name="algorithm" title="Algorithm Parameters" expanded="true"> + <param label="tolerance" name="tolerance" type="float" value="0.1" + help="Peaks will be considered a match when less than tolerance apart. Absolute m/z value, not in ppm."/> + <param label="mz_power" name="mz_power" type="float" value="0.0" + help="The power to raise mz to in the cosine function."/> + <param label="intensity_power" name="intensity_power" type="float" value="1.0" + help="The power to raise intensity to in the cosine function."/> + </section> + + <conditional name="ri_filtering"> + <param name="is_true" label="Apply RI filtering" type="boolean" truevalue="TRUE" falsevalue="FALSE" + checked="false"/> + <when value="TRUE"> + <param label="tolerance" name="tolerance" type="float" value="60" + help="Peaks will be considered a match when less than tolerance apart."/> + </when> + </conditional> + </inputs> + + <outputs> + <data label="$similarity_metric scores of ${on_string}" name="similarity_scores" format="tsv"/> + <data label="$similarity_metric matches of ${on_string}" name="similarity_matches" format="tsv"/> + </outputs> + + <tests> + <test> + <param name="references" value="similarity/fill.mgf" ftype="mgf"/> + <param name="queries" value="similarity/fill.msp" ftype="msp"/> + <param name="similarity_metric" value="CosineGreedy"/> + <output name="similarity_scores" file="similarity/scores_test1_out.tsv" ftype="tsv" + checksum="md5$1aff8d0777e2f4e565be2b1b393547ef"/> + <output name="similarity_matches" file="similarity/matches_test1_out.tsv" ftype="tsv" + checksum="md5$aab26ef4a0e80a53699832db72c06340"/> + </test> + <test> + <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/> + <param name="queries" value="similarity/fill.msp" ftype="msp"/> + <param name="similarity_metric" value="CosineGreedy"/> + <output name="similarity_scores" file="scores_test2_out.tsv" ftype="tsv" + checksum="md5$d2a5a01d9980636ce6a246d68834b84e"/> + <output name="similarity_matches" file="matches_test2_out.tsv" ftype="tsv" + checksum="md5$28dc16ce45105234437e53d59e240046"/> + </test> + <test> + <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/> + <param name="queries" value="similarity/fill.msp" ftype="msp"/> + <param name="similarity_metric" value="CosineHungarian"/> + <output name="similarity_scores" file="similarity/scores_test3_out.tsv" ftype="tsv" + checksum="md5$1341369778036e0a267ff723f8cfca9c"/> + <output name="similarity_matches" file="similarity/matches_test3_out.tsv" ftype="tsv" + checksum="md5$28dc16ce45105234437e53d59e240046"/> + </test> + <test> + <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/> + <param name="queries" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/> + <param name="similarity_metric" value="ModifiedCosine"/> + <output name="similarity_scores" file="similarity/scores_test4_out.tsv" ftype="tsv"/> + <output name="similarity_matches" file="similarity/matches_test4_out.tsv" ftype="tsv"/> + </test> + <test> + <param name="queries" value="similarity/fill.msp" ftype="msp"/> + <param name="similarity_metric" value="CosineHungarian"/> + <param name="is_symmetric" value="TRUE"/> + <output name="similarity_scores" file="similarity/scores_test5_out.tsv" ftype="tsv"/> + <output name="similarity_matches" file="similarity/matches_test5_out.tsv" ftype="tsv"/> + </test> + <test> + <param name="references" value="similarity/recetox_gc-ei_ms_20201028.msp" ftype="msp"/> + <param name="queries" value="similarity/fill2.msp" ftype="msp"/> + <param name="ri_filtering.is_true" value="TRUE" /> + <param name="ri_filtering.tolerance" value="60.0" /> + <param name="similarity_metric" value="CosineGreedy"/> + <output name="similarity_scores" file="similarity/scores_test6_out.tsv" ftype="tsv"/> + <output name="similarity_matches" file="similarity/matches_test6_out.tsv" ftype="tsv"/> + </test> + </tests> + + <help> + <![CDATA[ + @HELP_matchms@ + ]]> + </help> + + <citations> + <citation type="doi">10.5281/zenodo.4589154</citation> + <citation type="doi">10.21105/joss.02411</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 30e680e555d4 matchms_similarity_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matchms_similarity_wrapper.py Tue Mar 22 16:07:32 2022 +0000 |
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| @@ -0,0 +1,103 @@ +import argparse +import sys + +import numpy as np +from matchms import calculate_scores +from matchms.importing import load_from_mgf, load_from_msp +from matchms.similarity import CosineGreedy, CosineHungarian, MetadataMatch, ModifiedCosine +from pandas import DataFrame + + +def convert_precursor_mz(spectrum): + """ + Check the presence of precursor m/z since it is needed for ModifiedCosine similarity metric. Convert to float if + needed, raise error if missing. + """ + + if "precursor_mz" in spectrum.metadata: + metadata = spectrum.metadata + metadata["precursor_mz"] = float(metadata["precursor_mz"]) + spectrum.metadata = metadata + return spectrum + else: + raise ValueError("Precursor_mz missing. Apply 'add_precursor_mz' filter first.") + + +def main(argv): + parser = argparse.ArgumentParser(description="Compute MSP similarity scores") + parser.add_argument("-r", dest="ri_tolerance", type=float, help="Use RI filtering with given tolerance.") + parser.add_argument("-s", dest="symmetric", action='store_true', help="Computation is symmetric.") + parser.add_argument("--ref", dest="references_filename", type=str, help="Path to reference spectra library.") + parser.add_argument("--ref_format", dest="references_format", type=str, help="Reference spectra library file format.") + parser.add_argument("queries_filename", type=str, help="Path to query spectra.") + parser.add_argument("queries_format", type=str, help="Query spectra file format.") + parser.add_argument("similarity_metric", type=str, help='Metric to use for matching.') + parser.add_argument("tolerance", type=float, help="Tolerance to use for peak matching.") + parser.add_argument("mz_power", type=float, help="The power to raise mz to in the cosine function.") + parser.add_argument("intensity_power", type=float, help="The power to raise intensity to in the cosine function.") + parser.add_argument("output_filename_scores", type=str, help="Path where to store the output .tsv scores.") + parser.add_argument("output_filename_matches", type=str, help="Path where to store the output .tsv matches.") + args = parser.parse_args() + + if args.queries_format == 'msp': + queries_spectra = list(load_from_msp(args.queries_filename)) + elif args.queries_format == 'mgf': + queries_spectra = list(load_from_mgf(args.queries_filename)) + else: + raise ValueError(f'File format {args.queries_format} not supported for query spectra.') + + if args.symmetric: + reference_spectra = [] + else: + if args.references_format == 'msp': + reference_spectra = list(load_from_msp(args.references_filename)) + elif args.references_format == 'mgf': + reference_spectra = list(load_from_mgf(args.references_filename)) + else: + raise ValueError(f'File format {args.references_format} not supported for reference spectra library.') + + if args.similarity_metric == 'CosineGreedy': + similarity_metric = CosineGreedy(args.tolerance, args.mz_power, args.intensity_power) + elif args.similarity_metric == 'CosineHungarian': + similarity_metric = CosineHungarian(args.tolerance, args.mz_power, args.intensity_power) + elif args.similarity_metric == 'ModifiedCosine': + similarity_metric = ModifiedCosine(args.tolerance, args.mz_power, args.intensity_power) + reference_spectra = list(map(convert_precursor_mz, reference_spectra)) + queries_spectra = list(map(convert_precursor_mz, queries_spectra)) + else: + return -1 + + print("Calculating scores...") + scores = calculate_scores( + references=queries_spectra if args.symmetric else reference_spectra, + queries=queries_spectra, + similarity_function=similarity_metric, + is_symmetric=args.symmetric + ) + + if args.ri_tolerance is not None: + print("RI filtering with tolerance ", args.ri_tolerance) + ri_matches = calculate_scores(reference_spectra, queries_spectra, MetadataMatch("retention_index", "difference", args.ri_tolerance)).scores + scores.scores["score"] = np.where(ri_matches, scores.scores["score"], 0.0) + + write_outputs(args, scores) + return 0 + + +def write_outputs(args, scores): + print("Storing outputs...") + query_names = [spectra.metadata['compound_name'] for spectra in scores.queries] + reference_names = [spectra.metadata['compound_name'] for spectra in scores.references] + + # Write scores to dataframe + dataframe_scores = DataFrame(data=[entry["score"] for entry in scores.scores], index=reference_names, columns=query_names) + dataframe_scores.to_csv(args.output_filename_scores, sep='\t') + + # Write number of matches to dataframe + dataframe_matches = DataFrame(data=[entry["matches"] for entry in scores.scores], index=reference_names, columns=query_names) + dataframe_matches.to_csv(args.output_filename_matches, sep='\t') + + +if __name__ == "__main__": + main(argv=sys.argv[1:]) + pass |
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| diff -r 000000000000 -r 30e680e555d4 test-data/filtering/clean_metadata.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtering/clean_metadata.msp Tue Mar 22 16:07:32 2022 +0000 |
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| @@ -0,0 +1,197 @@ +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C001 +RETENTION_TIME: 38.74 +RETENTION_INDEX: None +NUM PEAKS: 57 +138.9121 10186226.0 +148.9337 1008656.0 +175.0641 26780143.0 +186.1095 2675456.0 +196.8658 21390430.0 +198.8647 21688594.0 +200.8848 7742528.0 +206.9034 26130980.0 +216.9205 32607700.0 +234.0134 2550129.0 +254.8252 23747536.0 +256.8215 31377637.0 +258.8237 15532799.0 +266.8652 9805546.0 +268.8537 3090354.0 +306.9914 3169316.0 +312.7841 10051801.0 +316.7777 10734168.0 +322.8157 6317648.0 +324.9549 8619910.0 +334.849 4178412.0 +342.8093 3285552.0 +349.9455 2050695.0 +350.9875 6150799.0 +351.941 1965882.0 +366.8281 3253770.0 +370.7418 9765463.0 +372.7383 19374863.0 +382.8218 12815572.0 +384.8177 8311500.0 +392.7685 10913351.0 +413.2664 3965867.0 +426.7772 5431633.0 +428.7834 8554675.0 +434.7287 9943329.0 +436.8161 3705247.0 +440.7322 10603010.0 +442.7401 8271752.0 +450.7016 8762673.0 +460.7076 4528973.0 +462.7862 2123666.0 +484.7242 4273989.0 +486.7743 4886062.0 +488.6825 12267966.0 +492.744 7662344.0 +494.8953 7188793.0 +498.8794 6811405.0 +500.8484 6520691.0 +502.7832 3567833.0 +510.763 4989757.0 +518.7415 4243468.0 +546.6093 7177067.0 +550.6949 6104789.0 +566.5977 5171811.0 +612.6927 2005587.0 +676.6436 1982714.0 +800.4451 2792137.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C002 +RETENTION_TIME: 520.25 +RETENTION_INDEX: 1234.5 +NUM PEAKS: 35 +131.1733 1971789.0 +267.2688 6103973.0 +279.0196 1946255.0 +289.6491 46498377.0 +301.1565 15185412.0 +309.1649 18045974.0 +310.1623 295359836.0 +311.1658 13124727.0 +312.0296 38757284.0 +330.6757 12666597.0 +525.375 1073323842.0 +526.3783 181668883.0 +527.3812 23642795.0 +551.3321 111616808.0 +552.3348 28340614.0 +553.3314 2609936.0 +562.3269 7538206.0 +578.2905 7578406.0 +619.3008 4742103.0 +624.296 11790213.0 +813.5403 25060147.0 +814.5336 5865975.0 +955.1171 2322927.0 +1047.7378 150394804.0 +1048.7399 90978863.0 +1049.7432 29946438.0 +1050.7453 6807767.0 +1069.7158 5074652.0 +1074.1979 3402288.0 +1075.1968 33352763.0 +1076.2004 10417953.0 +1101.6535 2023916.0 +1206.3127 3738816.0 +1216.8041 4439324.0 +1217.807 3565334.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C003 +RETENTION_TIME: 483.67 +RETENTION_INDEX: None +NUM PEAKS: 26 +265.2529 11366224.0 +266.2564 1420444.0 +279.6362 29849749.0 +280.6546 8848921.0 +288.6414 202172046.0 +378.2093 15309961.0 +379.1966 2902366.0 +522.3565 4089569222.0 +523.354 1201714423.0 +549.3267 63300808.0 +576.2749 7386007.0 +577.3074 2354251.0 +617.2778 2323470.0 +625.4543 4040374.0 +796.9808 13576738.0 +797.9841 6368973.0 +809.9883 12596682.0 +810.9916 6601055.0 +1043.7028 144351468.0 +1044.7068 83271854.0 +1045.706 27998321.0 +1046.7131 6505178.0 +1058.1594 20718345.0 +1059.1626 6608764.0 +1071.1639 15461047.0 +1072.1671 5096642.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C004 +RETENTION_TIME: 473.48 +RETENTION_INDEX: None +NUM PEAKS: 24 +124.1405 6517662.0 +170.2437 1237313.0 +275.6336 28001849.0 +296.147 190395687.0 +482.3247 145772322.0 +483.3283 36245876.0 +496.34 12577588056.0 +497.3442 3337125302.0 +498.3462 532285213.0 +499.3493 68176083.0 +770.964 49250157.0 +771.9675 22666873.0 +783.9721 9839299.0 +784.9749 3622908.0 +949.6233 8009033.0 +950.6274 3674694.0 +991.6726 1420557258.0 +992.6749 763118028.0 +993.6787 239161906.0 +994.6801 53549573.0 +1017.6897 168186952.0 +1018.6656 120599518.0 +1019.6555 57647644.0 +1020.6591 12469103.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C005 +RETENTION_TIME: 41.72 +RETENTION_INDEX: None +NUM PEAKS: 20 +218.1386 14009249.0 +337.0623 88672453.0 +338.0654 8770055.0 +353.0361 37061354.0 +359.0443 48435582.0 +360.0459 5025128.0 +375.018 29159485.0 +376.0216 2740193.0 +381.0261 13522755.0 +396.9999 10317665.0 +417.0027 13822994.0 +418.9966 4386311.0 +432.9764 9779399.0 +438.9851 11307111.0 +440.9796 3364168.0 +454.9592 9820452.0 +456.9603 3774845.0 +470.9263 3632486.0 +512.8989 4072570.0 +572.871 3485486.0 + |
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| diff -r 000000000000 -r 30e680e555d4 test-data/filtering/default_filters.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtering/default_filters.msp Tue Mar 22 16:07:32 2022 +0000 |
| b |
| @@ -0,0 +1,199 @@ +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C001 +RETENTION_TIME: 38.74 +RETENTION_INDEX: None +CHARGE: -1 +NUM PEAKS: 57 +138.9121 10186226.0 +148.9337 1008656.0 +175.0641 26780143.0 +186.1095 2675456.0 +196.8658 21390430.0 +198.8647 21688594.0 +200.8848 7742528.0 +206.9034 26130980.0 +216.9205 32607700.0 +234.0134 2550129.0 +254.8252 23747536.0 +256.8215 31377637.0 +258.8237 15532799.0 +266.8652 9805546.0 +268.8537 3090354.0 +306.9914 3169316.0 +312.7841 10051801.0 +316.7777 10734168.0 +322.8157 6317648.0 +324.9549 8619910.0 +334.849 4178412.0 +342.8093 3285552.0 +349.9455 2050695.0 +350.9875 6150799.0 +351.941 1965882.0 +366.8281 3253770.0 +370.7418 9765463.0 +372.7383 19374863.0 +382.8218 12815572.0 +384.8177 8311500.0 +392.7685 10913351.0 +413.2664 3965867.0 +426.7772 5431633.0 +428.7834 8554675.0 +434.7287 9943329.0 +436.8161 3705247.0 +440.7322 10603010.0 +442.7401 8271752.0 +450.7016 8762673.0 +460.7076 4528973.0 +462.7862 2123666.0 +484.7242 4273989.0 +486.7743 4886062.0 +488.6825 12267966.0 +492.744 7662344.0 +494.8953 7188793.0 +498.8794 6811405.0 +500.8484 6520691.0 +502.7832 3567833.0 +510.763 4989757.0 +518.7415 4243468.0 +546.6093 7177067.0 +550.6949 6104789.0 +566.5977 5171811.0 +612.6927 2005587.0 +676.6436 1982714.0 +800.4451 2792137.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C002 +RETENTION_TIME: 520.25 +RETENTION_INDEX: 1234.5 +CHARGE: -1 +NUM PEAKS: 35 +131.1733 1971789.0 +267.2688 6103973.0 +279.0196 1946255.0 +289.6491 46498377.0 +301.1565 15185412.0 +309.1649 18045974.0 +310.1623 295359836.0 +311.1658 13124727.0 +312.0296 38757284.0 +330.6757 12666597.0 +525.375 1073323842.0 +526.3783 181668883.0 +527.3812 23642795.0 +551.3321 111616808.0 +552.3348 28340614.0 +553.3314 2609936.0 +562.3269 7538206.0 +578.2905 7578406.0 +619.3008 4742103.0 +624.296 11790213.0 +813.5403 25060147.0 +814.5336 5865975.0 +955.1171 2322927.0 +1047.7378 150394804.0 +1048.7399 90978863.0 +1049.7432 29946438.0 +1050.7453 6807767.0 +1069.7158 5074652.0 +1074.1979 3402288.0 +1075.1968 33352763.0 +1076.2004 10417953.0 +1101.6535 2023916.0 +1206.3127 3738816.0 +1216.8041 4439324.0 +1217.807 3565334.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C003 +RETENTION_TIME: 483.67 +CHARGE: -1 +NUM PEAKS: 26 +265.2529 11366224.0 +266.2564 1420444.0 +279.6362 29849749.0 +280.6546 8848921.0 +288.6414 202172046.0 +378.2093 15309961.0 +379.1966 2902366.0 +522.3565 4089569222.0 +523.354 1201714423.0 +549.3267 63300808.0 +576.2749 7386007.0 +577.3074 2354251.0 +617.2778 2323470.0 +625.4543 4040374.0 +796.9808 13576738.0 +797.9841 6368973.0 +809.9883 12596682.0 +810.9916 6601055.0 +1043.7028 144351468.0 +1044.7068 83271854.0 +1045.706 27998321.0 +1046.7131 6505178.0 +1058.1594 20718345.0 +1059.1626 6608764.0 +1071.1639 15461047.0 +1072.1671 5096642.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C004 +RETENTION_TIME: 473.48 +CHARGE: -1 +NUM PEAKS: 24 +124.1405 6517662.0 +170.2437 1237313.0 +275.6336 28001849.0 +296.147 190395687.0 +482.3247 145772322.0 +483.3283 36245876.0 +496.34 12577588056.0 +497.3442 3337125302.0 +498.3462 532285213.0 +499.3493 68176083.0 +770.964 49250157.0 +771.9675 22666873.0 +783.9721 9839299.0 +784.9749 3622908.0 +949.6233 8009033.0 +950.6274 3674694.0 +991.6726 1420557258.0 +992.6749 763118028.0 +993.6787 239161906.0 +994.6801 53549573.0 +1017.6897 168186952.0 +1018.6656 120599518.0 +1019.6555 57647644.0 +1020.6591 12469103.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C005 +RETENTION_TIME: 41.72 +CHARGE: -1 +NUM PEAKS: 20 +218.1386 14009249.0 +337.0623 88672453.0 +338.0654 8770055.0 +353.0361 37061354.0 +359.0443 48435582.0 +360.0459 5025128.0 +375.018 29159485.0 +376.0216 2740193.0 +381.0261 13522755.0 +396.9999 10317665.0 +417.0027 13822994.0 +418.9966 4386311.0 +432.9764 9779399.0 +438.9851 11307111.0 +440.9796 3364168.0 +454.9592 9820452.0 +456.9603 3774845.0 +470.9263 3632486.0 +512.8989 4072570.0 +572.871 3485486.0 + |
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/filtering/input.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtering/input.msp Tue Mar 22 16:07:32 2022 +0000 |
| b |
| @@ -0,0 +1,193 @@ +NAME:C001 +IONMODE:Negative +RETENTIONTIME:38.74 +RETENTIONINDEX: -1 +SPECTRUMTYPE:Centroid +Num Peaks:57 +216.9205 32607700 +256.8215 31377637 +175.0641 26780143 +206.9034 26130980 +254.8252 23747536 +198.8647 21688594 +196.8658 21390430 +372.7383 19374863 +258.8237 15532799 +382.8218 12815572 +488.6825 12267966 +392.7685 10913351 +316.7777 10734168 +440.7322 10603010 +138.9121 10186226 +312.7841 10051801 +434.7287 9943329 +266.8652 9805546 +370.7418 9765463 +450.7016 8762673 +324.9549 8619910 +428.7834 8554675 +384.8177 8311500 +442.7401 8271752 +200.8848 7742528 +492.744 7662344 +494.8953 7188793 +546.6093 7177067 +498.8794 6811405 +500.8484 6520691 +322.8157 6317648 +350.9875 6150799 +550.6949 6104789 +426.7772 5431633 +566.5977 5171811 +510.763 4989757 +486.7743 4886062 +460.7076 4528973 +484.7242 4273989 +518.7415 4243468 +334.849 4178412 +413.2664 3965867 +436.8161 3705247 +502.7832 3567833 +342.8093 3285552 +366.8281 3253770 +306.9914 3169316 +268.8537 3090354 +800.4451 2792137 +186.1095 2675456 +234.0134 2550129 +462.7862 2123666 +349.9455 2050695 +612.6927 2005587 +676.6436 1982714 +351.941 1965882 +148.9337 1008656 + +NAME:C002 +IONMODE:Negative +RETENTIONTIME:520.25 +RETENTIONINDEX: 1234.5 +SPECTRUMTYPE:Centroid +Num Peaks:35 +525.375 1073323842 +310.1623 295359836 +526.3783 181668883 +1047.7378 150394804 +551.3321 111616808 +1048.7399 90978863 +289.6491 46498377 +312.0296 38757284 +1075.1968 33352763 +1049.7432 29946438 +552.3348 28340614 +813.5403 25060147 +527.3812 23642795 +309.1649 18045974 +301.1565 15185412 +311.1658 13124727 +330.6757 12666597 +624.296 11790213 +1076.2004 10417953 +578.2905 7578406 +562.3269 7538206 +1050.7453 6807767 +267.2688 6103973 +814.5336 5865975 +1069.7158 5074652 +619.3008 4742103 +1216.8041 4439324 +1206.3127 3738816 +1217.807 3565334 +1074.1979 3402288 +553.3314 2609936 +955.1171 2322927 +1101.6535 2023916 +131.1733 1971789 +279.0196 1946255 + +NAME:C003 +IONMODE:Negative +RETENTIONTIME:483.67 +SPECTRUMTYPE:Centroid +Num Peaks:26 +522.3565 4089569222 +523.354 1201714423 +288.6414 202172046 +1043.7028 144351468 +1044.7068 83271854 +549.3267 63300808 +279.6362 29849749 +1045.706 27998321 +1058.1594 20718345 +1071.1639 15461047 +378.2093 15309961 +796.9808 13576738 +809.9883 12596682 +265.2529 11366224 +280.6546 8848921 +576.2749 7386007 +1059.1626 6608764 +810.9916 6601055 +1046.7131 6505178 +797.9841 6368973 +1072.1671 5096642 +625.4543 4040374 +379.1966 2902366 +577.3074 2354251 +617.2778 2323470 +266.2564 1420444 + +NAME:C004 +IONMODE:Negative +RETENTIONTIME:473.48 +SPECTRUMTYPE:Centroid +Num Peaks:24 +496.34 12577588056 +497.3442 3337125302 +991.6726 1420557258 +992.6749 763118028 +498.3462 532285213 +993.6787 239161906 +296.147 190395687 +1017.6897 168186952 +482.3247 145772322 +1018.6656 120599518 +499.3493 68176083 +1019.6555 57647644 +994.6801 53549573 +770.964 49250157 +483.3283 36245876 +275.6336 28001849 +771.9675 22666873 +1020.6591 12469103 +783.9721 9839299 +949.6233 8009033 +124.1405 6517662 +950.6274 3674694 +784.9749 3622908 +170.2437 1237313 + +NAME:C005 +IONMODE:Negative +RETENTIONTIME:41.72 +SPECTRUMTYPE:Centroid +Num Peaks:20 +337.0623 88672453 +359.0443 48435582 +353.0361 37061354 +375.018 29159485 +218.1386 14009249 +417.0027 13822994 +381.0261 13522755 +438.9851 11307111 +396.9999 10317665 +454.9592 9820452 +432.9764 9779399 +338.0654 8770055 +360.0459 5025128 +418.9966 4386311 +512.8989 4072570 +456.9603 3774845 +470.9263 3632486 +572.871 3485486 +440.9796 3364168 +376.0216 2740193 |
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/filtering/mz_range.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtering/mz_range.msp Tue Mar 22 16:07:32 2022 +0000 |
| b |
| @@ -0,0 +1,129 @@ +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C001 +RETENTION_TIME: 38.74 +RETENTION_INDEX: None +NUM PEAKS: 41 +306.9914 3169316.0 +312.7841 10051801.0 +316.7777 10734168.0 +322.8157 6317648.0 +324.9549 8619910.0 +334.849 4178412.0 +342.8093 3285552.0 +349.9455 2050695.0 +350.9875 6150799.0 +351.941 1965882.0 +366.8281 3253770.0 +370.7418 9765463.0 +372.7383 19374863.0 +382.8218 12815572.0 +384.8177 8311500.0 +392.7685 10913351.0 +413.2664 3965867.0 +426.7772 5431633.0 +428.7834 8554675.0 +434.7287 9943329.0 +436.8161 3705247.0 +440.7322 10603010.0 +442.7401 8271752.0 +450.7016 8762673.0 +460.7076 4528973.0 +462.7862 2123666.0 +484.7242 4273989.0 +486.7743 4886062.0 +488.6825 12267966.0 +492.744 7662344.0 +494.8953 7188793.0 +498.8794 6811405.0 +500.8484 6520691.0 +502.7832 3567833.0 +510.763 4989757.0 +518.7415 4243468.0 +546.6093 7177067.0 +550.6949 6104789.0 +566.5977 5171811.0 +612.6927 2005587.0 +676.6436 1982714.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C002 +RETENTION_TIME: 520.25 +RETENTION_INDEX: 1234.5 +NUM PEAKS: 16 +301.1565 15185412.0 +309.1649 18045974.0 +310.1623 295359836.0 +311.1658 13124727.0 +312.0296 38757284.0 +330.6757 12666597.0 +525.375 1073323842.0 +526.3783 181668883.0 +527.3812 23642795.0 +551.3321 111616808.0 +552.3348 28340614.0 +553.3314 2609936.0 +562.3269 7538206.0 +578.2905 7578406.0 +619.3008 4742103.0 +624.296 11790213.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C003 +RETENTION_TIME: 483.67 +NUM PEAKS: 11 +378.2093 15309961.0 +379.1966 2902366.0 +522.3565 4089569222.0 +523.354 1201714423.0 +549.3267 63300808.0 +576.2749 7386007.0 +577.3074 2354251.0 +617.2778 2323470.0 +625.4543 4040374.0 +796.9808 13576738.0 +797.9841 6368973.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C004 +RETENTION_TIME: 473.48 +NUM PEAKS: 10 +482.3247 145772322.0 +483.3283 36245876.0 +496.34 12577588056.0 +497.3442 3337125302.0 +498.3462 532285213.0 +499.3493 68176083.0 +770.964 49250157.0 +771.9675 22666873.0 +783.9721 9839299.0 +784.9749 3622908.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C005 +RETENTION_TIME: 41.72 +NUM PEAKS: 19 +337.0623 88672453.0 +338.0654 8770055.0 +353.0361 37061354.0 +359.0443 48435582.0 +360.0459 5025128.0 +375.018 29159485.0 +376.0216 2740193.0 +381.0261 13522755.0 +396.9999 10317665.0 +417.0027 13822994.0 +418.9966 4386311.0 +432.9764 9779399.0 +438.9851 11307111.0 +440.9796 3364168.0 +454.9592 9820452.0 +456.9603 3774845.0 +470.9263 3632486.0 +512.8989 4072570.0 +572.871 3485486.0 + |
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/filtering/normalise_intensities.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtering/normalise_intensities.msp Tue Mar 22 16:07:32 2022 +0000 |
| b |
| @@ -0,0 +1,194 @@ +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C001 +RETENTION_TIME: 38.74 +RETENTION_INDEX: None +NUM PEAKS: 57 +138.9121 0.31238713555387226 +148.9337 0.03093306182282099 +175.0641 0.8212827951680125 +186.1095 0.08204982258791635 +196.8658 0.6559932163262051 +198.8647 0.6651371915222478 +200.8848 0.23744477531380626 +206.9034 0.8013745219687375 +216.9205 1.0 +234.0134 0.0782063439003671 +254.8252 0.7282800074828951 +256.8215 0.9622769161885076 +258.8237 0.4763537140000675 +266.8652 0.30071259242448867 +268.8537 0.09477374975849262 +306.9914 0.09719532503059093 +312.7841 0.30826464301376666 +316.7777 0.3291912033047409 +322.8157 0.1937471210787636 +324.9549 0.2643519782137348 +334.849 0.12814188059875428 +342.8093 0.10076000453880525 +349.9455 0.06288990023828728 +350.9875 0.18863026217733847 +351.941 0.06028888882073866 +366.8281 0.09978532677864431 +370.7418 0.29948334289140294 +372.7383 0.5941806076478868 +382.8218 0.3930228749651156 +384.8177 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| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/filtering/relative_intensity.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtering/relative_intensity.msp Tue Mar 22 16:07:32 2022 +0000 |
| b |
| @@ -0,0 +1,51 @@ +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C001 +RETENTION_TIME: 38.74 +RETENTION_INDEX: None +NUM PEAKS: 16 +138.9121 10186226.0 +175.0641 26780143.0 +196.8658 21390430.0 +198.8647 21688594.0 +206.9034 26130980.0 +254.8252 23747536.0 +258.8237 15532799.0 +266.8652 9805546.0 +312.7841 10051801.0 +316.7777 10734168.0 +372.7383 19374863.0 +382.8218 12815572.0 +392.7685 10913351.0 +434.7287 9943329.0 +440.7322 10603010.0 +488.6825 12267966.0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C002 +RETENTION_TIME: 520.25 +RETENTION_INDEX: 1234.5 +NUM PEAKS: 0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C003 +RETENTION_TIME: 483.67 +NUM PEAKS: 0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C004 +RETENTION_TIME: 473.48 +NUM PEAKS: 0 + +IONMODE: negative +SPECTRUMTYPE: Centroid +COMPOUND_NAME: C005 +RETENTION_TIME: 41.72 +NUM PEAKS: 3 +353.0361 37061354.0 +359.0443 48435582.0 +375.018 29159485.0 + |
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/formatter/test2_threshold_formatting.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/formatter/test2_threshold_formatting.tsv Tue Mar 22 16:07:32 2022 +0000 |
| [ |
| @@ -0,0 +1,19 @@ +query reference matches score +C007 Benzo[b]naphtho[2,1-d]thiophene 3 0.4302304171927885 +C023 Butylated hydroxytoluene 3 0.4899347755610658 +C016 Drometrizole 3 0.5535081364244014 +C040 Deltamethrin 4 0.5995685829585914 +C040 cis-Cypermethrin_isomer1 3 0.7514936043388737 +C040 cis-Cypermethrin_isomer2 3 0.6205879323732599 +C043 Carbofuran phenol 3 0.5173781620618291 +C023 Alachlor 4 0.4289634841639738 +C012 Chlorpyrifos 3 0.43976068904478827 +C016 Atrazine 5 0.4399647084473271 +C029 Metolachlor 3 0.8624580271763471 +C073 Praziquantel 3 0.6840766738581763 +C034 Carbaryl 3 0.4781026376526427 +C043 Carbofuran 3 0.5212598550187718 +C013 Indoxacarb 5 0.4827488304818007 +C073 Oxadixyl 4 0.7910256109540179 +C073 Amitraz 4 0.5270236660009217 +C008 Spirotetramat 5 0.40641914075077024 |
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/formatter/test2_topk_formatting.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/formatter/test2_topk_formatting.tsv Tue Mar 22 16:07:32 2022 +0000 |
| [ |
| b"@@ -0,0 +1,523 @@\n+query\treference\tmatches\tscore\n+C001\tChlorpyrifos\t7\t0.2439698460078672\n+C001\ttrans-Chlordane\t10\t0.1709889053423956\n+C001\tcis-Chlordane\t10\t0.16934374734008048\n+C002\tCarfentrazone-ethyl\t1\t0.023438813553203555\n+C002\t2,2',3,3',4,5',6,6'-Octachlorobiphenyl\t2\t0.012935401162453864\n+C002\tPyridaben\t4\t0.011168624908917228\n+C003\tPerylene_2H12\t2\t0.0005256270959446041\n+C003\tMetalaxyl\t1\t1.7567415612900304e-06\n+C003\tPerylene\t0\t0.0\n+C004\t17-alpha-Ethynylestradiol\t2\t0.002716713573623163\n+C004\tCoronene\t1\t0.0009680981940665212\n+C004\tProgesterone\t2\t0.0007924296222333303\n+C005\tTetraconazole\t3\t0.12154746411094572\n+C005\tSulfentrazone\t1\t0.05393598836706972\n+C005\tIndoxacarb\t1\t0.0441412960627566\n+C006\tTris(4-tert-butylphenyl) phosphate\t2\t0.12426514943875827\n+C006\tPerylene_2H12\t0\t0.0\n+C006\tPerylene\t0\t0.0\n+C007\tBenzo[b]naphtho[2,1-d]thiophene\t3\t0.4302304171927885\n+C007\t2-Chlorobiphenyl\t2\t0.30327152545734354\n+C007\tRetene\t3\t0.16318259462298138\n+C008\tSpirotetramat\t5\t0.40641914075077024\n+C008\tEthofumesate\t4\t0.17576877383827938\n+C008\t2,4-Di-tert-butyl-6-(5-chloro-2H-benzotriazol-2-yl)phenol\t3\t0.1419543758042326\n+C009\tPicoxystrobin\t1\t0.0006870380110630028\n+C009\tTris(isopropylphenyl)phosphate\t1\t0.00023550942343171069\n+C009\tTebufenpyrad\t1\t0.00017257075992195458\n+C010\tcis-Permethrin\t1\t0.008724226797557697\n+C010\ttrans-Permethrin\t1\t0.008418860878033153\n+C010\tcis-Phenothrin\t1\t0.005882714253167312\n+C011\tFuberidazole\t1\t0.2308319926807784\n+C011\tPrometryn\t2\t0.1773186209832549\n+C011\tBenzoximate\t1\t0.07676637011355666\n+C012\tChlorpyrifos\t3\t0.43976068904478827\n+C012\tTerbufos\t1\t0.4006683041096004\n+C012\t2,6-Dichloro-4-nitroaniline\t1\t0.20998341159494333\n+C013\tIndoxacarb\t5\t0.4827488304818007\n+C013\tTemephos\t2\t0.32810153796559577\n+C013\tNuarimol\t2\t0.2936210041931014\n+C014\tChlorferone\t1\t0.5119124308782732\n+C014\tPiperonyl butoxide\t1\t0.4857177881241794\n+C014\t2,6-Dichloro-4-nitroaniline\t2\t0.33898957004708385\n+C015\tMetazachlor\t1\t0.0011434403294572687\n+C015\talpha-Amylcinnamyl alcohol\t1\t0.0005805859933790689\n+C015\tPendimethalin\t1\t0.0005015386924657569\n+C016\tDrometrizole\t3\t0.5535081364244014\n+C016\tAcenaphthylene\t2\t0.540073031173669\n+C016\tAtrazine\t5\t0.4399647084473271\n+C017\t4-tert-Octylphenol\t1\t0.9088788152148044\n+C017\tPropargite_isomer2\t1\t0.8953233485170952\n+C017\tPropargite_isomer1\t1\t0.8942159049307404\n+C018\tTris(4-tert-butylphenyl) phosphate\t1\t0.189695375366971\n+C018\tPerylene_2H12\t0\t0.0\n+C018\tPerylene\t0\t0.0\n+C019\tTriclosan\t1\t0.13434903881343435\n+C019\tTerbufos\t1\t0.08080384965580391\n+C019\tEpoxiconazole\t2\t0.07313225916488224\n+C020\tTris(isopropylphenyl)phosphate\t2\t0.2520159660977677\n+C020\tAmitraz\t2\t0.1245102870796828\n+C020\tMetribuzin\t1\t0.05224979683560159\n+C021\tTebuthiuron\t2\t0.9340205348244696\n+C021\t1,5-Dimethylnaphthalene\t1\t0.6803608761410861\n+C021\t2,6-Dimethylnaphthalene\t1\t0.6264160291669295\n+C022\t2-Bromoallyl(2,4,6-tribromophenyl) ether\t1\t0.11311229152083695\n+C022\t2,3,4,5,6-Pentabromobenzyl alcohol\t2\t0.07003350703850979\n+C022\tAllyl 2,4,6-tribromophenyl ether\t1\t0.06571493640420596\n+C023\tPhenanthrene_2H10\t1\t0.7408591267092633\n+C023\t2-Chlorobiphenyl\t1\t0.6159214014775711\n+C023\tButylated hydroxytoluene\t3\t0.4899347755610658\n+C024\tMepronil\t2\t0.18000248105004787\n+C024\tSpirotetramat\t8\t0.17523909122675907\n+C024\tEstrone\t7\t0.17146514923780354\n+C025\tTris(4-tert-butylphenyl) phosphate\t2\t0.2957673370199089\n+C025\tPerylene_2H12\t0\t0.0\n+C025\tPerylene\t0\t0.0\n+C026\tIsodecyl diphenyl phosphate\t2\t0.4122773057565717\n+C026\tDicofol\t1\t0.32235849897575225\n+C026\tTris(isopropylphenyl)phosphate\t2\t0.18207675907106227\n+C027\tFenobucarb\t1\t0.058048257187677615\n+C027\tIsoprocarb\t1\t0.056638368345330564\n+C027\tDioxacarb\t1\t0.041723437047250914\n+C028\tPhosmet\t1\t0.7848313885767587\n+C028\tAlachlor\t1\t0.5400260886224933\n+C028\tButafenacil\t2\t0.5287006460619553\n+C029\tMetolachlor\t3\t0.8624580271763471\n+C029\tSafrole\t2\t0.591167446764124\n+C029\tAmitraz\t2\t0.4100617029164697\n+C030\tEthofumesate\t2\t0.1283368182166788\n+C030\tIprovalicarb isomer 1\t1\t0.1278518291141877\n+C030\tAcephate\t4\t0.12723099231343524\n+C031\tProgesterone\t1\t1.642699424"..b"\n+C138\tPhenanthrene_2H10\t0\t0.0\n+C139\tPerylene_2H12\t0\t0.0\n+C139\tPerylene\t0\t0.0\n+C139\tPhenanthrene_2H10\t0\t0.0\n+C140\tRotenone\t1\t0.0015990284859575886\n+C140\tPerylene_2H12\t0\t0.0\n+C140\tPerylene\t0\t0.0\n+C141\tTebufenpyrad\t2\t0.2938100129854653\n+C141\tTris(isopropylphenyl)phosphate\t2\t0.020202034111700597\n+C141\tIpconazole\t1\t0.017041584156450424\n+C142\tPerylene_2H12\t0\t0.0\n+C142\tPerylene\t0\t0.0\n+C142\tPhenanthrene_2H10\t0\t0.0\n+C143\tDimethomorph_isomer2\t1\t0.16685279162562694\n+C143\tDimethomorph _isomer1\t1\t0.16482807037456434\n+C143\t2,3,4,5,6-Pentabromotoluene\t1\t0.032682863992618404\n+C144\tEtoxazole\t2\t0.1027909809180103\n+C144\t2,4-Di-tert-butyl-6-(5-chloro-2H-benzotriazol-2-yl)phenol\t2\t0.04732776045289416\n+C144\tAzoxystrobin\t2\t0.035630773587232864\n+C145\tPerylene_2H12\t0\t0.0\n+C145\tPerylene\t0\t0.0\n+C145\tPhenanthrene_2H10\t0\t0.0\n+C146\tPropargite_isomer1\t1\t0.0633083562823998\n+C146\tPropargite_isomer2\t1\t0.05654738208679003\n+C146\t2,2',3,3',4,5',6,6'-Octachlorobiphenyl\t1\t0.035712333462604294\n+C147\t2,2',3,4,4',5',6-Heptabromodiphenyl ether\t1\t0.03047378825096018\n+C147\tChlorferone\t1\t0.01855122445019196\n+C147\tProgesterone\t2\t0.007867919703105094\n+C148\tBuprofezin\t1\t0.01875857752389424\n+C148\tPerylene_2H12\t0\t0.0\n+C148\tPerylene\t0\t0.0\n+C149\tMetalaxyl\t2\t0.29742589743178666\n+C149\t1,4-Naphthoquinone\t1\t0.2740480911849054\n+C149\tPraziquantel\t1\t0.260732240603901\n+C150\ttrans-Prallethrin\t1\t0.00633664692361121\n+C150\tPerylene_2H12\t0\t0.0\n+C150\tPerylene\t0\t0.0\n+C151\tSpirotetramat\t1\t0.011452966094891676\n+C151\tPerylene_2H12\t0\t0.0\n+C151\tPerylene\t0\t0.0\n+C152\tTris(3,5-xylenyl)phosphate\t1\t0.05756111981021594\n+C152\tTris(isopropylphenyl)phosphate\t1\t0.0449470954588726\n+C152\tPerylene_2H12\t0\t0.0\n+C153\tEthiofencarb\t1\t0.8284613374855048\n+C153\t1,1-Dibromo-2,3,3,4,4,5-hexachloro-2-cyclopenta-2,4-dien-1-ylcyclooctane\t1\t0.4257874890609336\n+C153\tIsomethyl-alpha-ionone\t1\t0.36103138237616267\n+C154\t7,12-Dimethylbenz[a]anthracene\t1\t0.29226381053937395\n+C154\tEnzacamene\t1\t0.14396940230197552\n+C154\tTriflumizole\t1\t0.10858411907186044\n+C155\tPerylene_2H12\t0\t0.0\n+C155\tPerylene\t0\t0.0\n+C155\tPhenanthrene_2H10\t0\t0.0\n+C156\t7,12-Dimethylbenz[a]anthracene\t1\t0.08248293081186396\n+C156\tMethoprotryne\t1\t0.0432082364937662\n+C156\tProgesterone\t1\t0.02316539180928352\n+C157\tPerylene_2H12\t0\t0.0\n+C157\tPerylene\t0\t0.0\n+C157\tPhenanthrene_2H10\t0\t0.0\n+C158\tTris(4-tert-butylphenyl) phosphate\t1\t0.012341356867974116\n+C158\tPerylene_2H12\t0\t0.0\n+C158\tPerylene\t0\t0.0\n+C159\tTrifluralin\t1\t0.1883562158254524\n+C159\tFenpropathrin\t1\t0.015975881134824614\n+C159\tEthiprole\t1\t0.007596489095240584\n+C160\tBumetrizole\t1\t0.04337092323628775\n+C160\ttrans-Cypermethrin_isomer2\t1\t0.030241071137562938\n+C160\tPerylene_2H12\t1\t0.029465908012253836\n+C161\tPerylene_2H12\t0\t0.0\n+C161\tPerylene\t0\t0.0\n+C161\tPhenanthrene_2H10\t0\t0.0\n+C162\tPerylene_2H12\t0\t0.0\n+C162\tPerylene\t0\t0.0\n+C162\tPhenanthrene_2H10\t0\t0.0\n+C163\tPerylene_2H12\t0\t0.0\n+C163\tPerylene\t0\t0.0\n+C163\tPhenanthrene_2H10\t0\t0.0\n+C164\t7,12-Dimethylbenz[a]anthracene\t1\t0.2284760273276565\n+C164\tEnzacamene\t1\t0.112547485896346\n+C164\tFenamidone\t1\t0.0486288864876461\n+C165\tBoscalid\t1\t0.08498662209290331\n+C165\tBuprofezin\t1\t0.08205704595848827\n+C165\tIpconazole\t1\t0.08152620214218925\n+C166\tTris(2-butoxyethyl) phosphate\t1\t0.008342150525801997\n+C166\tRotenone\t1\t0.0015006556689027325\n+C166\tPerylene_2H12\t0\t0.0\n+C167\tPerylene_2H12\t0\t0.0\n+C167\tPerylene\t0\t0.0\n+C167\tPhenanthrene_2H10\t0\t0.0\n+C168\tPerylene_2H12\t0\t0.0\n+C168\tPerylene\t0\t0.0\n+C168\tPhenanthrene_2H10\t0\t0.0\n+C169\tPerylene_2H12\t0\t0.0\n+C169\tPerylene\t0\t0.0\n+C169\tPhenanthrene_2H10\t0\t0.0\n+C170\tPerylene_2H12\t0\t0.0\n+C170\tPerylene\t0\t0.0\n+C170\tPhenanthrene_2H10\t0\t0.0\n+C171\t2,4-D butyl ester\t1\t0.6610587362108564\n+C171\tTerbutryn\t1\t0.6012657870951452\n+C171\tEstrone\t2\t0.31623371975319553\n+C172\tPerylene_2H12\t1\t0.06765194944236241\n+C172\t17-alpha-Ethynylestradiol\t1\t0.01884162876915315\n+C172\tProgesterone\t1\t0.01306130902820296\n+C173\tSpiromesifen\t1\t0.016586079079264453\n+C173\tRotenone\t1\t0.0025109428261963678\n+C173\tPerylene_2H12\t0\t0.0\n+C174\tPerylene_2H12\t0\t0.0\n+C174\tPerylene\t0\t0.0\n+C174\tPhenanthrene_2H10\t0\t0.0\n" |
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/matches_test2_out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/matches_test2_out.tsv Tue Mar 22 16:07:32 2022 +0000 |
| b |
| b'@@ -0,0 +1,387 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|
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/scores_test2_out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scores_test2_out.tsv Tue Mar 22 16:07:32 2022 +0000 |
| b |
| b'@@ -0,0 +1,387 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|
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/similarity/fill.mgf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/fill.mgf Tue Mar 22 16:07:32 2022 +0000 |
| b |
| b'@@ -0,0 +1,2513 @@\n+BEGIN IONS\n+NAME=C001\n+IONMODE=Negative\n+RETENTIONTIME=38.74\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=57\n+138.9121 10186226.0 \n+148.9337 1008656.0 \n+175.0641 26780143.0 \n+186.1095 2675456.0 \n+196.8658 21390430.0 \n+198.8647 21688594.0 \n+200.8848 7742528.0 \n+206.9034 26130980.0 \n+216.9205 32607700.0 \n+234.0134 2550129.0 \n+254.8252 23747536.0 \n+256.8215 31377637.0 \n+258.8237 15532799.0 \n+266.8652 9805546.0 \n+268.8537 3090354.0 \n+306.9914 3169316.0 \n+312.7841 10051801.0 \n+316.7777 10734168.0 \n+322.8157 6317648.0 \n+324.9549 8619910.0 \n+334.849 4178412.0 \n+342.8093 3285552.0 \n+349.9455 2050695.0 \n+350.9875 6150799.0 \n+351.941 1965882.0 \n+366.8281 3253770.0 \n+370.7418 9765463.0 \n+372.7383 19374863.0 \n+382.8218 12815572.0 \n+384.8177 8311500.0 \n+392.7685 10913351.0 \n+413.2664 3965867.0 \n+426.7772 5431633.0 \n+428.7834 8554675.0 \n+434.7287 9943329.0 \n+436.8161 3705247.0 \n+440.7322 10603010.0 \n+442.7401 8271752.0 \n+450.7016 8762673.0 \n+460.7076 4528973.0 \n+462.7862 2123666.0 \n+484.7242 4273989.0 \n+486.7743 4886062.0 \n+488.6825 12267966.0 \n+492.744 7662344.0 \n+494.8953 7188793.0 \n+498.8794 6811405.0 \n+500.8484 6520691.0 \n+502.7832 3567833.0 \n+510.763 4989757.0 \n+518.7415 4243468.0 \n+546.6093 7177067.0 \n+550.6949 6104789.0 \n+566.5977 5171811.0 \n+612.6927 2005587.0 \n+676.6436 1982714.0 \n+800.4451 2792137.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C002\n+IONMODE=Negative\n+RETENTIONTIME=520.25\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=35\n+131.1733 1971789.0 \n+267.2688 6103973.0 \n+279.0196 1946255.0 \n+289.6491 46498377.0 \n+301.1565 15185412.0 \n+309.1649 18045974.0 \n+310.1623 295359836.0 \n+311.1658 13124727.0 \n+312.0296 38757284.0 \n+330.6757 12666597.0 \n+525.375 1073323842.0 \n+526.3783 181668883.0 \n+527.3812 23642795.0 \n+551.3321 111616808.0 \n+552.3348 28340614.0 \n+553.3314 2609936.0 \n+562.3269 7538206.0 \n+578.2905 7578406.0 \n+619.3008 4742103.0 \n+624.296 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\n+353.0361 37061354.0 \n+359.0443 48435582.0 \n+360.0459 5025128.0 \n+375.018 29159485.0 \n+376.0216 2740193.0 \n+381.0261 13522755.0 \n+396.9999 10317665.0 \n+417.0027 13822994.0 \n+418.9966 4386311.0 \n+432'..b'TRUMTYPE=Centroid\n+NUM PEAKS=2\n+328.2481 11119434.0 \n+329.2519 2068394.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C152\n+IONMODE=Negative\n+RETENTIONTIME=385.78\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+409.1497 1369551.0 \n+427.1607 2275086.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C153\n+IONMODE=Negative\n+RETENTIONTIME=401.39\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+107.0557 2271180.0 \n+197.1612 1286942.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C154\n+IONMODE=Negative\n+RETENTIONTIME=388.72\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+239.1276 1743749.0 \n+286.9585 1645545.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C155\n+IONMODE=Negative\n+RETENTIONTIME=373.67\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+507.1617 6285930.0 \n+508.1657 1535734.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C156\n+IONMODE=Negative\n+RETENTIONTIME=378.37\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+257.2254 3302868.0 \n+777.6928 4522421.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C157\n+IONMODE=Negative\n+RETENTIONTIME=473.08\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+267.6425 11780168.0 \n+534.2949 13399261.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C158\n+IONMODE=Negative\n+RETENTIONTIME=508.15\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+380.2992 5790633.0 \n+423.2518 1386850.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C159\n+IONMODE=Negative\n+RETENTIONTIME=471.89\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+304.2357 21716257.0 \n+306.1523 8327492.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C160\n+IONMODE=Negative\n+RETENTIONTIME=465.45\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+193.1239 1274413.0 \n+295.1974 20379534.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C161\n+IONMODE=Negative\n+RETENTIONTIME=488.7\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+667.4214 3075774.0 \n+1189.7766 2040172.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C162\n+IONMODE=Negative\n+RETENTIONTIME=471.97\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+316.6601 7221684.0 \n+393.2201 8389493.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C163\n+IONMODE=Negative\n+RETENTIONTIME=465.16\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+422.3267 4962906.0 \n+431.3157 12163271.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C164\n+IONMODE=Negative\n+RETENTIONTIME=474.29\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+239.1779 8236995.0 \n+398.3268 11918127.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C165\n+IONMODE=Negative\n+RETENTIONTIME=477.74\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+249.1858 1576729.0 \n+307.15 1941191.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C166\n+IONMODE=Negative\n+RETENTIONTIME=494.51\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+355.2846 54372680.0 \n+373.2951 6108864.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C167\n+IONMODE=Negative\n+RETENTIONTIME=497.67\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+474.3486 2732000.0 \n+649.4483 2434649.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C168\n+IONMODE=Negative\n+RETENTIONTIME=498.02\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+459.2569 3550909.0 \n+539.4163 5285541.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C169\n+IONMODE=Negative\n+RETENTIONTIME=492.45\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+732.5452 4526953.0 \n+733.5465 1043642.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C170\n+IONMODE=Negative\n+RETENTIONTIME=497.3\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+450.3586 4210116.0 \n+451.3631 6446370.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C171\n+IONMODE=Negative\n+RETENTIONTIME=467.81\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+185.0776 5067455.0 \n+200.203 1398415.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C172\n+IONMODE=Negative\n+RETENTIONTIME=457.02\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+263.2347 3933284.0 \n+615.2633 1132491.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C173\n+IONMODE=Negative\n+RETENTIONTIME=443.89\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+370.2956 41596161.0 \n+371.304 9966707.0 \n+END IONS\n+\n+BEGIN IONS\n+NAME=C174\n+IONMODE=Negative\n+RETENTIONTIME=438.81\n+RETENTIONINDEX=\n+SPECTRUMTYPE=Centroid\n+NUM PEAKS=2\n+330.2563 5274387.0 \n+579.2938 6044865.0 \n+END IONS\n+\n' |
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/similarity/fill.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/fill.msp Tue Mar 22 16:07:32 2022 +0000 |
| b |
| b'@@ -0,0 +1,2165 @@\n+NAME:C001\n+IONMODE:Negative\n+RETENTIONTIME:38.74\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:57\n+216.9205 32607700\n+256.8215 31377637\n+175.0641 26780143\n+206.9034 26130980\n+254.8252 23747536\n+198.8647 21688594\n+196.8658 21390430\n+372.7383 19374863\n+258.8237 15532799\n+382.8218 12815572\n+488.6825 12267966\n+392.7685 10913351\n+316.7777 10734168\n+440.7322 10603010\n+138.9121 10186226\n+312.7841 10051801\n+434.7287 9943329\n+266.8652 9805546\n+370.7418 9765463\n+450.7016 8762673\n+324.9549 8619910\n+428.7834 8554675\n+384.8177 8311500\n+442.7401 8271752\n+200.8848 7742528\n+492.744 7662344\n+494.8953 7188793\n+546.6093 7177067\n+498.8794 6811405\n+500.8484 6520691\n+322.8157 6317648\n+350.9875 6150799\n+550.6949 6104789\n+426.7772 5431633\n+566.5977 5171811\n+510.763 4989757\n+486.7743 4886062\n+460.7076 4528973\n+484.7242 4273989\n+518.7415 4243468\n+334.849 4178412\n+413.2664 3965867\n+436.8161 3705247\n+502.7832 3567833\n+342.8093 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2322927\n+1101.6535 2023916\n+131.1733 1971789\n+279.0196 1946255\n+\n+NAME:C003\n+IONMODE:Negative\n+RETENTIONTIME:483.67\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:26\n+522.3565 4089569222\n+523.354 1201714423\n+288.6414 202172046\n+1043.7028 144351468\n+1044.7068 83271854\n+549.3267 63300808\n+279.6362 29849749\n+1045.706 27998321\n+1058.1594 20718345\n+1071.1639 15461047\n+378.2093 15309961\n+796.9808 13576738\n+809.9883 12596682\n+265.2529 11366224\n+280.6546 8848921\n+576.2749 7386007\n+1059.1626 6608764\n+810.9916 6601055\n+1046.7131 6505178\n+797.9841 6368973\n+1072.1671 5096642\n+625.4543 4040374\n+379.1966 2902366\n+577.3074 2354251\n+617.2778 2323470\n+266.2564 1420444\n+\n+NAME:C004\n+IONMODE:Negative\n+RETENTIONTIME:473.48\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:24\n+496.34 12577588056\n+497.3442 3337125302\n+991.6726 1420557258\n+992.6749 763118028\n+498.3462 532285213\n+993.6787 239161906\n+296.147 190395687\n+1017.6897 168186952\n+482.3247 145772322\n+1018.6656 120599518\n+499.3493 68176083\n+1019.6555 57647644\n+994.6801 53549573\n+770.964 49250157\n+483.3283 36245876\n+275.6336 28001849\n+771.9675 22666873\n+1020.6591 12469103\n+783.9721 9839299\n+949.6233 8009033\n+124.1405 6517662\n+950.6274 3674694\n+784.9749 3622908\n+170.2437 1237313\n+\n+NAME:C005\n+IONMODE:Negative\n+RETENTIONTIME:41.72\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:20\n+337.0623 88672453\n+359.0443 48435582\n+353.0361 37061354\n+375.018 29159485\n+218.1386 14009249\n+417.0027 13822994\n+381.0261 13522755\n+438.9851 11307111\n+396.9999 10317665\n+454.9592 9820452\n+432.9764 9779399\n+338.0654 8770055\n+360.0459 5025128\n+418.9966 4386311\n+512.8989 4072570\n+456.9603 3774845\n+470.9263 3632486\n+572.871 3485486\n+440.9796 3364168\n+376.0216 2740193\n+\n+NAME:C006\n+IONMODE:Negative\n+RETENTIONTIME:452.08\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:19\n+494.3249 803829845\n+495.3278 207959661\n+542.3239 193323900\n+543.3276 55501736\n+1087.6715 34676828\n+516.3076 24092471\n+274.6257 21694276\n+1088.6773 21466528\n+1001.658 11852076\n+1089.682 9948820\n+290.6256 9704443\n+1061.6562 9417442\n+987.6411 7453650\n+1037.6578 7076912\n+1062.6592 5657208\n+484.3311 5283943\n+265.6196 '..b'5.2288 1932289\n+\n+NAME:C147\n+IONMODE:Negative\n+RETENTIONTIME:563.22\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+282.2792 241362345\n+256.2615 19433189\n+\n+NAME:C148\n+IONMODE:Negative\n+RETENTIONTIME:548.47\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+305.2468 9633582\n+329.249 5814756\n+\n+NAME:C149\n+IONMODE:Negative\n+RETENTIONTIME:350.93\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+130.0643 7419216\n+190.0865 4433780\n+\n+NAME:C150\n+IONMODE:Negative\n+RETENTIONTIME:365.37\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+490.2083 5275418\n+465.1226 1763287\n+\n+NAME:C151\n+IONMODE:Negative\n+RETENTIONTIME:394.87\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+328.2481 11119434\n+329.2519 2068394\n+\n+NAME:C152\n+IONMODE:Negative\n+RETENTIONTIME:385.78\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+427.1607 2275086\n+409.1497 1369551\n+\n+NAME:C153\n+IONMODE:Negative\n+RETENTIONTIME:401.39\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+107.0557 2271180\n+197.1612 1286942\n+\n+NAME:C154\n+IONMODE:Negative\n+RETENTIONTIME:388.72\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+239.1276 1743749\n+286.9585 1645545\n+\n+NAME:C155\n+IONMODE:Negative\n+RETENTIONTIME:373.67\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+507.1617 6285930\n+508.1657 1535734\n+\n+NAME:C156\n+IONMODE:Negative\n+RETENTIONTIME:378.37\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+777.6928 4522421\n+257.2254 3302868\n+\n+NAME:C157\n+IONMODE:Negative\n+RETENTIONTIME:473.08\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+534.2949 13399261\n+267.6425 11780168\n+\n+NAME:C158\n+IONMODE:Negative\n+RETENTIONTIME:508.15\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+380.2992 5790633\n+423.2518 1386850\n+\n+NAME:C159\n+IONMODE:Negative\n+RETENTIONTIME:471.89\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+304.2357 21716257\n+306.1523 8327492\n+\n+NAME:C160\n+IONMODE:Negative\n+RETENTIONTIME:465.45\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+295.1974 20379534\n+193.1239 1274413\n+\n+NAME:C161\n+IONMODE:Negative\n+RETENTIONTIME:488.7\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+667.4214 3075774\n+1189.7766 2040172\n+\n+NAME:C162\n+IONMODE:Negative\n+RETENTIONTIME:471.97\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+393.2201 8389493\n+316.6601 7221684\n+\n+NAME:C163\n+IONMODE:Negative\n+RETENTIONTIME:465.16\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+431.3157 12163271\n+422.3267 4962906\n+\n+NAME:C164\n+IONMODE:Negative\n+RETENTIONTIME:474.29\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+398.3268 11918127\n+239.1779 8236995\n+\n+NAME:C165\n+IONMODE:Negative\n+RETENTIONTIME:477.74\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+307.15 1941191\n+249.1858 1576729\n+\n+NAME:C166\n+IONMODE:Negative\n+RETENTIONTIME:494.51\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+355.2846 54372680\n+373.2951 6108864\n+\n+NAME:C167\n+IONMODE:Negative\n+RETENTIONTIME:497.67\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+474.3486 2732000\n+649.4483 2434649\n+\n+NAME:C168\n+IONMODE:Negative\n+RETENTIONTIME:498.02\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+539.4163 5285541\n+459.2569 3550909\n+\n+NAME:C169\n+IONMODE:Negative\n+RETENTIONTIME:492.45\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+732.5452 4526953\n+733.5465 1043642\n+\n+NAME:C170\n+IONMODE:Negative\n+RETENTIONTIME:497.3\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+451.3631 6446370\n+450.3586 4210116\n+\n+NAME:C171\n+IONMODE:Negative\n+RETENTIONTIME:467.81\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+185.0776 5067455\n+200.203 1398415\n+\n+NAME:C172\n+IONMODE:Negative\n+RETENTIONTIME:457.02\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+263.2347 3933284\n+615.2633 1132491\n+\n+NAME:C173\n+IONMODE:Negative\n+RETENTIONTIME:443.89\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+370.2956 41596161\n+371.304 9966707\n+\n+NAME:C174\n+IONMODE:Negative\n+RETENTIONTIME:438.81\n+RETENTIONINDEX:\n+SPECTRUMTYPE:Centroid\n+Num Peaks:2\n+579.2938 6044865\n+330.2563 5274387\n+\n' |
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/similarity/fill2.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/fill2.msp Tue Mar 22 16:07:32 2022 +0000 |
| b |
| b'@@ -0,0 +1,5150 @@\n+NAME: C041\n+IONMODE: Negative\n+SPECTRUMTYPE: Centroid\n+RETENTIONTIME: 122.44\n+RETENTIONINDEX: 1079.198718\n+NUM PEAKS: 32\n+73.0841293753643 962537.0\n+92.9922681974622 25809589.0\n+93.5236243719193 7832508.0\n+93.9918503397022 4037554.0\n+94.9892593290089 9273560.0\n+102.528897846033 5258508.0\n+103.032878700634 5618676.0\n+106.048287181011 17919228.0\n+116.082937025519 19358163.0\n+116.088997408008 2749072817.0\n+116.093789141941 21174548.0\n+117.085953932526 5958559.0\n+117.088526521735 137197201.0\n+117.09226575013 144026411.0\n+117.095343138483 3078493.0\n+118.085738968471 93658275.0\n+118.091857064635 7792967.0\n+118.095506285782 3082221.0\n+120.088840757968 158124.0\n+129.052817882804 2757896.0\n+144.047597981883 6935455.0\n+154.03180616847 40749504.0\n+155.035134922158 4354801.0\n+156.011148185837 2560241.0\n+172.042203916163 16922092.0\n+178.047197818956 372134.0\n+190.107642341182 143044792.0\n+191.109992585577 20336483.0\n+192.104283767627 9359612.0\n+204.050979060253 4818700.0\n+205.059630310281 24572956.0\n+244.042971889438 1521120.0\n+\n+NAME: C078\n+IONMODE: Negative\n+SPECTRUMTYPE: Centroid\n+RETENTIONTIME: 123.01\n+RETENTIONINDEX: 1084.222756\n+NUM PEAKS: 19\n+75.010394066048 41579966.0\n+76.0137882041242 2876047.0\n+76.0181929768627 28340717.0\n+77.0259504577085 2087987.0\n+78.0338979909698 183026502.0\n+78.5690293876576 1621521.0\n+78.8681599478139 1487893.0\n+79.0376938452989 30093264.0\n+79.0416552579741 2825081311.0\n+79.0447459388332 28320503.0\n+79.0501993561375 4270687.0\n+79.2157179170819 1455165.0\n+79.5185598181509 1593839.0\n+80.0386557190469 10075569.0\n+80.0450063493877 149614748.0\n+81.0483295726077 3268158.0\n+89.9974943554148 1961794.0\n+95.0365701495921 4214292.0\n+96.0443688524812 20830699.0\n+\n+NAME: C115\n+IONMODE: Negative\n+SPECTRUMTYPE: Centroid\n+RETENTIONTIME: 123.7\n+RETENTIONINDEX: 1090.304487\n+NUM PEAKS: 12\n+77.9912808985361 1430046.0\n+78.0150262817737 37531039.0\n+84.0934034839136 3045143.0\n+85.1012069274801 7651144.0\n+86.1044999837715 502049.0\n+127.023946499139 21672536.0\n+155.015395274682 50181759.0\n+173.025818014551 19321056.0\n+225.059247121035 54449419.0\n+240.031884101672 47027617.0\n+278.105692656594 44448528.0\n+332.077037506685 36734393.0\n+\n+NAME: C072\n+IONMODE: Negative\n+SPECTRUMTYPE: Centroid\n+RETENTIONTIME: 126.02\n+RETENTIONINDEX: 1105.809524\n+NUM PEAKS: 20\n+75.026123979198 434239353.0\n+76.0294479264598 10769681.0\n+79.0184721827801 4406598.0\n+79.0228409649542 3040911.0\n+86.0420715774215 69402087.0\n+93.9412902191997 4117357.0\n+95.0446916434486 4401744.0\n+95.9392474302401 3764925.0\n+120.033807681496 1445863.0\n+122.943972830176 4871174.0\n+131.088643222278 12343251.0\n+134.108939486662 1310131.0\n+137.026000929413 1710939.0\n+168.950062688366 1235026.0\n+176.091958662459 68901069.0\n+177.09146256329 9695519.0\n+184.040024671153 13159137.0\n+206.084125728074 4028572.0\n+249.138642058545 13543889.0\n+251.137167813194 1490829.0\n+\n+NAME: C050\n+IONMODE: Negative\n+SPECTRUMTYPE: Centroid\n+RETENTIONTIME: 128.53\n+RETENTIONINDEX: 1117.761905\n+NUM PEAKS: 26\n+72.0264235348245 4721310.0\n+75.0234110401587 7374271.0\n+75.0288404069534 9420937.0\n+86.9717728755449 9553539.0\n+88.9509947069327 6380434.0\n+97.088645546243 920854.0\n+100.00330732202 18214503.0\n+102.073359041231 484549126.0\n+103.002973695426 21838182.0\n+105.0182950443 11385761.0\n+108.947110640446 3717342.0\n+111.104289675305 3'..b' 50206470.0\n+209.047732156056 2402702.0\n+224.063049376575 5028073.0\n+237.079282533047 3254126.0\n+249.987809880519 7068049.0\n+250.967699771612 4666725.0\n+250.985590439413 4155732.0\n+251.00396611366 4712547.0\n+252.983678728064 24136227.0\n+267.016209949758 5864415.0\n+283.063228005498 1245664.0\n+285.04434812945 5580645.0\n+285.079068565003 8168809.0\n+323.006809434282 4228442.0\n+342.088126205946 12649128.0\n+343.014343300482 13057700.0\n+343.066328014548 11668807.0\n+344.014693258176 2143320.0\n+400.005631091464 1275209.0\n+\n+NAME: C020\n+IONMODE: Negative\n+SPECTRUMTYPE: Centroid\n+RETENTIONTIME: 687.99\n+RETENTIONINDEX: 4135.089286\n+NUM PEAKS: 43\n+109.052235628516 1922885.0\n+111.044058476785 1730416.0\n+133.064909307365 1579533.0\n+137.041722086745 2474039.0\n+194.053642118165 5252308.0\n+212.061782732582 10437319.0\n+267.034768010352 4429084.0\n+267.068824022318 27744081.0\n+268.069192256745 2367920.0\n+310.970568727813 3126083.0\n+311.004219192148 2666091.0\n+325.055731606087 7634729.0\n+327.965549188207 5442532.0\n+328.962716535303 2722019.0\n+339.03821058645 6627839.0\n+341.051986399316 1671451.0\n+342.996634492902 3939816.0\n+345.115297423962 3938049.0\n+358.067243216398 3526875.0\n+361.025211906011 6516476.0\n+388.003000430725 3422825.0\n+388.073272089579 4224454.0\n+399.005054559559 4141766.0\n+401.984326631505 5585170.0\n+402.98179623463 3562508.0\n+416.036473280551 7221552.0\n+417.033665098569 4129234.0\n+417.087073648909 1945166.0\n+418.994970709551 2648178.0\n+430.088321970134 10765018.0\n+431.085366629672 6887942.0\n+473.09370665615 2502410.0\n+475.002854889036 2969642.0\n+475.14184210128 30625723.0\n+477.070907310139 2271450.0\n+489.055479984185 1973511.0\n+503.107930410573 2407435.0\n+549.092119293556 2513579.0\n+552.160354111203 1673065.0\n+565.143723544965 3485979.0\n+610.132183060405 1997085.0\n+625.181479977537 3872339.0\n+697.202597429349 2820429.0\n+\n+NAME: C019\n+IONMODE: Negative\n+SPECTRUMTYPE: Centroid\n+RETENTIONTIME: 688.11\n+RETENTIONINDEX: 4135.446429\n+NUM PEAKS: 45\n+70.261357375322 1769331.0\n+82.0777101637279 1721684.0\n+92.0256956423549 1063403.0\n+104.057597689888 2564581.0\n+106.07773010104 1697865.0\n+118.073139793174 3070732.0\n+135.080430341161 1465718.0\n+144.946939559008 1208427.0\n+145.046705119092 2856482.0\n+164.985419247789 16217649.0\n+179.033979756352 10865004.0\n+180.980322946522 4830502.0\n+191.070496682473 3188459.0\n+192.078428243192 3993484.0\n+194.04893073403 5942766.0\n+195.046783458568 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| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/similarity/matches_test1_out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/matches_test1_out.tsv Tue Mar 22 16:07:32 2022 +0000 |
| b |
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|
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/similarity/matches_test3_out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/matches_test3_out.tsv Tue Mar 22 16:07:32 2022 +0000 |
| b |
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|
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/similarity/matches_test4_out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/matches_test4_out.tsv Tue Mar 22 16:07:32 2022 +0000 |
| [ |
| b"@@ -0,0 +1,387 @@\n+\tPerylene_2H12\tPerylene\tPhenanthrene_2H10\tPhenanthrene\tAnthracene\tAcenaphthylene\tAcenaphthene\tFluoranthene\tPyrene\tpara-Terphenyl\tRetene\tBenzo[b]naphtho[2,1-d]thiophene\t2,3-Benzofluorene\tBenzo[ghi]fluoranthene\tTriphenylene\tBenzanthracene/Benzophenanthrene\tBenzofluoranthene\tBenzo(k)fluoranthene\tBenzo[e]pyrene\tBenzo(a)pyrene\tIndeno[1,2,3-cd]pyrene\tBenzo(g,h,i)perylene\tAnthanthrene\tDibenzanthracene\tCoronene\tDicofol\tBenzophenone\t2-tert-Butyl-4-methoxyphenol\tButylated hydroxytoluene\tBumetrizole\t4-Methylbenzophenone\t2,4,6-Tribromophenol\t2,6-Dichloro-4-nitroaniline\t1-Methylphenanthrene\tTriclosan\tDrometrizole\tEnzacamene\t2,4-Di-tert-butyl-6-(5-chloro-2H-benzotriazol-2-yl)phenol\tOctrizole\t1,2,7,9-Tetrachlorodibenzofuran\t2,2',3,4,5,5',6-Heptachlorobiphenyl\t2,4,6-Trichlorobiphenyl\t2,2',3,3',4,5',6,6'-Octachlorobiphenyl\tMirex\tbeta-Hexachlorocyclohexane\talpha-1,2,3,4,5,6-Hexachlorocyclohexane\tLindane\tdelta-Hexachlorocyclohexane\tepsilon-Hexachlorocyclohexane\tPentachlorobenzene\tHexachlorobenzene\t2,4'-Dichlorodiphenyldichloroethylene\t2,4'-Dichlorodiphenyldichloroethane\t2,4'-Dichlorodiphenyltrichloroethane\t1,2,7,9-Tetrachlorodibenzo-p-dioxin\t2,4,4'-Trichlorobiphenyl\t2,2',4,5,5'-Pentachlorobiphenyl\t2,3',4,4',5-Pentachlorobiphenyl\t2,2',3,4,4',5'-Hexachlorobiphenyl\t2,2',4,4',5,5'-Hexachlorobiphenyl\t2,2',3,4,4',5,5'-Heptachlorobiphenyl\t2,2',5,5'-Tetrachlorobiphenyl\t2,3',4,6-Tetrachlorobiphenyl\t2,3',5',6-Tetrachlorobiphenyl\t2,2',3,4',5-Pentachlorobiphenyl\t2,3,3',4,5-Pentachlorobiphenyl\t3,3',4,5,5'-Pentachlorobiphenyl\t2,3',4,4',5',6-Hexachlorobiphenyl\t2,3,3',4,5,6-Hexachlorobiphenyl\t2,3,3',4',5',6-Hexachlorobiphenyl\t2,3,3',4',5,6-Hexachlorobiphenyl\t2,3,3',4',5,5',6-Heptachlorobiphenyl\tcis-Prallethrin\ttrans-Prallethrin\tcis-Resmethrin\ttrans-Resmethrin\tcis-Tetramethrin\ttrans-Tetramethrin\tBifenthrin\tFenpropathrin\tcis-Phenothrin\ttrans-Phenothrin\tcis-Cyphenothrin\ttrans-Cyphenothrin\tFlucythrinate_isomer1\tFlucythrinate_isomer2\tcis-Fenvalerate\ttrans-Fenvalerate\tDeltamethrin\tChlorpyrifos oxon\tlambda-Cyhalothrin\tTefluthrin\tTransfluthrin\tcis-Permethrin\ttrans-Permethrin\tcis-Allethrin\ttrans-Allethrin\tcis-Cypermethrin_isomer1\ttrans-Cypermethrin_isomer1\tcis-Cypermethrin_isomer2\ttrans-Cypermethrin_isomer2\tcis-Cyfluthrin_isomer1\ttrans-Cyfluthrin_isomer1\tcis-Cyfluthrin_isomer2\ttrans-Cyfluthrin_Isomer2\t1,2,3,4,7,8-Hexachlorodibenzo-p-dioxin\t1,2,3,4,6,7,8-Heptachlorodibenzo-p-dioxin\tOctachlorodibenzo-p-dioxin\tOctachlorodibenzofuran\t1,2,3,7,8-Pentachlorodibenzofuran\t1,2,3,4,7,8-Hexachlorodibenzofuran\t1,2,3,4,6,7,8-Heptachlorodibenzofuran\t2,3,7,8-Tetrachlorodibenzofuran\t2,3,7,8-Tetrachlorodibenzo-p-dioxin\t1,2,3,7,8-Pentachlorodibenzo-p-dioxin\t2,3,4,5-Tetrabromo-6-chlorotoluene\t2,3,4,5,6-Pentabromotoluene\t2,3,4,5,6-Pentabromoethylbenzene\t2,3,5,6-Tetrabromo-p-xylene\tAllyl 2,4,6-tribromophenyl ether\t2-Bromoallyl(2,4,6-tribromophenyl) ether\tPentabromobenzene\tHexabromobenzene\t2,3,4,5,6-Pentabromobenzyl alcohol\t2-Ethylhexyl 2,3,4,5-Tetrabromobenzoate\tsyn-Dechlorane plus\tanti-Dechlorane plus\talpha-1,2-Dibromo-4-(1,2-dibromoethyl)cyclohexane\tbeta-1,2-Dibromo-4-(1,2-dibromoethyl)cyclohexane\t1,2,5,6-Tetrabromocyclooctane\t1,1-Dibromo-2,3,3,4,4,5-hexachloro-2-cyclopenta-2,4-dien-1-ylcyclooctane\talpha-Amylcinnamaldehyde\ttrans-Cinnamaldehyde\tCitral (Geranial)\t1-Fluronaphthalene\talpha-Hexylcinnamaldehyde\tLilial\talpha-Amylcinnamyl alcohol\tEugenol\tIsoeugenol\t4-Methoxybenzyl alcohol\tMethyleugenol\tCinnamyl alcohol\tBenzyl alcohol\tEstragole\tBenzyl benzoate\tBenzyl cinnamate\tBenzyl salicylate\tCamphor\tEucalyptol\tCoumarin\tLimonene\tIsomethyl-alpha-ionone\tdelta-Iraldeine\tSafrole\tCashmeran\tCelestolide\tPhantolide\tTonalide\tTraseolide\tGalaxolide\tAldrin\tEndosulfan\tHeptachlor\tcis-Heptachlor epoxide\tEndosulfan sulphate\tEndrin ketone\ttrans-Chlordane\tcis-Chlordane\tEndrin aldehyde\tEndrin\t4,4'-Dichlorodiphenyldichloroethylene\tMethoxychlor\t4,4'-Dichlorodiphenyldichloroethane\t4,4'-Dichlorodiphenyltrichloroethane\tTris(4-tert-butylphenyl) phosphate\tTri-n-butyl-phosphate\tTris(1,3-dichloro-2-propy"..b'39\t11\t10\t27\t32\t19\t34\t20\t25\t21\t47\t11\t36\t46\t25\t47\t36\t44\t37\t31\t33\t34\t39\t61\t9\t23\t30\t44\t15\t19\t21\t18\t18\t22\t14\t18\t22\t21\t24\t17\t16\t24\t29\t34\t31\t22\t45\t37\t26\t34\t36\t12\t12\t17\t49\t22\t30\t29\t13\t22\t57\t14\t33\t16\t17\t18\t22\t12\t6\t8\t17\t10\t55\t34\t40\t15\t9\t13\t49\t34\t22\t35\t7\t10\t19\t18\t26\t45\t23\t47\t38\t22\t19\t20\t7\t13\t37\t23\t7\t30\t22\t7\t12\t55\t52\t41\t39\t26\t37\t8\t12\t18\t16\t36\t32\t19\t31\t17\t2\t6\t35\t40\t19\t35\t29\t20\t16\t35\t47\t16\t31\t35\t18\t20\t19\t38\t24\t42\t27\t28\t17\t25\t60\t19\t20\t20\t34\t28\t36\t11\t16\t19\t14\t27\t21\t20\t13\t17\t30\t46\t75\t36\t3\t29\t10\t23\t45\t31\t21\t35\t18\t34\t10\t28\t51\t61\t56\t48\t62\t16\t8\t11\t44\t68\t80\t78\t26\t13\t88\t56\t85\t72\n+17-beta-Estradiol\t11\t11\t7\t12\t13\t9\t7\t13\t12\t16\t17\t15\t12\t12\t13\t14\t11\t12\t12\t12\t9\t9\t24\t12\t15\t16\t14\t28\t34\t34\t16\t18\t24\t13\t26\t21\t53\t22\t13\t13\t18\t13\t38\t1\t19\t19\t18\t20\t21\t4\t6\t11\t13\t10\t22\t12\t15\t12\t18\t18\t17\t13\t13\t12\t17\t13\t11\t15\t14\t15\t11\t17\t18\t22\t30\t27\t16\t7\t12\t30\t27\t25\t21\t19\t37\t28\t26\t27\t34\t18\t19\t12\t18\t19\t20\t13\t11\t31\t24\t26\t40\t23\t31\t28\t33\t9\t8\t8\t9\t13\t11\t12\t11\t13\t11\t6\t6\t10\t7\t31\t14\t9\t6\t21\t12\t16\t13\t7\t10\t5\t27\t38\t10\t23\t10\t25\t30\t31\t24\t27\t13\t29\t19\t10\t19\t17\t22\t6\t13\t21\t7\t13\t24\t19\t20\t42\t32\t29\t35\t13\t42\t21\t22\t16\t12\t9\t26\t7\t10\t48\t37\t11\t18\t12\t11\t20\t9\t6\t26\t27\t24\t12\t29\t20\t16\t18\t14\t1\t18\t14\t37\t17\t35\t14\t30\t8\t7\t21\t25\t15\t26\t17\t19\t25\t28\t11\t26\t30\t19\t39\t24\t35\t30\t23\t22\t28\t23\t50\t6\t14\t27\t37\t9\t20\t16\t14\t14\t15\t9\t14\t18\t16\t15\t11\t13\t18\t21\t25\t24\t16\t34\t31\t22\t23\t28\t11\t8\t13\t38\t14\t26\t26\t11\t18\t44\t9\t22\t10\t14\t13\t14\t10\t4\t4\t17\t7\t39\t31\t34\t15\t8\t11\t34\t27\t18\t30\t5\t9\t14\t16\t20\t35\t15\t37\t34\t17\t15\t13\t6\t14\t24\t13\t5\t28\t16\t6\t9\t46\t27\t31\t31\t18\t34\t6\t8\t15\t11\t27\t22\t12\t27\t15\t2\t6\t27\t28\t11\t34\t20\t11\t11\t20\t34\t13\t19\t26\t11\t14\t10\t31\t19\t35\t21\t20\t10\t16\t42\t17\t15\t16\t33\t17\t33\t12\t13\t14\t7\t17\t21\t13\t8\t13\t17\t30\t58\t28\t1\t17\t11\t23\t33\t28\t20\t24\t17\t28\t6\t26\t38\t47\t46\t41\t47\t12\t7\t11\t32\t50\t63\t63\t24\t9\t56\t67\t62\t60\n+Progesterone\t18\t10\t17\t16\t18\t13\t10\t14\t12\t23\t35\t19\t16\t13\t18\t17\t12\t13\t14\t13\t11\t10\t31\t14\t24\t28\t21\t46\t42\t64\t23\t38\t56\t21\t50\t27\t103\t32\t16\t21\t19\t28\t71\t2\t45\t42\t44\t42\t43\t12\t10\t24\t26\t24\t35\t20\t25\t19\t19\t22\t20\t25\t24\t21\t26\t18\t20\t21\t20\t20\t13\t18\t40\t51\t55\t48\t34\t21\t15\t59\t47\t45\t54\t47\t59\t48\t43\t55\t63\t38\t28\t21\t31\t24\t30\t47\t39\t52\t47\t51\t74\t42\t53\t52\t67\t20\t18\t14\t15\t16\t17\t20\t20\t17\t16\t13\t9\t18\t11\t61\t23\t13\t8\t51\t31\t22\t22\t15\t21\t15\t40\t48\t14\t43\t13\t40\t38\t39\t38\t39\t24\t43\t28\t16\t27\t19\t33\t8\t21\t33\t9\t24\t31\t31\t28\t65\t42\t40\t45\t16\t57\t50\t68\t27\t29\t21\t55\t17\t22\t112\t78\t29\t29\t23\t24\t30\t10\t15\t50\t41\t41\t17\t57\t44\t32\t32\t21\t5\t26\t37\t84\t30\t44\t22\t44\t11\t9\t29\t38\t20\t34\t23\t26\t42\t56\t15\t45\t68\t29\t62\t46\t58\t61\t34\t42\t41\t57\t81\t10\t30\t39\t56\t27\t24\t26\t28\t26\t28\t24\t21\t21\t22\t26\t20\t20\t21\t39\t45\t40\t22\t55\t39\t29\t43\t51\t12\t15\t25\t68\t25\t43\t42\t18\t20\t77\t14\t47\t24\t20\t18\t26\t14\t7\t9\t22\t14\t80\t44\t49\t19\t13\t10\t54\t34\t20\t43\t10\t14\t28\t20\t35\t59\t27\t58\t49\t31\t10\t24\t6\t15\t43\t34\t11\t40\t29\t9\t14\t83\t52\t50\t44\t35\t44\t9\t13\t21\t23\t44\t37\t27\t35\t19\t7\t16\t42\t52\t15\t46\t49\t34\t21\t52\t69\t18\t47\t44\t16\t37\t29\t51\t33\t52\t40\t38\t21\t30\t91\t23\t22\t29\t46\t36\t44\t14\t22\t31\t27\t32\t32\t28\t20\t28\t44\t59\t103\t43\t9\t33\t24\t44\t63\t43\t34\t55\t36\t52\t15\t43\t80\t101\t84\t86\t100\t16\t9\t14\t80\t81\t125\t95\t29\t13\t85\t62\t168\t125\n+Testosterone\t14\t8\t13\t13\t15\t12\t10\t14\t12\t24\t36\t18\t16\t10\t17\t16\t9\t9\t10\t9\t10\t9\t28\t12\t22\t25\t19\t44\t39\t48\t22\t35\t46\t19\t38\t25\t101\t27\t15\t18\t17\t26\t51\t2\t38\t36\t39\t37\t37\t8\t6\t20\t22\t21\t25\t18\t21\t16\t17\t15\t18\t23\t24\t19\t21\t15\t15\t16\t16\t16\t9\t15\t39\t46\t43\t44\t29\t20\t10\t46\t37\t36\t40\t34\t43\t36\t30\t41\t51\t33\t19\t20\t24\t17\t22\t41\t35\t38\t33\t36\t65\t34\t39\t36\t52\t13\t12\t10\t11\t11\t11\t13\t14\t14\t11\t7\t3\t10\t5\t51\t19\t7\t3\t41\t25\t19\t16\t11\t17\t14\t35\t48\t14\t41\t15\t35\t37\t37\t38\t37\t22\t44\t26\t15\t29\t16\t29\t8\t21\t32\t10\t24\t32\t30\t28\t63\t38\t34\t42\t16\t49\t41\t46\t19\t20\t15\t44\t13\t16\t91\t63\t24\t21\t19\t20\t27\t10\t13\t32\t27\t27\t15\t51\t30\t21\t27\t19\t3\t23\t35\t72\t29\t44\t18\t37\t8\t8\t26\t33\t17\t31\t21\t23\t32\t47\t13\t44\t56\t28\t60\t39\t52\t60\t37\t39\t38\t48\t78\t10\t26\t40\t49\t24\t22\t22\t24\t21\t24\t18\t15\t17\t18\t21\t15\t17\t17\t33\t39\t35\t18\t48\t38\t29\t39\t42\t12\t14\t18\t60\t23\t36\t36\t16\t16\t61\t13\t42\t21\t19\t16\t26\t14\t7\t8\t19\t14\t64\t41\t42\t19\t12\t11\t46\t34\t19\t40\t7\t15\t27\t20\t29\t49\t27\t55\t41\t30\t10\t21\t6\t15\t38\t28\t12\t37\t28\t7\t14\t75\t37\t43\t43\t33\t43\t9\t12\t20\t14\t39\t33\t21\t33\t18\t5\t13\t41\t45\t10\t44\t44\t28\t20\t43\t57\t15\t41\t38\t15\t30\t27\t46\t30\t49\t39\t36\t20\t27\t70\t22\t20\t25\t44\t27\t45\t13\t18\t26\t18\t26\t30\t21\t18\t25\t34\t45\t86\t38\t7\t24\t22\t32\t50\t37\t25\t48\t34\t47\t14\t37\t66\t81\t71\t74\t84\t15\t8\t12\t68\t60\t96\t82\t27\t13\t72\t60\t125\t130\n' |
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/similarity/matches_test5_out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/matches_test5_out.tsv Tue Mar 22 16:07:32 2022 +0000 |
| b |
| b'@@ -0,0 +1,175 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|
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/similarity/matches_test6_out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/matches_test6_out.tsv Tue Mar 22 16:07:32 2022 +0000 |
| [ |
| b'@@ -0,0 +1,387 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A\t1\t1\t0\t2\t5\t0\t1\t0\t2\t2\t3\t1\t5\t2\t12\t0\t3\t0\t2\t4\t4\t3\t4\t0\t2\t0\t3\t1\t3\t1\t3\t1\t2\t2\t5\t5\t4\t6\t2\t5\t1\t2\t2\t0\t0\t3\t1\t1\t9\t6\t0\t2\t2\t17\t6\t7\t0\t1\t9\t1\t4\t3\t14\t5\t6\t1\t2\t0\t0\t1\t0\t1\t14\t1\t5\t2\t1\t0\t1\t3\t2\t3\t1\t0\t3\t5\t3\t4\t1\t3\t3\t1\t10\t1\t0\t1\t1\t0\t2\t1\t1\t5\t3\t2\t1\t0\t0\t1\t1\t3\t1\t1\t0\t0\t0\t2\t11\t3\t6\t2\t1\t1\t2\t1\t1\t4\t2\t3\t3\t10\t4\t3\t3\t1\t2\t0\t0\t6\n+4-tert-Octylphenol\t1\t3\t0\t3\t3\t1\t2\t0\t1\t0\t2\t0\t3\t2\t5\t0\t0\t0\t1\t0\t1\t1\t1\t0\t0\t0\t0\t1\t0\t1\t0\t1\t2\t1\t1\t0\t0\t1\t1\t2\t0\t2\t0\t0\t0\t1\t1\t1\t2\t0\t0\t0\t1\t3\t3\t5\t1\t1\t5\t0\t0\t0\t0\t4\t3\t0\t0\t0\t0\t0\t0\t0\t3\t1\t0\t0\t2\t0\t0\t0\t0\t1\t0\t0\t0\t0\t2\t1\t0\t0\t0\t0\t2\t0\t0\t1\t0\t0\t0\t0\t1\t0\t0\t1\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t1\t1\t6\t1\t6\t0\t1\t0\t2\t0\t2\t1\t2\t3\t2\t4\t0\t1\t1\t0\t2\t0\t1\t1\n+Estrone\t12\t5\t4\t6\t11\t8\t5\t4\t7\t6\t3\t5\t20\t12\t23\t7\t6\t3\t5\t10\t7\t12\t8\t8\t4\t0\t4\t4\t9\t2\t4\t6\t11\t4\t6\t14\t6\t19\t5\t6\t4\t17\t5\t4\t2\t5\t6\t5\t14\t8\t1\t2\t3\t36\t14\t16\t3\t2\t31\t5\t9\t5\t38\t11\t11\t6\t6\t2\t3\t2\t2\t3\t49\t15\t9\t3\t2\t2\t1\t5\t1\t10\t7\t0\t5\t8\t5\t8\t4\t11\t7\t1\t27\t7\t2\t1\t2\t1\t3\t3\t6\t6\t11\t23\t2\t2\t2\t2\t6\t11\t5\t1\t2\t0\t2\t7\t32\t14\t21\t4\t4\t5\t7\t3\t6\t9\t4\t8\t4\t20\t2\t4\t4\t9\t7\t3\t2\t8\n+17-beta-Estradiol\t7\t2\t4\t4\t4\t3\t4\t1\t8\t3\t4\t6\t18\t7\t14\t5\t6\t3\t5\t8\t10\t10\t7\t5\t5\t0\t4\t4\t10\t4\t4\t3\t7\t4\t5\t12\t8\t16\t3\t3\t3\t12\t3\t2\t2\t3\t6\t3\t9\t8\t2\t2\t3\t33\t10\t9\t5\t2\t25\t5\t8\t6\t36\t8\t9\t5\t3\t3\t0\t1\t1\t4\t40\t8\t7\t1\t1\t1\t0\t2\t0\t6\t2\t0\t5\t8\t3\t9\t2\t9\t5\t1\t23\t7\t2\t2\t1\t1\t3\t1\t4\t6\t7\t17\t1\t2\t0\t2\t5\t9\t4\t1\t2\t0\t1\t4\t26\t9\t13\t4\t4\t4\t4\t1\t2\t6\t4\t3\t3\t12\t0\t1\t3\t4\t5\t1\t2\t5\n+Progesterone\t19\t7\t5\t11\t15\t11\t8\t1\t9\t6\t9\t7\t30\t15\t19\t7\t9\t5\t16\t11\t17\t21\t6\t10\t7\t0\t4\t7\t14\t10\t6\t10\t15\t5\t11\t15\t9\t40\t12\t11\t5\t23\t6\t4\t3\t6\t8\t7\t5\t11\t3\t3\t5\t51\t21\t30\t8\t7\t50\t8\t11\t11\t74\t17\t15\t8\t8\t7\t6\t3\t5\t11\t69\t20\t23\t7\t4\t3\t2\t3\t0\t18\t7\t3\t6\t10\t7\t12\t5\t15\t10\t3\t46\t12\t3\t8\t3\t3\t5\t6\t11\t16\t19\t32\t2\t1\t2\t5\t9\t17\t7\t1\t2\t0\t1\t10\t73\t29\t28\t4\t9\t5\t11\t15\t9\t9\t8\t9\t5\t20\t1\t5\t7\t6\t8\t3\t5\t11\n+Testosterone\t16\t7\t2\t9\t14\t10\t6\t0\t8\t6\t7\t8\t24\t12\t13\t7\t6\t5\t12\t12\t19\t19\t2\t11\t4\t0\t3\t6\t10\t11\t7\t7\t13\t3\t9\t9\t11\t34\t10\t8\t4\t23\t4\t4\t2\t4\t7\t4\t3\t9\t3\t2\t3\t42\t11\t27\t4\t4\t41\t5\t11\t10\t55\t12\t14\t6\t7\t3\t3\t2\t2\t8\t47\t17\t17\t4\t2\t1\t1\t4\t0\t13\t7\t2\t6\t7\t4\t9\t2\t11\t5\t1\t33\t7\t3\t6\t1\t2\t7\t4\t10\t10\t16\t26\t1\t2\t3\t4\t9\t13\t6\t1\t4\t0\t1\t6\t69\t21\t25\t3\t6\t4\t6\t11\t4\t9\t7\t7\t3\t16\t1\t3\t3\t5\t6\t3\t5\t8\n' |
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/similarity/recetox_gc-ei_ms_20201028.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/recetox_gc-ei_ms_20201028.msp Tue Mar 22 16:07:32 2022 +0000 |
| [ |
| b'@@ -0,0 +1,31986 @@\n+NAME: Perylene_2H12\r\n+SCANNUMBER: -1\r\n+RETENTIONTIME: -1\r\n+RETENTIONINDEX: 2876\r\n+PRECURSORMZ: 264.16858\r\n+PRECURSORTYPE: [M]+\r\n+IONMODE: Positive\r\n+SPECTRUMTYPE: Centroid\r\n+FORMULA: C20H12\r\n+INCHIKEY: CSHWQDPOILHKBI-AQZSQYOVSA-N\r\n+INCHI: \r\n+SMILES: [2H]C1=C(C2=C3C(=C1[2H])C4=C(C(=C(C5=C4C(=C(C(=C5[2H])[2H])[2H])C3=C(C(=C2[2H])[2H])[2H])[2H])[2H])[2H])[2H]\r\n+AUTHORS: Price et al., RECETOX, Masaryk University (CZ)\r\n+COLLISIONENERGY: 70eV\r\n+INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS\r\n+INSTRUMENTTYPE: GC-EI-Orbitrap\r\n+IONIZATION: EI+\r\n+LICENSE: CC BY-NC\r\n+COMMENT: \r\n+Num Peaks: 33\r\n+116.05576\t29277\r\n+118.06992\t49651\r\n+128.0558\t37001\r\n+130.06996\t78584\r\n+130.57159\t17533\r\n+132.08408\t65686\r\n+132.5858\t12593\r\n+207.0322\t39569\r\n+222.08282\t13141\r\n+223.06346\t20762\r\n+225.04277\t18058\r\n+227.02202\t26370\r\n+232.11204\t30354\r\n+236.1405\t22796\r\n+252.09322\t8564\r\n+256.11212\t41765\r\n+257.11557\t8688\r\n+258.12622\t21742\r\n+259.13446\t11564\r\n+260.14041\t248997\r\n+261.14358\t51721\r\n+262.15466\t33597\r\n+263.16254\t63732\r\n+264.16858\t829577\r\n+265.01968\t18286\r\n+265.17191\t176460\r\n+266.17523\t18876\r\n+283.03036\t10261\r\n+287.00632\t11352\r\n+295.10288\t26727\r\n+299.06152\t33379\r\n+359.0282\t67046\r\n+400.98447\t17406\r\n+\r\n+NAME: Perylene\r\n+SCANNUMBER: -1\r\n+RETENTIONTIME: -1\r\n+RETENTIONINDEX: 2886.9\r\n+PRECURSORMZ: 252.09323\r\n+PRECURSORTYPE: [M]+\r\n+IONMODE: Positive\r\n+SPECTRUMTYPE: Centroid\r\n+FORMULA: C20H12\r\n+INCHIKEY: CSHWQDPOILHKBI-UHFFFAOYSA-N\r\n+INCHI: \r\n+SMILES: C1=CC2=C3C(=C1)C1=CC=CC4=C1C(=CC=C4)C3=CC=C2\r\n+AUTHORS: Price et al., RECETOX, Masaryk University (CZ)\r\n+COLLISIONENERGY: 70eV\r\n+INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS\r\n+INSTRUMENTTYPE: GC-EI-Orbitrap\r\n+IONIZATION: EI+\r\n+LICENSE: CC BY-NC\r\n+COMMENT: \r\n+Num Peaks: 19\r\n+112.03071\t49892\r\n+113.03854\t87510\t"Theoretical m/z 113.039125, Mass diff 0 (0 ppm), Formula C9H5"\r\n+124.03076\t100146\r\n+124.53242\t24923\r\n+125.03855\t179254\t"Theoretical m/z 125.039125, Mass diff 0 (0 ppm), Formula C10H5"\r\n+125.54019\t49039\r\n+126.04636\t131679\r\n+126.54804\t36313\r\n+222.04645\t28905\r\n+224.06192\t55632\r\n+226.04175\t37413\r\n+246.04646\t23286\r\n+248.06204\t140007\r\n+249.07072\t62236\t"Theoretical m/z 249.070425, Mass diff -0.001 (0 ppm), Formula C20H9"\r\n+250.07765\t641789\r\n+251.07967\t137600\r\n+252.09323\t1955166\t"Theoretical m/z 252.093354, Mass diff 0 (0.49 ppm), SMILES C1=CC=2C=CC=C3C4=CC=CC5=CC=CC(C(=C1)C23)=C54, Annotation [C20H12]+, Rule of HR False"\r\n+253.09656\t402252\r\n+254.09985\t39987\r\n+\r\n+NAME: Phenanthrene_2H10\r\n+SCANNUMBER: -1\r\n+RETENTIONTIME: -1\r\n+RETENTIONINDEX: 1827.1\r\n+PRECURSORMZ: 188.14029\r\n+PRECURSORTYPE: [M]+\r\n+IONMODE: Positive\r\n+SPECTRUMTYPE: Centroid\r\n+FORMULA: C14H10\r\n+INCHIKEY: YNPNZTXNASCQKK-LHNTUAQVSA-N\r\n+INCHI: \r\n+SMILES: [2H]C1=C(C(=C2C(=C1[2H])C(=C(C3=C(C(=C(C(=C32)[2H])[2H])[2H])[2H])[2H])[2H])[2H])[2H]\r\n+AUTHORS: Price et al., RECETOX, Masaryk University (CZ)\r\n+COLLISIONENERGY: 70eV\r\n+INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS\r\n+INSTRUMENTTYPE: GC-EI-Orbitrap\r\n+IONIZATION: EI+\r\n+LICENSE: CC BY-NC\r\n+COMMENT: \r\n+Num Peaks: 17\r\n+76.02767\t185421\r\n+78.0418\t256858\r\n+80.05586\t881271\r\n+90.04181\t200162\r\n+92.06206\t537968\r\n+94.06999\t628791\r\n+156.08402\t836513\r\n+158.09808\t477819\r\n+160.11218\t2421148\r\n+161.11554\t310248\r\n+176.10866\t308983\r\n+184.11224\t2784543\r\n+185.11562\t445833\r\n+186.12637\t1283282\r\n+188.14029\t15115275\r\n+189.1436\t2312386\r\n+190.14688\t151400\r\n+\r\n+NAME: Phenanthrene\r\n+SCANNUMBER: -1\r\n+RETENTIONTIME: -1\r\n+RETENTIONINDEX: 1832.9\r\n+PRECURSORMZ: 178.0775\r\n+PRECURSORTYPE: [M]+\r\n+IONMODE: Positive\r\n+SPECTRUMTYPE: Centroid\r\n+FORMULA: C14H10\r\n+INCHIKEY: YNPNZTXNASCQKK-UHFFFAOYSA-N\r\n+INCHI: \r\n+SMILES: C1=CC2=C(C=C1)C1=C(C=CC=C1)C=C2\r\n+AUTHORS: Price et al., RECETOX, Masaryk University (CZ)\r\n+COLLISIONENERGY: 70eV\r\n+INSTRUMENT: Q Exactive GC Orbitrap GC-MS/MS\r\n+INSTRUMENTTYPE: GC-EI-Orbitrap\r\n+IONIZATION: EI+\r\n+LICENSE: CC BY-NC\r\n+COMMENT: \r\n+Num Peaks: 19\r\n+74.01508\t137808\t"Theoretical m/z 74.01565, Mass diff 0 (0 ppm), Formula C6H2"\r\n+75.02295\t278714\t"Theoretical m/z 75.023475, Mass diff 0 (0 ppm), Formula C6H3"\r\n+76.03075\t6'..b'pm), SMILES C=C2CCC1CC(C)CCC1C2(C)C, Annotation [C14H24-7H]+, Rule of HR True"\r\n+187.14806\t422332\t"Theoretical m/z 187.148122, Mass diff 0 (0.33 ppm), SMILES CC2CCC1C(CCCC1(C)(C))C2(C), Annotation [C14H26-7H]+, Rule of HR True"\r\n+188.1559\t151252\t"Theoretical m/z 188.155947, Mass diff 0 (0.25 ppm), SMILES CC2CCC1C(CCCC1(C)(C))C2(C), Annotation [C14H26-6H]+, Rule of HR False"\r\n+189.12735\t68862\t"Theoretical m/z 189.127389, Mass diff 0 (0.21 ppm), SMILES O=C2C=C1CCCC(CC)C1(C)CC2, Annotation [C13H20O-3H]+, Rule of HR True"\r\n+189.16364\t163919\t"Theoretical m/z 189.163772, Mass diff 0 (0.7 ppm), SMILES CC2CCC1C(CCCC1(C)(C))C2(C), Annotation [C14H26-5H]+, Rule of HR True"\r\n+190.13504\t97146\r\n+195.11685\t57370\t"Theoretical m/z 195.117375, Mass diff 0 (0 ppm), Formula C15H15"\r\n+197.13249\t50230\t"Theoretical m/z 197.132481, Mass diff 0 (0.04 ppm), SMILES C=C3CCC2C(CCC1CCCC12)C3C, Annotation [C15H24-7H]+, Rule of HR True"\r\n+199.14803\t221936\t"Theoretical m/z 199.148122, Mass diff 0 (0.46 ppm), SMILES C=C2CCC1C(C)C(C)CCC1C2(C)C, Annotation [C15H26-7H]+, Rule of HR True"\r\n+200.15579\t108028\r\n+201.16364\t216321\t"Theoretical m/z 201.163772, Mass diff 0 (0.65 ppm), SMILES C=C2CCC1C(C)C(C)CCC1C2(C)C, Annotation [C15H26-5H]+, Rule of HR True"\r\n+202.17162\t208618\r\n+203.14304\t1200123\t"Theoretical m/z 203.143035, Mass diff 0 (0.02 ppm), SMILES OC3CCC2C3(CCC1C(C)CCCC12), Annotation [C14H24O-5H]+, Rule of HR True"\r\n+204.14627\t283454\r\n+206.16646\t32118\r\n+209.13243\t45976\t"Theoretical m/z 209.133026, Mass diff 0 (0 ppm), Formula C16H17"\r\n+211.14809\t272618\t"Theoretical m/z 211.148132, Mass diff 0 (-0.2 ppm), SMILES CC1=C(C)C2=C([CH+]CCC=C(C)\\C=C/2)C=C1, Annotation [C16H19]+, Rule of HR True"\r\n+212.15134\t57168\r\n+213.16373\t355360\t"Theoretical m/z 213.163773, Mass diff 0 (-0.2 ppm), SMILES CC1=C(C)C2=C([CH+]CCC=C(C)CC2)C=C1, Annotation [C16H21]+, Rule of HR True"\r\n+214.16698\t92310\r\n+215.143\t60304\t"Theoretical m/z 215.143035, Mass diff 0 (0.16 ppm), SMILES OC3CCC2C3(CCC1C(C(=C)CCC12)C), Annotation [C15H24O-5H]+, Rule of HR True"\r\n+216.15102\t55312\r\n+217.15874\t113508\t"Theoretical m/z 217.158691, Mass diff 0 (0.23 ppm), SMILES OC3CCC2C3(CCC1C2(CCCC1(C)(C))), Annotation [C15H26O-5H]+, Rule of HR True"\r\n+218.16704\t51076\r\n+226.17177\t37673\r\n+227.1797\t204277\t"Theoretical m/z 227.179433, Mass diff 0 (1.18 ppm), SMILES C=C2CCC1C(CC)C(C)CCC1C2(C)CC, Annotation [C17H30-7H]+, Rule of HR True"\r\n+228.1873\t842856\r\n+229.1588\t359919\t"Theoretical m/z 229.158691, Mass diff 0 (0.48 ppm), SMILES OC3CCC2C3(CCC1C2(CCC(=C)C1(C)(C))), Annotation [C16H26O-5H]+, Rule of HR True"\r\n+230.16186\t41138\r\n+231.17433\t428563\t"Theoretical m/z 231.174335, Mass diff 0 (0.02 ppm), SMILES O=C3C=C2CCC1C(C)CCCC1C2(C)CC3, Annotation [C16H24O-H]+, Rule of HR True"\r\n+232.17703\t61957\r\n+237.16373\t184777\t"Theoretical m/z 237.164326, Mass diff 0 (0 ppm), Formula C18H21"\r\n+238.16693\t38109\r\n+241.15854\t66162\t"Theoretical m/z 241.158691, Mass diff 0 (0.62 ppm), SMILES O=C3C=C2CCC1C(CC)CCCC1C2(C)CC3, Annotation [C17H26O-5H]+, Rule of HR True"\r\n+242.16649\t51489\r\n+245.19052\t102650\t"Theoretical m/z 245.189996, Mass diff 0.001 (2.14 ppm), SMILES OC1CCC2C3CCC(=C)C(C)(C)C3(CCC12(C)), Annotation [C17H28O-3H]+, Rule of HR True"\r\n+246.19786\t1126362\r\n+247.2011\t212107\r\n+252.18724\t143505\r\n+255.17436\t288345\t"Theoretical m/z 255.174341, Mass diff 0 (0.08 ppm), SMILES O=C3C=C2CCC1C4CCCC4(CCC1C2(C)CC3), Annotation [C18H26O-3H]+, Rule of HR True"\r\n+256.17764\t54890\r\n+259.16943\t50245\t"Theoretical m/z 259.169244, Mass diff 0 (0.72 ppm), SMILES O=C3C=C2CCC1C(C)C(CO)CCC1C2(C)CC3, Annotation [C17H26O2-3H]+, Rule of HR True"\r\n+260.17758\t70396\r\n+270.19791\t397018\r\n+271.20062\t89701\r\n+273.18549\t199263\t"Theoretical m/z 273.184894, Mass diff 0.001 (2.18 ppm), SMILES O=C3C=C2CCC1C4CCC(O)C4(CCC1C2(C)CC3), Annotation [C18H26O2-H]+, Rule of HR True"\r\n+274.18863\t88305\r\n+288.20841\t1123316\t"Theoretical m/z 288.208375, Mass diff 0 (0.12 ppm), SMILES O=C4C=C3CCC1C(CCC2(C)(C(O)CCC12))C3(C)CC4, Annotation [C19H28O2]+, Rule of HR False"\r\n+289.21173\t220898\r\n+\r\n+\r\n' |
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/similarity/scores_test1_out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/scores_test1_out.tsv Tue Mar 22 16:07:32 2022 +0000 |
| b |
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|
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/similarity/scores_test3_out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/scores_test3_out.tsv Tue Mar 22 16:07:32 2022 +0000 |
| b |
| b'@@ -0,0 +1,387 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53443328694\t0.005947519671344408\t0.0\t0.0005356814581771544\t0.006215857342936553\t0.0\t0.009417667003961789\t0.009918679539108183\t0.00023339501999512072\t0.02671768716952186\t0.00030790986345821436\t0.0\t0.0\t0.0013743163821902838\t0.01723317359032806\t0.0\t0.031565466787107484\t0.012448459343477094\t0.0\t0.007750527312298496\t0.0070234525583043545\t0.02059761160321701\t0.023913761352649478\t0.011281962106545012\t1.6426994248357484e-05\t0.0\t0.03697516657930819\t0.033662224880288756\t0.0\t0.0\t0.023540677910418206\t0.0\t0.036138976947232074\t0.02542494090112982\t0.0\t0.0\t0.011503400057545196\t0.0\t0.00020822196303031898\t0.0\t0.0\t0.0\t0.0\t0.0014763317286047445\t0.0\t0.0012583838846539634\t0.0\t0.003999037208194656\t0.013710430439412245\t0.0013524730258847118\t0.007867754340786993\t0.040527384587716785\t0.010996257146538806\t0.0\t0.0\t0.06835446607134321\t0.0\t0.0\t0.008591363167784043\t0.0\t0.0\t0.0\t0.0\t0.0\t0.007090284250167511\t0.008465564938609326\t0.08040814196887734\t0.0\t0.028294996723359764\t0.0\t0.0\t0.0038398141926578064\t0.16023981186600048\t0.04805946943116568\t0.037035561711554706\t0.0\t0.0005120942309216829\t0.0\t0.0\t0.03494182656191998\t0.0\t0.0\t0.027888357150312005\t0.01258535522221259\t0.03740123828771993\t0.008517825868349588\t0.00913703375472102\t0.0\t0.0\t0.0\t0.0\t0.0\t0.029300775267851735\t0.0\t0.0\t0.0\t0.01295087988307018\t0.0005955124138932553\t0.0\t0.0\t0.0\t0.005304965226057589\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.039134050766579234\t0.2714869727438596\t0.003527160692631183\t0.0\t0.0\t0.020497841819279862\t0.0\t0.002511329287084922\t0.0\t0.3500845873047567\t0.0\t0.002239902702309837\t0.0\t0.005491138035803363\t0.0\t0.0\t0.011672805021412769\t0.02568290039984708\t0.07006608189710377\t0.018632962351792192\t0.0\t0.04153373284622605\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.00786791970310509\t0.0\t0.047481418502903334\t0.0\t0.0\t0.0\t0.10974594417370813\t0.034291658672408076\t0.0\t0.023165391809283516\t0.0\t0.0\t0.0\t0.0002833417563650782\t0.0\t0.0\t0.0\t0.026807362599866824\t0.003975994609085822\t0.0\t0.0\t0.0\t0.0\t0.0\t0.06458445415629567\t0.013061309028202963\t0.0\t0.0\n+Testosterone\t0.00963321193050066\t0.00024864315729290006\t0.0\t0.00023222574210458811\t0.0009261428396286391\t0.0\t0.0\t0.00040034384039336243\t0.0\t6.734322542065858e-05\t0.0016889974488375878\t0.0\t0.1780813812315969\t0.007271975837211051\t0.0001534940265342155\t0.027912903539727703\t0.0\t0.0\t0.0\t0.0005797401705402813\t0.01109882605223559\t0.0\t0.024485309434567656\t0.020836980610370613\t0.0\t0.004730656796420955\t0.009055625850088012\t0.01764485751937845\t0.0342974876068616\t0.003171910470299864\t0.0\t0.0\t0.039580956813763224\t0.008699485073663131\t0.0\t0.0\t0.027921629937492445\t0.0\t0.011883152521337894\t0.00473955367711716\t0.0\t0.0\t0.06041370798509162\t0.0\t0.042697154051077546\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0028714022903154834\t0.021418156386493012\t0.0015186515255164064\t0.006270179831850896\t0.029915893967898583\t0.00688460931497788\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.001333543171051696\t0.0\t0.08702752210600657\t0.0\t0.03171198034450119\t0.0\t0.0\t0.0\t0.0\t0.0007660193758873158\t0.010813507002141582\t0.0\t0.0\t0.0\t0.0\t0.004200894168035819\t0.0\t0.0\t0.02349484368553467\t0.01816654272894712\t0.06339867284692742\t0.00859117181156952\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.11646566920503162\t0.0\t0.0\t0.0\t0.0\t0.0031342530947578136\t0.0\t0.15489171142643712\t0.0\t0.013048242174815912\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.001658310433454475\t0.03949452321180806\t0.0\t0.0\t0.0\t0.021990926351807643\t0.0\t0.13014922112429483\t0.0\t0.18331721895001493\t0.0\t0.0014411200837741657\t0.0\t0.0\t0.0\t0.0\t0.010921053413542842\t0.00943243671087211\t0.06421886680272976\t0.025882956568067213\t0.0\t0.03618383380922253\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0006655628265325035\t0.0\t0.026485058850513155\t0.0\t0.0\t0.0\t0.10783284756046711\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.12344754627650137\t0.0\t0.0\t0.0\n' |
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/similarity/scores_test4_out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/scores_test4_out.tsv Tue Mar 22 16:07:32 2022 +0000 |
| [ |
| b"@@ -0,0 +1,387 @@\n+\tPerylene_2H12\tPerylene\tPhenanthrene_2H10\tPhenanthrene\tAnthracene\tAcenaphthylene\tAcenaphthene\tFluoranthene\tPyrene\tpara-Terphenyl\tRetene\tBenzo[b]naphtho[2,1-d]thiophene\t2,3-Benzofluorene\tBenzo[ghi]fluoranthene\tTriphenylene\tBenzanthracene/Benzophenanthrene\tBenzofluoranthene\tBenzo(k)fluoranthene\tBenzo[e]pyrene\tBenzo(a)pyrene\tIndeno[1,2,3-cd]pyrene\tBenzo(g,h,i)perylene\tAnthanthrene\tDibenzanthracene\tCoronene\tDicofol\tBenzophenone\t2-tert-Butyl-4-methoxyphenol\tButylated hydroxytoluene\tBumetrizole\t4-Methylbenzophenone\t2,4,6-Tribromophenol\t2,6-Dichloro-4-nitroaniline\t1-Methylphenanthrene\tTriclosan\tDrometrizole\tEnzacamene\t2,4-Di-tert-butyl-6-(5-chloro-2H-benzotriazol-2-yl)phenol\tOctrizole\t1,2,7,9-Tetrachlorodibenzofuran\t2,2',3,4,5,5',6-Heptachlorobiphenyl\t2,4,6-Trichlorobiphenyl\t2,2',3,3',4,5',6,6'-Octachlorobiphenyl\tMirex\tbeta-Hexachlorocyclohexane\talpha-1,2,3,4,5,6-Hexachlorocyclohexane\tLindane\tdelta-Hexachlorocyclohexane\tepsilon-Hexachlorocyclohexane\tPentachlorobenzene\tHexachlorobenzene\t2,4'-Dichlorodiphenyldichloroethylene\t2,4'-Dichlorodiphenyldichloroethane\t2,4'-Dichlorodiphenyltrichloroethane\t1,2,7,9-Tetrachlorodibenzo-p-dioxin\t2,4,4'-Trichlorobiphenyl\t2,2',4,5,5'-Pentachlorobiphenyl\t2,3',4,4',5-Pentachlorobiphenyl\t2,2',3,4,4',5'-Hexachlorobiphenyl\t2,2',4,4',5,5'-Hexachlorobiphenyl\t2,2',3,4,4',5,5'-Heptachlorobiphenyl\t2,2',5,5'-Tetrachlorobiphenyl\t2,3',4,6-Tetrachlorobiphenyl\t2,3',5',6-Tetrachlorobiphenyl\t2,2',3,4',5-Pentachlorobiphenyl\t2,3,3',4,5-Pentachlorobiphenyl\t3,3',4,5,5'-Pentachlorobiphenyl\t2,3',4,4',5',6-Hexachlorobiphenyl\t2,3,3',4,5,6-Hexachlorobiphenyl\t2,3,3',4',5',6-Hexachlorobiphenyl\t2,3,3',4',5,6-Hexachlorobiphenyl\t2,3,3',4',5,5',6-Heptachlorobiphenyl\tcis-Prallethrin\ttrans-Prallethrin\tcis-Resmethrin\ttrans-Resmethrin\tcis-Tetramethrin\ttrans-Tetramethrin\tBifenthrin\tFenpropathrin\tcis-Phenothrin\ttrans-Phenothrin\tcis-Cyphenothrin\ttrans-Cyphenothrin\tFlucythrinate_isomer1\tFlucythrinate_isomer2\tcis-Fenvalerate\ttrans-Fenvalerate\tDeltamethrin\tChlorpyrifos oxon\tlambda-Cyhalothrin\tTefluthrin\tTransfluthrin\tcis-Permethrin\ttrans-Permethrin\tcis-Allethrin\ttrans-Allethrin\tcis-Cypermethrin_isomer1\ttrans-Cypermethrin_isomer1\tcis-Cypermethrin_isomer2\ttrans-Cypermethrin_isomer2\tcis-Cyfluthrin_isomer1\ttrans-Cyfluthrin_isomer1\tcis-Cyfluthrin_isomer2\ttrans-Cyfluthrin_Isomer2\t1,2,3,4,7,8-Hexachlorodibenzo-p-dioxin\t1,2,3,4,6,7,8-Heptachlorodibenzo-p-dioxin\tOctachlorodibenzo-p-dioxin\tOctachlorodibenzofuran\t1,2,3,7,8-Pentachlorodibenzofuran\t1,2,3,4,7,8-Hexachlorodibenzofuran\t1,2,3,4,6,7,8-Heptachlorodibenzofuran\t2,3,7,8-Tetrachlorodibenzofuran\t2,3,7,8-Tetrachlorodibenzo-p-dioxin\t1,2,3,7,8-Pentachlorodibenzo-p-dioxin\t2,3,4,5-Tetrabromo-6-chlorotoluene\t2,3,4,5,6-Pentabromotoluene\t2,3,4,5,6-Pentabromoethylbenzene\t2,3,5,6-Tetrabromo-p-xylene\tAllyl 2,4,6-tribromophenyl ether\t2-Bromoallyl(2,4,6-tribromophenyl) ether\tPentabromobenzene\tHexabromobenzene\t2,3,4,5,6-Pentabromobenzyl alcohol\t2-Ethylhexyl 2,3,4,5-Tetrabromobenzoate\tsyn-Dechlorane plus\tanti-Dechlorane plus\talpha-1,2-Dibromo-4-(1,2-dibromoethyl)cyclohexane\tbeta-1,2-Dibromo-4-(1,2-dibromoethyl)cyclohexane\t1,2,5,6-Tetrabromocyclooctane\t1,1-Dibromo-2,3,3,4,4,5-hexachloro-2-cyclopenta-2,4-dien-1-ylcyclooctane\talpha-Amylcinnamaldehyde\ttrans-Cinnamaldehyde\tCitral (Geranial)\t1-Fluronaphthalene\talpha-Hexylcinnamaldehyde\tLilial\talpha-Amylcinnamyl alcohol\tEugenol\tIsoeugenol\t4-Methoxybenzyl alcohol\tMethyleugenol\tCinnamyl alcohol\tBenzyl alcohol\tEstragole\tBenzyl benzoate\tBenzyl cinnamate\tBenzyl salicylate\tCamphor\tEucalyptol\tCoumarin\tLimonene\tIsomethyl-alpha-ionone\tdelta-Iraldeine\tSafrole\tCashmeran\tCelestolide\tPhantolide\tTonalide\tTraseolide\tGalaxolide\tAldrin\tEndosulfan\tHeptachlor\tcis-Heptachlor epoxide\tEndosulfan sulphate\tEndrin ketone\ttrans-Chlordane\tcis-Chlordane\tEndrin aldehyde\tEndrin\t4,4'-Dichlorodiphenyldichloroethylene\tMethoxychlor\t4,4'-Dichlorodiphenyldichloroethane\t4,4'-Dichlorodiphenyltrichloroethane\tTris(4-tert-butylphenyl) phosphate\tTri-n-butyl-phosphate\tTris(1,3-dichloro-2-propy"..b'99004\t0.25699522150266857\t0.10086896866641386\t0.19470204063894617\t0.11098877289750769\t0.006075991834095414\t0.12927366381808264\t0.2082286991025265\t0.27240094810916426\t0.1654349689057302\t0.19840999142874\t0.16569982850423232\t0.2161122709425279\t0.14188794086609754\t0.13892041895889107\t0.163316162934255\t0.19714612348281121\t0.11328276368401106\t0.1797393737639574\t0.11912510425789868\t0.1513410655357927\t0.17376963876857818\t0.11727276196549535\t0.18242398225791773\t0.42587475586474854\t0.26019712746688456\t0.14368704499704515\t0.2071878076412335\t0.09453837918890001\t0.17883495196186588\t0.230407695094039\t0.2003708220640954\t0.28221288790938787\t0.1632240149541304\t0.33569524175870596\t0.3064105089065634\t0.06757663229398125\t0.1875387758604876\t0.14809372567415943\t0.0852574772349589\t0.038518437729193764\t0.1694183013806351\t0.15289185256222845\t0.1323269305931256\t0.14183815846488648\t0.11892832652180535\t0.12040055943475189\t0.055133306975097635\t0.059734777165814525\t0.0566711436003959\t0.10411276944449463\t0.09983202384693853\t0.038921466584489514\t0.0866119306764878\t0.06992238111265867\t0.09431159408139042\t0.0938643626333852\t0.08034523157647287\t0.30621301093750836\t0.1961893280957181\t0.1611360617918086\t0.23758939346985095\t0.12271395237074852\t0.1430157698712594\t0.0833933983294341\t0.035843502317569234\t0.1633740133739675\t0.1483671806190231\t0.13613729576468475\t0.13641339521522466\t0.10219746530932572\t0.24528101783913517\t0.22010021314888892\t0.17232404535039347\t0.17930641471345765\t0.15547769438760414\t0.1764623247344844\t0.08065948881320073\t0.19144552461877729\t0.3183099871734532\t0.06306342224555873\t0.05987974210984678\t0.05740354384209485\t0.20721138046115542\t0.328456758896439\t0.32098885468030136\t0.23821868337793292\t0.07145396369303544\t0.19081119513093286\t0.057616601871621285\t0.2340183931599587\t0.23822558856834722\t0.06797270073648182\t0.43003853617809873\t0.02792424887822149\t0.18822156250959438\t0.16114686619257262\t0.22810608062777601\t0.0838224184080167\t0.08443319924123477\t0.1894850392430079\t0.265083072227541\t0.10874839217026484\t0.21783385621466414\t0.006793839193263404\t0.08475249990448121\t0.12988582068761828\t0.2837084520725496\t0.07764215735572715\t0.08398679648212394\t0.09380315448372266\t0.21450922103222061\t0.27742281155579906\t0.04435157844941482\t0.35472454340204307\t0.3010423011492258\t0.06572111033523048\t0.35449933960739016\t0.184212014644299\t0.16510341696367972\t0.22650136131747978\t0.08545503348016772\t0.054746540083621745\t0.07158142375321293\t0.05222918108605921\t0.29873505869435935\t0.1592048730563699\t0.12242150172343544\t0.06834825436267856\t0.11787482883203612\t0.06533075716795377\t0.29220597270428633\t0.3204987910247821\t0.23075740046511872\t0.16013387140172308\t0.1031810078648983\t0.11609557607181138\t0.06536501695877456\t0.07528353746322132\t0.14631099884719126\t0.31686299036015636\t0.15686508283056178\t0.2502894060505306\t0.15632555985381263\t0.06157073783891902\t0.17850524434839174\t0.15082352190116588\t0.10496525194001774\t0.0328681907045638\t0.24179240409750177\t0.20560588522808376\t0.2271655674450096\t0.218989372412798\t0.09854462852017379\t0.1117782001836314\t0.32586231433297036\t0.16492586594387235\t0.1863221551020623\t0.23621550072877454\t0.12483921692480258\t0.16889581762525904\t0.03249926663036536\t0.015295084861858975\t0.20368054392043403\t0.18965962379608556\t0.1016530064450796\t0.12816683398762763\t0.06555661306024704\t0.022930759762077174\t0.019231613914197573\t0.15747279820504434\t0.088105124422038\t0.34732800952940357\t0.12915213761674713\t0.026497694389320044\t0.07320003712462311\t0.15992895420273134\t0.04418658553634053\t0.22031587132600947\t0.10334439566995825\t0.054857312240601364\t0.14588090116315752\t0.0720775597079632\t0.2322377084263006\t0.009182131128330325\t0.08725499132616112\t0.23335439715459685\t0.26456927574996886\t0.20593724958472245\t0.16953436023943352\t0.2915911520785385\t0.1972305838560561\t0.061557676013784396\t0.08503438513801481\t0.16053915107475406\t0.14738299237590127\t0.3485715331892874\t0.331614755581215\t0.149139047638064\t0.14441111333967438\t0.3881349843527812\t0.3574090148392564\t0.8662836910447197\t1.0\n' |
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/similarity/scores_test5_out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/scores_test5_out.tsv Tue Mar 22 16:07:32 2022 +0000 |
| b |
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|
| b |
| diff -r 000000000000 -r 30e680e555d4 test-data/similarity/scores_test6_out.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/similarity/scores_test6_out.tsv Tue Mar 22 16:07:32 2022 +0000 |
| b |
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|