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Changeset 2:f151ee133612 (2020-07-14)

Previous changeset 1:9ee2e2ceb2c9 (2020-03-19)

Commit message:
"planemo upload for repository https://github.com/computational-metabolomics/metfrag-galaxy commit b337c6296968848e3214f4b51df3d86776f84b6a"

modified:
metfrag.py
metfrag.xml
test-data/RP022611.tabular
test-data/RP022611_all_col.tabular
test-data/RP022611_suspect_default.txt
test-data/metfrag_massbank.tabular
test-data/metfrag_msp.tabular
test-data/winter_pos.tabular

added:
test-data/RP022611_all_adducts.tabular

diff -r 9ee2e2ceb2c9 -r f151ee133612 metfrag.py
--- a/metfrag.py Thu Mar 19 06:04:18 2020 -0400
+++ b/metfrag.py Tue Jul 14 07:41:53 2020 -0400

[

b'@@ -1,6 +1,11 @@\n from __future__ import absolute_import, print_function\n \n-import ConfigParser\n+try:\n+ from configparser import ConfigParser\n+except ImportError as e:\n+ print(e)\n+ from ConfigParser import ConfigParser\n+\n import argparse\n import csv\n import glob\n@@ -14,137 +19,6 @@\n \n import six\n \n-print(sys.version)\n-\n-parser = argparse.ArgumentParser()\n-parser.add_argument(\'--input_pth\')\n-parser.add_argument(\'--result_pth\', default=\'metfrag_result.csv\')\n-\n-parser.add_argument(\'--temp_dir\')\n-parser.add_argument(\'--polarity\', default=\'pos\')\n-parser.add_argument(\'--minMSMSpeaks\', default=1)\n-\n-parser.add_argument(\'--MetFragDatabaseType\', default=\'PubChem\')\n-parser.add_argument(\'--LocalDatabasePath\', default=\'\')\n-parser.add_argument(\'--LocalMetChemDatabaseServerIp\', default=\'\')\n-\n-parser.add_argument(\'--DatabaseSearchRelativeMassDeviation\', default=5)\n-parser.add_argument(\'--FragmentPeakMatchRelativeMassDeviation\', default=10)\n-parser.add_argument(\'--FragmentPeakMatchAbsoluteMassDeviation\', default=0.001)\n-parser.add_argument(\'--NumberThreads\', default=1)\n-parser.add_argument(\'--UnconnectedCompoundFilter\', action=\'store_true\')\n-parser.add_argument(\'--IsotopeFilter\', action=\'store_true\')\n-\n-parser.add_argument(\'--FilterMinimumElements\', default=\'\')\n-parser.add_argument(\'--FilterMaximumElements\', default=\'\')\n-parser.add_argument(\'--FilterSmartsInclusionList\', default=\'\')\n-parser.add_argument(\'--FilterSmartsExclusionList\', default=\'\')\n-parser.add_argument(\'--FilterIncludedElements\', default=\'\')\n-parser.add_argument(\'--FilterExcludedElements\', default=\'\')\n-parser.add_argument(\'--FilterIncludedExclusiveElements\', default=\'\')\n-\n-parser.add_argument(\'--score_thrshld\', default=0)\n-parser.add_argument(\'--pctexplpeak_thrshld\', default=0)\n-parser.add_argument(\'--schema\')\n-parser.add_argument(\'--cores_top_level\', default=1)\n-parser.add_argument(\'--chunks\', default=1)\n-parser.add_argument(\'--meta_select_col\', default=\'name\')\n-parser.add_argument(\'--skip_invalid_adducts\', action=\'store_true\')\n-\n-parser.add_argument(\'--ScoreSuspectLists\', default=\'\')\n-parser.add_argument(\'--MetFragScoreTypes\',\n- default="FragmenterScore,OfflineMetFusionScore")\n-parser.add_argument(\'--MetFragScoreWeights\', default="1.0,1.0")\n-\n-args = parser.parse_args()\n-print(args)\n-\n-config = ConfigParser.ConfigParser()\n-config.read(\n- os.path.join(os.path.dirname(os.path.abspath(__file__)), \'config.ini\'))\n-\n-if os.stat(args.input_pth).st_size == 0:\n- print(\'Input file empty\')\n- exit()\n-\n-# Create temporary working directory\n-if args.temp_dir:\n- wd = args.temp_dir\n-else:\n- wd = tempfile.mkdtemp()\n-\n-if os.path.exists(wd):\n- shutil.rmtree(wd)\n- os.makedirs(wd)\n-else:\n- os.makedirs(wd)\n-\n-######################################################################\n-# Setup regular expressions for MSP parsing dictionary\n-######################################################################\n-regex_msp = {}\n-regex_msp[\'name\'] = [r\'^Name(?:=|:)(.*)$\']\n-regex_msp[\'polarity\'] = [r\'^ion.*mode(?:=|:)(.*)$\',\n- r\'^ionization.*mode(?:=|:)(.*)$\',\n- r\'^polarity(?:=|:)(.*)$\']\n-regex_msp[\'precursor_mz\'] = [r\'^precursor.*m/z(?:=|:)\\s*(\\d*[.,]?\\d*)$\',\n- r\'^precursor.*mz(?:=|:)\\s*(\\d*[.,]?\\d*)$\']\n-regex_msp[\'precursor_type\'] = [r\'^precursor.*type(?:=|:)(.*)$\',\n- r\'^adduct(?:=|:)(.*)$\',\n- r\'^ADDUCTIONNAME(?:=|:)(.*)$\']\n-regex_msp[\'num_peaks\'] = [r\'^Num.*Peaks(?:=|:)\\s*(\\d*)$\']\n-regex_msp[\'msp\'] = [r\'^Name(?:=|:)(.*)$\'] # Flag for standard MSP format\n-\n-regex_massbank = {}\n-regex_massbank[\'name\'] = [r\'^RECORD_TITLE:(.*)$\']\n-regex_massbank[\'polarity\'] = [r\'^AC\\$MASS_SPECTROMETRY:\\s+ION_MODE\\s+(.*)$\']\n-regex_massbank[\'precursor_mz\'] = [\n- r\'^MS\\$FOCUSED_ION:\\s+PRECURSOR_M/Z\\s+(\\d*[.,]?\\d*)$\']\n-regex_massbank[\'precursor_type\'] = [\n- r\'^MS\\$FOCUSED_ION:\\s+PRECURSOR_TYPE\\s+(.*)$\']\n-regex_massbank[\'num_peaks\'] = [r'..b'=\'"\')\n+ dwriter.writeheader()\n+\n+ for fn in outfiles:\n+ with open(fn) as infile:\n+ reader = csv.DictReader(infile, delimiter=\',\', quotechar=\'"\')\n+ for line in reader:\n+ bewrite = True\n+ for key, value in line.items():\n+ # Filter when no MS/MS peak matched\n+ if key == "ExplPeaks":\n+ if float(args.pctexplpeak_thrshld) > 0 \\\n+ and value and "NA" in value:\n+ bewrite = False\n+ # Filter with a score threshold\n+ elif key == "Score":\n+ if value and float(value) <= float(\n+ args.score_thrshld):\n+ bewrite = False\n+ elif key == "NoExplPeaks":\n+ nbfindpeak = float(value)\n+ elif key == "NumberPeaksUsed":\n+ totpeaks = float(value)\n+ # Filter with a relative number of peak matched\n+ try:\n+ pctexplpeak = nbfindpeak / totpeaks * 100\n+ except ZeroDivisionError:\n+ bewrite = False\n+ else:\n+ if pctexplpeak < float(args.pctexplpeak_thrshld):\n bewrite = False\n- elif key == "NoExplPeaks":\n- nbfindpeak = float(value)\n- elif key == "NumberPeaksUsed":\n- totpeaks = float(value)\n- # Filter with a relative number of peak matched\n- try:\n- pctexplpeak = nbfindpeak / totpeaks * 100\n- except ZeroDivisionError:\n- bewrite = False\n- else:\n- if pctexplpeak < float(args.pctexplpeak_thrshld):\n- bewrite = False\n+\n+ # Write the line if it pass all filters\n+ if bewrite:\n+ bfn = os.path.basename(fn)\n+ bfn = bfn.replace(".csv", "")\n+ line[\'sample_name\'] = paramds[bfn][\'SampleName\']\n+ ad = paramds[bfn][\'additional_details\']\n \n- # Write the line if it pass all filters\n- if bewrite:\n- bfn = os.path.basename(fn)\n- bfn = bfn.replace(".csv", "")\n- line[\'sample_name\'] = paramds[bfn][\'SampleName\']\n- ad = paramds[bfn][\'additional_details\']\n+ if args.MetFragDatabaseType == "MetChem":\n+ # for some reason the metchem database option does\n+ # not report the full inchikey (at least in the\n+ # Bham setup. This ensures we always get\n+ # the fully inchikey\n+ line[\'InChIKey\'] = \'{}-{}-{}\'.format(\n+ line[\'InChIKey1\'],\n+ line[\'InChIKey2\'],\n+ line[\'InChIKey3\'])\n \n- if args.MetFragDatabaseType == "MetChem":\n- # for some reason the metchem database option does\n- # not report the full inchikey (at least in the Bham\n- # setup. This ensures we always get the fully inchikey\n- line[\'InChIKey\'] = \'{}-{}-{}\'.format(line[\'InChIKey1\'],\n- line[\'InChIKey2\'],\n- line[\'InChIKey3\'])\n-\n- line.update(ad)\n- dwriter.writerow(line)\n+ line.update(ad)\n+ dwriter.writerow(line)\n'

diff -r 9ee2e2ceb2c9 -r f151ee133612 metfrag.xml
--- a/metfrag.xml Thu Mar 19 06:04:18 2020 -0400
+++ b/metfrag.xml Tue Jul 14 07:41:53 2020 -0400

[

b'@@ -1,4 +1,4 @@\n-<tool id="metfrag" name="MetFrag" version="2.4.5+galaxy2" profile="18.01">\n+<tool id="metfrag" name="MetFrag" version="2.4.5+galaxy3" profile="18.01">\n <description>\n in silico fragmentor for compound annotation of mass spectrometry fragmentation spectra\n </description>\n@@ -51,6 +51,8 @@\n --minMSMSpeaks $minMSMSpeaks\n --schema $schema\n \n+ $output_cl\n+\n $PreProcessFilter.UnconnectedCompoundFilter\n $PreProcessFilter.IsotopeFilter\n \n@@ -62,6 +64,28 @@\n --FilterExcludedElements \'$PreProcessFilter.FilterExcludedElements\'\n --FilterIncludedExclusiveElements \'$PreProcessFilter.FilterIncludedExclusiveElements\'\n \n+ #if $adducts_cond.adducts_selector == \'select\':\n+ #for $a in $adducts_cond.adducts\n+ --adducts $a\n+ #end for\n+ #elif $adducts_cond.adducts_selector == \'all\':\n+ #if $polarity == \'pos\':\n+ --adducts [M+H]+\n+ --adducts [M+NH4]+\n+ --adducts [M+Na]+\n+ --adducts [M+K]+\n+ --adducts [M+CH3OH+H]+\n+ --adducts [M+ACN+H]+\n+ --adducts [M+ACN+Na]+\n+ --adducts [M+2ACN+H]+\n+ #elif $polarity == \'neg\':\n+ --adducts [M-H]-\n+ --adducts [M+Cl]-\n+ --adducts [M+HCOO]-\n+ --adducts [M+CH3COO]-\n+ #end if\n+ #end if\n+\n $skip_invalid_adducts\n --score_thrshld $PostProcessFilter.score_thrshld\n --pctexplpeak_thrshld $PostProcessFilter.pctexplpeak_thrshld\n@@ -101,6 +125,7 @@\n <option value="pos" selected="true">Positive</option>\n <option value="neg">Negative</option>\n </param>\n+\n <param argument="--schema" type="select" label="Schema"\n help="The schema used for the MSP file (auto will try automatically determine the schema)">\n <option value="auto" selected="True">Auto</option>\n@@ -110,12 +135,12 @@\n <param argument="--meta_select_col" type="select"\n label="Choose how additional metadata columns are extracted"\n help="The MetFrag output can have additional meta data columns added, these can be either extracted\n- from all MSP parameters or from the \'Name\' and \'RECORD_TITLE\' MSP parameter. Additionally, columns\n+ from the MSP parameters or from the \'Name\' and \'RECORD_TITLE\' MSP parameter. Additionally, columns\n can be added from the \'Name\' or \'RECORD_TITLE\' parameter by splitting on | and :\n e.g. \'MZ:100.2 | RT:20 | xcms_grp_id:1\' would create MZ,RT and xcms_grp_id columns">\n- <option value="name" selected="true">Extra metadata columns from the Name or RECORD_TITLE</option>\n+ <option value="name" >Extra metadata columns from the Name or RECORD_TITLE</option>\n <option value="name_split">Extra metadata columns from the Name or RECORD_TITLE (each column is split on "|" and ":" ) </option>\n- <option value="all">Extra metadata columns from all MSP parameters</option>\n+ <option value="all" selected="true">Extra metadata columns from MSP parameters</option>\n </param>\n <conditional name="suspectlist">\n <param name="suspectselector" type="select" label="Suspect list"\n@@ -143,12 +168,47 @@\n <expand macro="metfrag_scoring" suspectlistscore="False" weights="1.0,1.0"/>\n </when>\n </conditional>\n- <param argument="--minMSMSpeaks" type="integer" label="Minimum number of MS/MS peaks" value="0"/>\n+\n+ <conditional name="adducts_cond">\n+ <param name="adducts_selector" type="select" label="How to handle adducts"\n+ help="Choose whether to include a suspect list">\n+ '..b'" type="integer" label="Minimum number of MS/MS peaks" value="0"/>\n+ <param argument="--output_cl" type="boolean" checked="true"\n+ truevalue="--output_cl" falsevalue=""\n+ label="Output the MetFrag command line call" help="This will output all the parameters used\n+ for each MetFrag command line call (including the fragment peaks)"/>\n <section name="PreProcessFilter" title="PreProcessing filters" expanded="False">\n <param argument="--UnconnectedCompoundFilter" type="boolean" checked="false"\n truevalue="--UnconnectedCompoundFilter" falsevalue=""\n@@ -213,6 +273,8 @@\n <param name="MetFragDatabaseType" value="PubChem"/>\n <param name="MetFragDatabaseType" value="LocalCSV"/>\n <param name="LocalDatabasePath" value="demo_db.csv"/>\n+ <param name="meta_select_col" value="name"/>\n+ <param name="output_cl" value="false"/>\n <output name="results" file="metfrag_massbank.tabular"/>\n </test>\n <test>\n@@ -224,6 +286,8 @@\n <param name="MetFragDatabaseType" value="LocalCSV"/>\n <param name="LocalDatabasePath" value="demo_db.csv"/>\n <output name="results" file="metfrag_msp.tabular"/>\n+ <param name="meta_select_col" value="name"/>\n+ <param name="output_cl" value="false"/>\n </test>\n <test>\n \n@@ -239,6 +303,8 @@\n <param name="input" value="RP022611.txt"/>\n <param name="MetFragDatabaseType" value="LocalCSV"/>\n <param name="LocalDatabasePath" value="demo_db.csv"/>\n+ <param name="meta_select_col" value="name"/>\n+ <param name="output_cl" value="false"/>\n <output name="results" file="RP022611.tabular"/>\n </test>\n <test>\n@@ -247,7 +313,7 @@\n <param name="schema" value="massbank"/>\n <param name="MetFragDatabaseType" value="LocalCSV"/>\n <param name="LocalDatabasePath" value="demo_db.csv"/>\n- <param name="meta_select_col" value="all"/>\n+ <param name="output_cl" value="false"/>\n <output name="results" file="RP022611_all_col.tabular"/>\n </test>\n <test>\n@@ -260,14 +326,34 @@\n <param name="includesuspects_default_bool" value="true"/>\n </conditional>\n </conditional>\n+ <param name="meta_select_col" value="name"/>\n+ <param name="output_cl" value="false"/>\n <output name="results" file="RP022611_suspect_default.txt"/>\n </test>\n <test>\n \n <param name="input" value="invalid_adduct.msp"/>\n <param name="skip_invalid_adducts" value="true"/>\n+ <param name="meta_select_col" value="name"/>\n+ <param name="output_cl" value="false"/>\n <output name="results" file="invalid_adduct_result.txt" ftype="tabular"/>\n </test>\n+ <test>\n+ \n+ <param name="input" value="RP022611.txt"/>\n+ <param name="schema" value="massbank"/>\n+ <param name="polarity" value="neg"/>\n+ <param name="skip_invalid_adducts" value="false"/>\n+ <param name="MetFragDatabaseType" value="PubChem"/>\n+ <param name="MetFragDatabaseType" value="LocalCSV"/>\n+ <param name="LocalDatabasePath" value="demo_db.csv"/>\n+ <param name="meta_select_col" value="name"/>\n+ <param name="output_cl" value="false"/>\n+ <output name="results" file="RP022611_all_adducts.tabular"/>\n+ <conditional name="adducts_cond">\n+ <param name="adducts_selector" value="all"/>\n+ </conditional>\n+ </test>\n </tests>\n <help>\n -------\n'

diff -r 9ee2e2ceb2c9 -r f151ee133612 test-data/RP022611.tabular
--- a/test-data/RP022611.tabular Thu Mar 19 06:04:18 2020 -0400
+++ b/test-data/RP022611.tabular Tue Jul 14 07:41:53 2020 -0400

[

@@ -1,2 +1,2 @@
adduct name sample_name ExplPeaks FormulasOfExplPeaks FragmenterScore FragmenterScore_Values Identifier InChI InChIKey InChIKey1 InChIKey2 InChIKey3 MaximumTreeDepth MolecularFormula MonoisotopicMass Name NoExplPeaks NumberPeaksUsed OfflineMetFusionScore SMILES Score
-[M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- 1_metfrag_result 59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- 105.84456906313766 696.0;1156.0;696.0;1156.0 5793 InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1 WQZGKKKJIJFFOK-GASJEMHNSA-N WQZGKKKJIJFFOK GASJEMHNSA N 2 C6H12O6 180.0633881 D-Glucose 4 5 2.8456682842407846 C(C1C(C(C(C(O1)O)O)O)O)O 2.0
+[M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- 1_metfrag_result 59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- 105.84456906313768 696.0;1156.0;696.0;1156.0 5793 InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1 WQZGKKKJIJFFOK-GASJEMHNSA-N WQZGKKKJIJFFOK GASJEMHNSA N 2 C6H12O6 180.0633881 D-Glucose 4 5 2.8456682842407846 C(C1C(C(C(C(O1)O)O)O)O)O 2.0

diff -r 9ee2e2ceb2c9 -r f151ee133612 test-data/RP022611_all_adducts.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RP022611_all_adducts.tabular Tue Jul 14 07:41:53 2020 -0400

[

@@ -0,0 +1,2 @@
+adduct name sample_name CompoundName ExplPeaks FormulasOfExplPeaks FragmenterScore FragmenterScore_Values Identifier InChI InChIKey InChIKey1 InChIKey2 InChIKey3 MaximumTreeDepth MolecularFormula MonoisotopicMass Name NoExplPeaks NumberPeaksUsed OfflineMetFusionScore SMILES Score
+[M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- 1_metfrag_result 59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- 105.84456906313768 696.0;1156.0;696.0;1156.0 5793 InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1 WQZGKKKJIJFFOK-GASJEMHNSA-N WQZGKKKJIJFFOK GASJEMHNSA N 2 C6H12O6 180.0633881 D-Glucose 4 5 2.8456682842407846 C(C1C(C(C(C(O1)O)O)O)O)O 2.0

diff -r 9ee2e2ceb2c9 -r f151ee133612 test-data/RP022611_all_col.tabular
--- a/test-data/RP022611_all_col.tabular Thu Mar 19 06:04:18 2020 -0400
+++ b/test-data/RP022611_all_col.tabular Tue Jul 14 07:41:53 2020 -0400

[

@@ -1,2 +1,2 @@
-polarity adduct massbank name cols num_peaks sample_name precursor_type precursor_mz ExplPeaks FormulasOfExplPeaks FragmenterScore FragmenterScore_Values Identifier InChI InChIKey InChIKey1 InChIKey2 InChIKey3 MaximumTreeDepth MolecularFormula MonoisotopicMass Name NoExplPeaks NumberPeaksUsed OfflineMetFusionScore SMILES Score
-NEGATIVE [M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- m/z int. rel.int. 5 1_metfrag_result [M-H]- 179.0561 59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- 105.84456906313766 696.0;1156.0;696.0;1156.0 5793 InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1 WQZGKKKJIJFFOK-GASJEMHNSA-N WQZGKKKJIJFFOK GASJEMHNSA N 2 C6H12O6 180.0633881 D-Glucose 4 5 2.8456682842407846 C(C1C(C(C(C(O1)O)O)O)O)O 2.0
+name num_peaks polarity precursor_mz precursor_type retention_time sample_name ExplPeaks FormulasOfExplPeaks FragmenterScore FragmenterScore_Values Identifier InChI InChIKey InChIKey1 InChIKey2 InChIKey3 MaximumTreeDepth MolecularFormula MonoisotopicMass Name NoExplPeaks NumberPeaksUsed OfflineMetFusionScore SMILES Score
+D-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]- 5 NEGATIVE 179.0561 [M-H]- 0.604 1_metfrag_result 59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0 59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H- 105.84456906313768 696.0;1156.0;696.0;1156.0 5793 InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1 WQZGKKKJIJFFOK-GASJEMHNSA-N WQZGKKKJIJFFOK GASJEMHNSA N 2 C6H12O6 180.0633881 D-Glucose 4 5 2.8456682842407846 C(C1C(C(C(C(O1)O)O)O)O)O 2.0

diff -r 9ee2e2ceb2c9 -r f151ee133612 test-data/RP022611_suspect_default.txt
--- a/test-data/RP022611_suspect_default.txt Thu Mar 19 06:04:18 2020 -0400
+++ b/test-data/RP022611_suspect_default.txt Tue Jul 14 07:41:53 2020 -0400

[

b'@@ -1,1328 +1,1330 @@\n adduct\tname\tsample_name\tExplPeaks\tFormulasOfExplPeaks\tFragmenterScore\tFragmenterScore_Values\tIUPACName\tIdentifier\tInChI\tInChIKey\tInChIKey1\tInChIKey2\tMaximumTreeDepth\tMolecularFormula\tMonoisotopicMass\tNoExplPeaks\tNumberPeaksUsed\tOfflineMetFusionScore\tSMILES\tScore\tSuspectListScore\tXlogP3\r\n-[M-H]-\tD-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]-\t1_metfrag_result\t59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0\t59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H-\t105.84456906313766\t696.0;1156.0;696.0;1156.0\t6-(hydroxymethyl)oxane-2,3,4,5-tetrol\t206\tInChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2\tWQZGKKKJIJFFOK-UHFFFAOYSA-N\tWQZGKKKJIJFFOK\tUHFFFAOYSA\t2\tC6H12O6\t180.063388\t4\t5\t2.8456682842407846\tC(C1C(C(C(C(O1)O)O)O)O)O\t1.8267821960344066\t1.0\t-2.6\r\n-[M-H]-\tD-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]-\t1_metfrag_result\t59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0\t59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H-\t105.84456906313766\t696.0;1156.0;696.0;1156.0\t(3R,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol\t5793\tInChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1\tWQZGKKKJIJFFOK-GASJEMHNSA-N\tWQZGKKKJIJFFOK\tGASJEMHNSA\t2\tC6H12O6\t180.063388\t4\t5\t2.8456682842407846\tC([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)O)O)O\t1.8267821960344066\t1.0\t-2.6\r\n-[M-H]-\tD-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]-\t1_metfrag_result\t59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0\t59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H-\t105.84456906313766\t696.0;1156.0;696.0;1156.0\t(3R,4S,5R,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol\t6036\tInChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3+,4+,5-,6?/m1/s1\tWQZGKKKJIJFFOK-SVZMEOIVSA-N\tWQZGKKKJIJFFOK\tSVZMEOIVSA\t2\tC6H12O6\t180.063388\t4\t5\t2.8456682842407846\tC([C@@H]1[C@@H]([C@@H]([C@H](C(O1)O)O)O)O)O\t1.8267821960344066\t1.0\t-2.6\r\n-[M-H]-\tD-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]-\t1_metfrag_result\t59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0\t59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H-\t105.84456906313766\t696.0;1156.0;696.0;1156.0\t(3S,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol\t18950\tInChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5+,6?/m1/s1\tWQZGKKKJIJFFOK-QTVWNMPRSA-N\tWQZGKKKJIJFFOK\tQTVWNMPRSA\t2\tC6H12O6\t180.063388\t4\t5\t2.8456682842407846\tC([C@@H]1[C@H]([C@@H]([C@@H](C(O1)O)O)O)O)O\t1.8267821960344066\t1.0\t-2.6\r\n-[M-H]-\tD-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]-\t1_metfrag_result\t59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0\t59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H-\t105.84456906313766\t696.0;1156.0;696.0;1156.0\t(2R,3R,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol\t64689\tInChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6-/m1/s1\tWQZGKKKJIJFFOK-VFUOTHLCSA-N\tWQZGKKKJIJFFOK\tVFUOTHLCSA\t2\tC6H12O6\t180.063388\t4\t5\t2.8456682842407846\tC([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O)O\t1.8267821960344066\t1.0\t-2.6\r\n-[M-H]-\tD-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]-\t1_metfrag_result\t59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0\t59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H-\t105.84456906313766\t696.0;1156.0;696.0;1156.0\t(2S,3R,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol\t79025\tInChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6+/m1/s1\tWQZGKKKJIJFFOK-DVKNGEFBSA-N\tWQZGKKKJIJFFOK\tDVKNGEFBSA\t2\tC6H12O6\t180.063388\t4\t5\t2.8456682842407846\tC([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)O\t1.8267821960344066\t1.0\t-2.6\r\n-[M-H]-\tD-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]-\t1_metfrag_result\t59.0138_715.8;71.014_679.7;89.0251_999.0;101.0234_103.0\t59.0138:[C2H4O2]-H-;71.014:[C3H5O2-H]-H-;89.0251:[C3H6O3]-H-;101.0234:[C4H7O3-H]-H-\t105.84456906313766\t696.0;1156.0;696.0;1156.0\t(2S,3S,4S,5R,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol\t81696\tInChI=1S/C6H12'..b'619776061033\tCC1=C(C=NN1C(C)C#N)[N+](=O)[O-]\t0.09487814168347423\t0.0\t0.8\r\n [M-H]-\tD-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]-\t1_metfrag_result\tNA\tNA\t0.0\tNA\t2-(5-methyl-3-nitropyrazol-1-yl)propanenitrile\t130496629\tInChI=1S/C7H8N4O2/c1-5-3-7(11(12)13)9-10(5)6(2)4-8/h3,6H,1-2H3\tXQAVMQDOBJVPGM-UHFFFAOYSA-N\tXQAVMQDOBJVPGM\tUHFFFAOYSA\t2\tC7H8N4O2\t180.064726\t0\t5\t0.4499354978039307\tCC1=CC(=NN1C(C)C#N)[N+](=O)[O-]\t0.09486745176076741\t0.0\t1.1\r\n@@ -2506,8 +2511,8 @@\n [M-H]-\tD-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]-\t1_metfrag_result\tNA\tNA\t0.0\tNA\t2-amino-5-nitrobenzenecarboximidamide\t23570805\tInChI=1S/C7H8N4O2/c8-6-2-1-4(11(12)13)3-5(6)7(9)10/h1-3H,8H2,(H3,9,10)\tSANYQLJUVTZWIM-UHFFFAOYSA-N\tSANYQLJUVTZWIM\tUHFFFAOYSA\t2\tC7H8N4O2\t180.064726\t0\t5\t0.4405038611414184\tC1=CC(=C(C=C1[N+](=O)[O-])C(=N)N)N\t0.0928788215227152\t0.0\t1.1\r\n [M-H]-\tD-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]-\t1_metfrag_result\tNA\tNA\t0.0\tNA\t2-amino-4-nitrobenzenecarboximidamide\t130121705\tInChI=1S/C7H8N4O2/c8-6-3-4(11(12)13)1-2-5(6)7(9)10/h1-3H,8H2,(H3,9,10)\tNTCIMCGJFBXXJK-UHFFFAOYSA-N\tNTCIMCGJFBXXJK\tUHFFFAOYSA\t2\tC7H8N4O2\t180.064726\t0\t5\t0.4405038611414184\tC1=CC(=C(C=C1[N+](=O)[O-])N)C(=N)N\t0.0928788215227152\t0.0\t1.3\r\n [M-H]-\tD-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]-\t1_metfrag_result\tNA\tNA\t0.0\tNA\tN-(methyldiazenyl)-2-nitroaniline\t71366356\tInChI=1S/C7H8N4O2/c1-8-10-9-6-4-2-3-5-7(6)11(12)13/h2-5H,1H3,(H,8,9)\tXTLWCVOSWCIKQY-UHFFFAOYSA-N\tXTLWCVOSWCIKQY\tUHFFFAOYSA\t2\tC7H8N4O2\t180.064726\t0\t5\t0.4394875049285973\tCN=NNC1=CC=CC=C1[N+](=O)[O-]\t0.0926645260860089\t0.0\t2.6\r\n-[M-H]-\tD-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]-\t1_metfrag_result\tNA\tNA\t0.0\tNA\t[3-(4-formylpyrrol-1-ium-3-yl)phenyl]boron\t123325304\tInChI=1S/C11H7BNO/c12-10-3-1-2-8(4-10)11-6-13-5-9(11)7-14/h1-7H/q+1\tITSFZGAUQXSQLQ-UHFFFAOYSA-N\tITSFZGAUQXSQLQ\tUHFFFAOYSA\t2\tC11H7BNO\t180.062069\t0\t5\t0.4393393288146\t[B]C1=CC(=CC=C1)C2=C(C=[N+]=C2)C=O\t0.09263328362922267\t0.0\tNA\r\n-[M-H]-\tD-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]-\t1_metfrag_result\tNA\tNA\t0.0\tNA\t[6-chloro-5-(propan-2-ylamino)pyridin-3-yl]boron\t88247312\tInChI=1S/C8H10BClN2/c1-5(2)12-7-3-6(9)4-11-8(7)10/h3-5,12H,1-2H3\tKARJYHBOTAPAEP-UHFFFAOYSA-N\tKARJYHBOTAPAEP\tUHFFFAOYSA\t2\tC8H10BClN2\t180.062556\t0\t5\t0.43923442980502786\t[B]C1=CC(=C(N=C1)Cl)NC(C)C\t0.09261116601063309\t0.0\tNA\r\n+[M-H]-\tD-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]-\t1_metfrag_result\tNA\tNA\t0.0\tNA\tNA\t123325304\tInChI=1S/C11H7BNO/c12-10-3-1-2-8(4-10)11-6-13-5-9(11)7-14/h1-7H/q+1\tITSFZGAUQXSQLQ-UHFFFAOYSA-N\tITSFZGAUQXSQLQ\tUHFFFAOYSA\t2\tC11H7BNO\t180.062069\t0\t5\t0.4393393288146\t[B]C1=CC(=CC=C1)C2=C(C=[N+]=C2)C=O\t0.09263328362922267\t0.0\tNA\r\n+[M-H]-\tD-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]-\t1_metfrag_result\tNA\tNA\t0.0\tNA\tNA\t88247312\tInChI=1S/C8H10BClN2/c1-5(2)12-7-3-6(9)4-11-8(7)10/h3-5,12H,1-2H3\tKARJYHBOTAPAEP-UHFFFAOYSA-N\tKARJYHBOTAPAEP\tUHFFFAOYSA\t2\tC8H10BClN2\t180.062556\t0\t5\t0.43923442980502786\t[B]C1=CC(=C(N=C1)Cl)NC(C)C\t0.09261116601063309\t0.0\tNA\r\n [M-H]-\tD-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]-\t1_metfrag_result\tNA\tNA\t0.0\tNA\tN-(methyldiazenyl)-4-nitroaniline\t94508\tInChI=1S/C7H8N4O2/c1-8-10-9-6-2-4-7(5-3-6)11(12)13/h2-5H,1H3,(H,8,9)\tBDSNQOSDUXHMCI-UHFFFAOYSA-N\tBDSNQOSDUXHMCI\tUHFFFAOYSA\t2\tC7H8N4O2\t180.064726\t0\t5\t0.4388490767373334\tCN=NNC1=CC=C(C=C1)[N+](=O)[O-]\t0.09252991555642621\t0.0\t2.2\r\n [M-H]-\tD-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]-\t1_metfrag_result\tNA\tNA\t0.0\tNA\t1-(2,5-difluorophenyl)-1H-pyrrol-1-ium\t23123375\tInChI=1S/C10H7F2N/c11-8-3-4-9(12)10(7-8)13-5-1-2-6-13/h1-7H/p+1\tHYQPJXOHMPYAIQ-UHFFFAOYSA-O\tHYQPJXOHMPYAIQ\tUHFFFAOYSA\t2\tC10H8F2N\t180.062481\t0\t5\t0.4385212371694085\tC1=C[NH+](C=C1)C2=C(C=CC(=C2)F)F\t0.09246079163855978\t0.0\t2.8\r\n [M-H]-\tD-Glucose; LC-ESI-QTOF; MS2; CE: 10; R=; [M-H]-\t1_metfrag_result\tNA\tNA\t0.0\tNA\t1-(2,3-difluorophenyl)-1H-pyrrol-1-ium\t23123435\tInChI=1S/C10H7F2N/c11-8-4-3-5-9(10(8)12)13-6-1-2-7-13/h1-7H/p+1\tBVZJJASLXCRPHD-UHFFFAOYSA-O\tBVZJJASLXCRPHD\tUHFFFAOYSA\t2\tC10H8F2N\t180.062481\t0\t5\t0.4385212371694085\tC1=C[NH+](C=C1)C2=C(C(=CC=C2)F)F\t0.09246079163855978\t0.0\t2.8\r\n'

diff -r 9ee2e2ceb2c9 -r f151ee133612 test-data/metfrag_massbank.tabular
--- a/test-data/metfrag_massbank.tabular Thu Mar 19 06:04:18 2020 -0400
+++ b/test-data/metfrag_massbank.tabular Tue Jul 14 07:41:53 2020 -0400

[

@@ -1,13 +1,13 @@
adduct name sample_name CompoundName ExplPeaks FormulasOfExplPeaks FragmenterScore FragmenterScore_Values Identifier InChI InChIKey InChIKey1 InChIKey2 InChIKey3 MaximumTreeDepth MolecularFormula MonoisotopicMass Name NoExplPeaks NumberPeaksUsed OfflineMetFusionScore SMILES Score
-[M+H]+ MZ:79.0219 | RT:177 | XCMS_group:9 | file:1 | scan:NA 5_metfrag_result 61.0115814208984_84.2;62.9908714294434_97.8;63.9986305236816_999.0 61.0115814208984:[C2H6S-H]+;62.9908714294434:[CH3OS]+;63.9986305236816:[CH3OS]+H+ 282.1697651393817 622.0;272.0;272.0 679 InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 IAZDPXIOMUYVGZ-UHFFFAOYSA-N IAZDPXIOMUYVGZ UHFFFAOYSA N 2 C2H6OS 78.014 test 3 5 0.21393611414493724 CS(=O)C 2.0
-[M+H]+ MZ:79.0219 | RT:177 | XCMS_group:9 | file:1 | scan:NA 5_metfrag_result 61.0115814208984_84.2;62.9908714294434_97.8;63.9986305236816_999.0 61.0115814208984:[C2H6S-H]+;62.9908714294434:[CH3OS]+;63.9986305236816:[CH3OS]+H+ 282.1697651393817 622.0;272.0;272.0 HMDB0002151 InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 IAZDPXIOMUYVGZ-UHFFFAOYSA-N IAZDPXIOMUYVGZ UHFFFAOYSA N 2 C2H6OS 78.0139355 Dimethyl sulfoxide 3 5 0.21393611414493724 CS(C)=O 2.0
-[M+H]+ MZ:79.0219 | RT:184 | XCMS_group:9 | file:1 | scan:NA 6_metfrag_result 62.9906845092773_74.1;63.9986686706543_999.0 62.9906845092773:[CH3OS]+;63.9986686706543:[CH3OS]+H+ 245.34661903929023 272.0;272.0 679 InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 IAZDPXIOMUYVGZ-UHFFFAOYSA-N IAZDPXIOMUYVGZ UHFFFAOYSA N 2 C2H6OS 78.014 test 2 4 0.14080908903149097 CS(=O)C 2.0
-[M+H]+ MZ:79.0219 | RT:184 | XCMS_group:9 | file:1 | scan:NA 6_metfrag_result 62.9906845092773_74.1;63.9986686706543_999.0 62.9906845092773:[CH3OS]+;63.9986686706543:[CH3OS]+H+ 245.34661903929023 272.0;272.0 HMDB0002151 InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 IAZDPXIOMUYVGZ-UHFFFAOYSA-N IAZDPXIOMUYVGZ UHFFFAOYSA N 2 C2H6OS 78.0139355 Dimethyl sulfoxide 2 4 0.14080908903149097 CS(C)=O 2.0
-[M+H]+ MZ:79.0219 | RT:212 | XCMS_group:9 | file:1 | scan:NA 7_metfrag_result 61.0115776062012_88.7;62.9908828735352_67.4;63.9986190795898_999.0 61.0115776062012:[C2H6S-H]+;62.9908828735352:[CH3OS]+;63.9986190795898:[CH3OS]+H+ 273.21939470601694 622.0;272.0;272.0 679 InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 IAZDPXIOMUYVGZ-UHFFFAOYSA-N IAZDPXIOMUYVGZ UHFFFAOYSA N 2 C2H6OS 78.014 test 3 8 0.21833426500502406 CS(=O)C 2.0
-[M+H]+ MZ:79.0219 | RT:212 | XCMS_group:9 | file:1 | scan:NA 7_metfrag_result 61.0115776062012_88.7;62.9908828735352_67.4;63.9986190795898_999.0 61.0115776062012:[C2H6S-H]+;62.9908828735352:[CH3OS]+;63.9986190795898:[CH3OS]+H+ 273.21939470601694 622.0;272.0;272.0 HMDB0002151 InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 IAZDPXIOMUYVGZ-UHFFFAOYSA-N IAZDPXIOMUYVGZ UHFFFAOYSA N 2 C2H6OS 78.0139355 Dimethyl sulfoxide 3 8 0.21833426500502406 CS(C)=O 2.0
+[M+H]+ MZ:79.0219 | RT:177 | XCMS_group:9 | file:1 | scan:NA 5_metfrag_result 61.0115814208984_84.2;62.9908714294434_97.8;63.9986305236816_999.0 61.0115814208984:[C2H6S-H]+;62.9908714294434:[CH3OS]+;63.9986305236816:[CH3OS]+H+ 282.1697651392046 622.0;272.0;272.0 679 InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 IAZDPXIOMUYVGZ-UHFFFAOYSA-N IAZDPXIOMUYVGZ UHFFFAOYSA N 2 C2H6OS 78.014 test 3 5 0.21393611414493724 CS(=O)C 2.0
+[M+H]+ MZ:79.0219 | RT:177 | XCMS_group:9 | file:1 | scan:NA 5_metfrag_result 61.0115814208984_84.2;62.9908714294434_97.8;63.9986305236816_999.0 61.0115814208984:[C2H6S-H]+;62.9908714294434:[CH3OS]+;63.9986305236816:[CH3OS]+H+ 282.1697651392046 622.0;272.0;272.0 HMDB0002151 InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 IAZDPXIOMUYVGZ-UHFFFAOYSA-N IAZDPXIOMUYVGZ UHFFFAOYSA N 2 C2H6OS 78.0139355 Dimethyl sulfoxide 3 5 0.21393611414493724 CS(C)=O 2.0
+[M+H]+ MZ:79.0219 | RT:184 | XCMS_group:9 | file:1 | scan:NA 6_metfrag_result 62.9906845092773_74.1;63.9986686706543_999.0 62.9906845092773:[CH3OS]+;63.9986686706543:[CH3OS]+H+ 245.3466190392 272.0;272.0 679 InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 IAZDPXIOMUYVGZ-UHFFFAOYSA-N IAZDPXIOMUYVGZ UHFFFAOYSA N 2 C2H6OS 78.014 test 2 4 0.14080908903149097 CS(=O)C 2.0
+[M+H]+ MZ:79.0219 | RT:184 | XCMS_group:9 | file:1 | scan:NA 6_metfrag_result 62.9906845092773_74.1;63.9986686706543_999.0 62.9906845092773:[CH3OS]+;63.9986686706543:[CH3OS]+H+ 245.3466190392 272.0;272.0 HMDB0002151 InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 IAZDPXIOMUYVGZ-UHFFFAOYSA-N IAZDPXIOMUYVGZ UHFFFAOYSA N 2 C2H6OS 78.0139355 Dimethyl sulfoxide 2 4 0.14080908903149097 CS(C)=O 2.0
+[M+H]+ MZ:79.0219 | RT:212 | XCMS_group:9 | file:1 | scan:NA 7_metfrag_result 61.0115776062012_88.7;62.9908828735352_67.4;63.9986190795898_999.0 61.0115776062012:[C2H6S-H]+;62.9908828735352:[CH3OS]+;63.9986190795898:[CH3OS]+H+ 273.2193947059513 622.0;272.0;272.0 679 InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 IAZDPXIOMUYVGZ-UHFFFAOYSA-N IAZDPXIOMUYVGZ UHFFFAOYSA N 2 C2H6OS 78.014 test 3 8 0.21833426500502406 CS(=O)C 2.0
+[M+H]+ MZ:79.0219 | RT:212 | XCMS_group:9 | file:1 | scan:NA 7_metfrag_result 61.0115776062012_88.7;62.9908828735352_67.4;63.9986190795898_999.0 61.0115776062012:[C2H6S-H]+;62.9908828735352:[CH3OS]+;63.9986190795898:[CH3OS]+H+ 273.2193947059513 622.0;272.0;272.0 HMDB0002151 InChI=1S/C2H6OS/c1-4(2)3/h1-2H3 IAZDPXIOMUYVGZ-UHFFFAOYSA-N IAZDPXIOMUYVGZ UHFFFAOYSA N 2 C2H6OS 78.0139355 Dimethyl sulfoxide 3 8 0.21833426500502406 CS(C)=O 2.0
[M+H]+ MZ:86.0607 | RT:1497 | XCMS_group:19 | file:1 | scan:NA 9_metfrag_result NA NA 0.0 NA HMDB0002039 InChI=1S/C4H7NO/c6-4-2-1-3-5-4/h1-3H2,(H,5,6) HNJBEVLQSNELDL-UHFFFAOYSA-N HNJBEVLQSNELDL UHFFFAOYSA N 2 C4H7NO 85.05276385 2-Pyrrolidinone 0 3 1.382021738987827 O=C1CCCN1 1.0
[M+H]+ MZ:86.0607 | RT:1497 | XCMS_group:19 | file:1 | scan:NA 9_metfrag_result NA NA 0.0 NA HMDB0060427 InChI=1S/C4H7NO/c1-4(2,6)3-5/h6H,1-2H3 MWFMGBPGAXYFAR-UHFFFAOYSA-N MWFMGBPGAXYFAR UHFFFAOYSA N 2 C4H7NO 85.05276385 Acetone cyanohydrin 0 3 1.259881333913003 CC(C)(O)C#N 0.9116219364506684
-[M+H]+ MZ:86.0606 | RT:1498 | XCMS_group:19 | file:1 | scan:NA 10_metfrag_result 53.9984169006348_183.7 53.9984169006348:[C2HNO-H]+ 28.14129547353099 796.0 HMDB0060427 InChI=1S/C4H7NO/c1-4(2,6)3-5/h6H,1-2H3 MWFMGBPGAXYFAR-UHFFFAOYSA-N MWFMGBPGAXYFAR UHFFFAOYSA N 2 C4H7NO 85.05276385 Acetone cyanohydrin 1 10 1.5355220212517242 CC(C)(O)C#N 1.9157496211754683
+[M+H]+ MZ:86.0606 | RT:1498 | XCMS_group:19 | file:1 | scan:NA 10_metfrag_result 53.9984169006348_183.7 53.9984169006348:[C2HNO-H]+ 28.141295473506776 796.0 HMDB0060427 InChI=1S/C4H7NO/c1-4(2,6)3-5/h6H,1-2H3 MWFMGBPGAXYFAR-UHFFFAOYSA-N MWFMGBPGAXYFAR UHFFFAOYSA N 2 C4H7NO 85.05276385 Acetone cyanohydrin 1 10 1.5355220212517242 CC(C)(O)C#N 1.9157496211754683
[M+H]+ MZ:86.0606 | RT:1498 | XCMS_group:19 | file:1 | scan:NA 10_metfrag_result NA NA 0.0 NA HMDB0002039 InChI=1S/C4H7NO/c6-4-2-1-3-5-4/h1-3H2,(H,5,6) HNJBEVLQSNELDL-UHFFFAOYSA-N HNJBEVLQSNELDL UHFFFAOYSA N 2 C4H7NO 85.05276385 2-Pyrrolidinone 0 10 1.6767924176487323 O=C1CCCN1 1.0
[M+H]+ MZ:86.0607 | RT:1500 | XCMS_group:19 | file:1 | scan:NA 11_metfrag_result NA NA 0.0 NA HMDB0002039 InChI=1S/C4H7NO/c6-4-2-1-3-5-4/h1-3H2,(H,5,6) HNJBEVLQSNELDL-UHFFFAOYSA-N HNJBEVLQSNELDL UHFFFAOYSA N 2 C4H7NO 85.05276385 2-Pyrrolidinone 0 5 1.3746691837774077 O=C1CCCN1 1.0
[M+H]+ MZ:86.0607 | RT:1500 | XCMS_group:19 | file:1 | scan:NA 11_metfrag_result NA NA 0.0 NA HMDB0060427 InChI=1S/C4H7NO/c1-4(2,6)3-5/h6H,1-2H3 MWFMGBPGAXYFAR-UHFFFAOYSA-N MWFMGBPGAXYFAR UHFFFAOYSA N 2 C4H7NO 85.05276385 Acetone cyanohydrin 0 5 1.2539223673403028 CC(C)(O)C#N 0.9121630004789162

diff -r 9ee2e2ceb2c9 -r f151ee133612 test-data/metfrag_msp.tabular
--- a/test-data/metfrag_msp.tabular Thu Mar 19 06:04:18 2020 -0400
+++ b/test-data/metfrag_msp.tabular Tue Jul 14 07:41:53 2020 -0400

[

diff -r 9ee2e2ceb2c9 -r f151ee133612 test-data/winter_pos.tabular
--- a/test-data/winter_pos.tabular Thu Mar 19 06:04:18 2020 -0400
+++ b/test-data/winter_pos.tabular Tue Jul 14 07:41:53 2020 -0400

[

b'@@ -1,45 +1,45 @@\n-adduct\tname\tsample_name\tExplPeaks\tFormulasOfExplPeaks\tFragmenterScore\tFragmenterScore_Values\tIUPACName\tIdentifier\tInChI\tInChIKey\tInChIKey1\tInChIKey2\tMaximumTreeDepth\tMolecularFormula\tMonoisotopicMass\tNoExplPeaks\tNumberPeaksUsed\tOfflineMetFusionScore\tSMILES\tScore\tXlogP3\r\n-[M+H]+\tpos_27_winter_Marpol_27_2.E.3_01_17272:1\t1_metfrag_result\tNA\tNA\t0.0\tNA\tdimethyl(dipropyl)-lambda4-sulfane\t71774044\tInChI=1S/C8H20S/c1-5-7-9(3,4)8-6-2/h5-8H2,1-4H3\tOPMSGHPOQIQQRS-UHFFFAOYSA-N\tOPMSGHPOQIQQRS\tUHFFFAOYSA\t2\tC8H20S\t148.128572\t0\t1\t0.37031226614982965\tCCCS(C)(C)CCC\t1.0\t2.7\r\n-[M+H]+\tpos_27_winter_Marpol_27_2.E.3_01_17272:1\t1_metfrag_result\tNA\tNA\t0.0\tNA\tbutyl-ethyl-dimethyl-lambda4-sulfane\t90984195\tInChI=1S/C8H20S/c1-5-7-8-9(3,4)6-2/h5-8H2,1-4H3\tHCGXHQGSWBNABQ-UHFFFAOYSA-N\tHCGXHQGSWBNABQ\tUHFFFAOYSA\t2\tC8H20S\t148.128572\t0\t1\t0.37031226614982965\tCCCCS(C)(C)CC\t1.0\t2.5\r\n-[M+H]+\tpos_27_winter_Marpol_27_2.E.3_01_17272:1\t1_metfrag_result\tNA\tNA\t0.0\tNA\ttrimethyl(3-methylbutyl)-lambda4-sulfane\t118334050\tInChI=1S/C8H20S/c1-8(2)6-7-9(3,4)5/h8H,6-7H2,1-5H3\tDFXVYXYADDYUJD-UHFFFAOYSA-N\tDFXVYXYADDYUJD\tUHFFFAOYSA\t2\tC8H20S\t148.128572\t0\t1\t0.3692650195260169\tCC(C)CCS(C)(C)C\t0.9971719904536216\t2.6\r\n-[M+H]+\tpos_27_winter_Marpol_27_2.E.3_01_17272:1\t1_metfrag_result\tNA\tNA\t0.0\tNA\tbutyl-trimethyl-methylidene-lambda6-sulfane\t123293059\tInChI=1S/C8H20S/c1-6-7-8-9(2,3,4)5/h2,6-8H2,1,3-5H3\tVKPVIYIHVYLQST-UHFFFAOYSA-N\tVKPVIYIHVYLQST\tUHFFFAOYSA\t2\tC8H20S\t148.128572\t0\t1\t0.3684934475101417\tCCCCS(=C)(C)(C)C\t0.9950884191371828\t2.8\r\n-[M+H]+\tpos_27_winter_Marpol_27_2.E.3_01_17272:1\t1_metfrag_result\tNA\tNA\t0.0\tNA\ttrimethyl(pentyl)-lambda4-sulfane\t123234955\tInChI=1S/C8H20S/c1-5-6-7-8-9(2,3)4/h5-8H2,1-4H3\tDOMKJZGKNOYRJJ-UHFFFAOYSA-N\tDOMKJZGKNOYRJJ\tUHFFFAOYSA\t2\tC8H20S\t148.128572\t0\t1\t0.36833824834252354\tCCCCCS(C)(C)C\t0.9946693156350715\t2.7\r\n-[M+H]+\tpos_27_winter_Marpol_27_2.E.3_01_17272:1\t1_metfrag_result\tNA\tNA\t0.0\tNA\ttrimethyl(2-methylbutyl)-lambda4-sulfane\t89554176\tInChI=1S/C8H20S/c1-6-8(2)7-9(3,4)5/h8H,6-7H2,1-5H3\tVYPWEAXBOOOKCI-UHFFFAOYSA-N\tVYPWEAXBOOOKCI\tUHFFFAOYSA\t2\tC8H20S\t148.128572\t0\t1\t0.3670899392001932\tCCC(C)CS(C)(C)C\t0.9912983521093177\t2.6\r\n-[M+H]+\tpos_27_winter_Marpol_27_2.E.3_01_17272:1\t1_metfrag_result\tNA\tNA\t0.0\tNA\tethyl-dimethyl-(2-methylpropyl)-lambda4-sulfane\t123581531\tInChI=1S/C8H20S/c1-6-9(4,5)7-8(2)3/h8H,6-7H2,1-5H3\tHCQWOWHBTFNYPP-UHFFFAOYSA-N\tHCQWOWHBTFNYPP\tUHFFFAOYSA\t2\tC8H20S\t148.128572\t0\t1\t0.3670899392001932\tCCS(C)(C)CC(C)C\t0.9912983521093177\t2.6\r\n-[M+H]+\tpos_27_winter_Marpol_27_2.E.3_01_17272:1\t1_metfrag_result\tNA\tNA\t0.0\tNA\tdiethyl-methyl-propyl-lambda4-sulfane\t87264764\tInChI=1S/C8H20S/c1-5-8-9(4,6-2)7-3/h5-8H2,1-4H3\tFEBVEQKYAVNHNG-UHFFFAOYSA-N\tFEBVEQKYAVNHNG\tUHFFFAOYSA\t2\tC8H20S\t148.128572\t0\t1\t0.3665198706303188\tCCCS(C)(CC)CC\t0.9897589254632564\t2.5\r\n-[M+H]+\tpos_27_winter_Marpol_27_2.E.3_01_17272:1\t1_metfrag_result\tNA\tNA\t0.0\tNA\tdimethyl-propan-2-yl-propyl-lambda4-sulfane\t123984437\tInChI=1S/C8H20S/c1-6-7-9(4,5)8(2)3/h8H,6-7H2,1-5H3\tYKCWUJTZJUTSRN-UHFFFAOYSA-N\tYKCWUJTZJUTSRN\tUHFFFAOYSA\t2\tC8H20S\t148.128572\t0\t1\t0.36642602760587445\tCCCS(C)(C)C(C)C\t0.9895055095410131\t2.6\r\n-[M+H]+\tpos_27_winter_Marpol_27_2.E.3_01_17272:1\t1_metfrag_result\tNA\tNA\t0.0\tNA\ttrimethyl(pentan-2-yl)-lambda4-sulfane\t123872005\tInChI=1S/C8H20S/c1-6-7-8(2)9(3,4)5/h8H,6-7H2,1-5H3\tKBFUVSMTQRNXGQ-UHFFFAOYSA-N\tKBFUVSMTQRNXGQ\tUHFFFAOYSA\t2\tC8H20S\t148.128572\t0\t1\t0.366385855541442\tCCCC(C)S(C)(C)C\t0.9893970279483019\t2.6\r\n-[M+H]+\tpos_27_winter_Marpol_27_2.E.3_01_17272:1\t1_metfrag_result\tNA\tNA\t0.0\tNA\ttert-butyl-ethyl-dimethyl-lambda4-sulfane\t123948136\tInChI=1S/C8H20S/c1-7-9(5,6)8(2,3)4/h7H2,1-6H3\tZYNXVEVNBFJHMI-UHFFFAOYSA-N\tZYNXVEVNBFJHMI\tUHFFFAOYSA\t2\tC8H20S\t148.128572\t0\t1\t0.3656746377878431\tCCS(C)(C)C(C)(C)C\t0.9874764387088648\t2.3\r\n-[M+H]+\tpos_27_winter_Marpol_27_2.E.3_01_17272:1\t1_metfrag_result\tNA\tNA\t0.0\tNA\t2,2-dimethylpropyl(trimethyl)-lambda4-sulfane\t123803452\tInChI=1S/C8H20S/c1-8(2,3)7-9(4,5)6/h7H2,1-6H3\tZHZXMNSILACQJD-UHFFFAOYSA-N\tZHZXMNSILACQJD\tUHFFFAOYSA\t2\tC8H20S\t148.128572\t0\t1\t0.3645577651'..b'214\t[M+H]+\t650.574\t2_metfrag_result\tNA\tNA\t0.0\tNA\t1-(difluoromethyl)-1-methylpiperidin-1-ium\t24750697\tInChI=1S/C7H14F2N/c1-10(7(8)9)5-3-2-4-6-10/h7H,2-6H2,1H3/q+1\tSIBIOKOZJHIJMS-UHFFFAOYSA-N\tSIBIOKOZJHIJMS\tUHFFFAOYSA\t2\tC7H14F2N\t150.109431\t0\t1\t0.023002603052633866\tC[N+]1(CCCCC1)C(F)F\t0.9962080355465082\t2.1\r\n+2\tmetfrag MetFragDatabaseType=PubChem FragmentPeakMatchAbsoluteMassDeviation=0.001 FragmentPeakMatchRelativeMassDeviation=5.0 DatabaseSearchRelativeMassDeviation=10.0 SampleName=2_metfrag_result ResultsPath=./temp/ IsPositiveIonMode=True PrecursorIonMode=1 MetFragCandidateWriter=CSV NumberThreads=1 MetFragScoreTypes=FragmenterScore,OfflineMetFusionScore MetFragScoreWeights=1.0,1.0 PeakListPath=./temp/2_tmpspec.txt NeutralPrecursorMass=150.10841614 PeakListString=136.090178471023_168;151.110697295085_1052;152.117423567352_136\tpos_27_winter_Marpol_27_2.E.3_01_17272:2\t3\t151.11569214\t[M+H]+\t650.574\t2_metfrag_result\tNA\tNA\t0.0\tNA\t[(2S)-1-(3,3-difluorocyclobutyl)propan-2-yl]azanium\t144763422\tInChI=1S/C7H13F2N/c1-5(10)2-6-3-7(8,9)4-6/h5-6H,2-4,10H2,1H3/p+1/t5-/m0/s1\tPFPVDGBOJWFZCE-YFKPBYRVSA-O\tPFPVDGBOJWFZCE\tYFKPBYRVSA\t2\tC7H14F2N\t150.109431\t0\t1\t0.022930394247447423\tC[C@@H](CC1CC(C1)(F)F)[NH3+]\t0.9930807811310254\t1.5\r\n+3\tmetfrag MetFragDatabaseType=PubChem FragmentPeakMatchAbsoluteMassDeviation=0.001 FragmentPeakMatchRelativeMassDeviation=5.0 DatabaseSearchRelativeMassDeviation=10.0 SampleName=3_metfrag_result ResultsPath=./temp/ IsPositiveIonMode=True PrecursorIonMode=1 MetFragCandidateWriter=CSV NumberThreads=1 MetFragScoreTypes=FragmenterScore,OfflineMetFusionScore MetFragScoreWeights=1.0,1.0 PeakListPath=./temp/3_tmpspec.txt NeutralPrecursorMass=165.08485657 PeakListString=121.067062911877_262;131.049505932606_146;137.060202192821_531;149.059561491169_254;166.08537028381_545\tpos_27_winter_Marpol_27_2.E.3_01_17272:3\t5\t166.09213257\t[M+H]+\t42.174\t3_metfrag_result\tNA\tNA\t0.0\tNA\t[1-(2,2-difluoroethylcarbamoyl)cyclopropyl]azanium\t140645036\tInChI=1S/C6H10F2N2O/c7-4(8)3-10-5(11)6(9)1-2-6/h4H,1-3,9H2,(H,10,11)/p+1\tVBDLBVWQUBMPID-UHFFFAOYSA-O\tVBDLBVWQUBMPID\tUHFFFAOYSA\t2\tC6H11F2N2O\t165.083944\t0\t4\t1.5659197717037268\tC1CC1(C(=O)NCC(F)F)[NH3+]\t1.0\t-0.2\r\n+3\tmetfrag MetFragDatabaseType=PubChem FragmentPeakMatchAbsoluteMassDeviation=0.001 FragmentPeakMatchRelativeMassDeviation=5.0 DatabaseSearchRelativeMassDeviation=10.0 SampleName=3_metfrag_result ResultsPath=./temp/ IsPositiveIonMode=True PrecursorIonMode=1 MetFragCandidateWriter=CSV NumberThreads=1 MetFragScoreTypes=FragmenterScore,OfflineMetFusionScore MetFragScoreWeights=1.0,1.0 PeakListPath=./temp/3_tmpspec.txt NeutralPrecursorMass=165.08485657 PeakListString=121.067062911877_262;131.049505932606_146;137.060202192821_531;149.059561491169_254;166.08537028381_545\tpos_27_winter_Marpol_27_2.E.3_01_17272:3\t5\t166.09213257\t[M+H]+\t42.174\t3_metfrag_result\tNA\tNA\t0.0\tNA\t2-methylphosphanyl-N-(2-methylphosphanylethyl)ethanamine\t5366868\tInChI=1S/C6H17NP2/c1-8-5-3-7-4-6-9-2/h7-9H,3-6H2,1-2H3\tRVTLJXOPJDPRHE-UHFFFAOYSA-N\tRVTLJXOPJDPRHE\tUHFFFAOYSA\t2\tC6H17NP2\t165.083624\t0\t4\t1.4513834802368626\tCPCCNCCPC\t0.9268568584824444\t-0.8\r\n+3\tmetfrag MetFragDatabaseType=PubChem FragmentPeakMatchAbsoluteMassDeviation=0.001 FragmentPeakMatchRelativeMassDeviation=5.0 DatabaseSearchRelativeMassDeviation=10.0 SampleName=3_metfrag_result ResultsPath=./temp/ IsPositiveIonMode=True PrecursorIonMode=1 MetFragCandidateWriter=CSV NumberThreads=1 MetFragScoreTypes=FragmenterScore,OfflineMetFusionScore MetFragScoreWeights=1.0,1.0 PeakListPath=./temp/3_tmpspec.txt NeutralPrecursorMass=165.08485657 PeakListString=121.067062911877_262;131.049505932606_146;137.060202192821_531;149.059561491169_254;166.08537028381_545\tpos_27_winter_Marpol_27_2.E.3_01_17272:3\t5\t166.09213257\t[M+H]+\t42.174\t3_metfrag_result\tNA\tNA\t0.0\tNA\tNA\t58378282\tInChI=1S/C7H10BN2O2/c1-10(2)7-4-3-6(5-9-7)12-8-11/h3-5,11H,1-2H3\tQHOASYSLTRWFLE-UHFFFAOYSA-N\tQHOASYSLTRWFLE\tUHFFFAOYSA\t2\tC7H10BN2O2\t165.083533\t0\t4\t1.4368216184360907\t[B](O)OC1=CN=C(C=C1)N(C)C\t0.9175576197449906\tNA\r\n'