Mercurial > repos > gmat > isocor
changeset 0:96f7617b4848 draft
planemo upload
| author | gmat |
|---|---|
| date | Mon, 27 May 2019 03:33:36 -0400 |
| parents | |
| children | fa183805db31 |
| files | isocor.xml test-data/Data_example.tsv test-data/Derivatives.dat test-data/Isotopes.dat test-data/Metabolites.dat test-data/results.log test-data/results.tsv |
| diffstat | 7 files changed, 399 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/isocor.xml Mon May 27 03:33:36 2019 -0400 @@ -0,0 +1,116 @@ +<tool id="isocor" name="Isotope Correction for mass spectrometry labeling experiments" version="0.1.2"> + <requirements> + <requirement type="package" version="2.1.3">isocor</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + isocorcli -t "$tracer" -M "$input1" -D "$input2" -I "$input3" +#if $tracer_purity: + -p $tracer_purity +#end if +#if $resolution: + -r $resolution +#end if +#if $mz: + -m $mz +#end if +#if $resolution_formula_code: + -f $resolution_formula_code +#end if +#if $correct_na_tracer: + -n +#end if +#if $verbose_log: + -v +#end if + "$input4" > "$output1" 2> "$output2" + ]]></command> + <inputs> + <param type="text" name="tracer" argument="-t" label="the isotopic tracer (e.g. '13C')" /> + <param type="data" name="input1" argument="-M" label="metabolites db" format="tabular" /> + <param type="data" name="input2" argument="-D" label="derivatives db" format="tabular" /> + <param type="data" name="input3" argument="-I" label="isotopes db" format="csv" /> + <param type="integer" optional="true" argument="-r" name="resolution" label="HR only: resolution of the mass spectrometer (e.g. 1e4)" /> + <param type="integer" optional="true" argument="-m" name="mz" label="HR only: mz at which resolution is given (e.g. '400')" /> + <param type="boolean" optional="true" argument="-n" name="correct_na_tracer" label="flag to correct tracer natural abundance" /> + <param type="boolean" optional="true" argument="-v" name="verbose_log" label="flag to enable verbose logs" /> + <param type="text" optional="true" argument="-p" name="tracer_purity" label="purity vector of the tracer" /> + + <param name="resolution_formula_code" optional="true" argument="-f" type="select" label="HR only: spectrometer formula code"> + <option value="orbitrap">Orbitrap</option> + <option value="ft-icr">ft-icr</option> + <option value="constant">Constant</option> + <option value="datafile">Datafile</option> + </param> + + <param type="data" name="input4" label="measurements Data file" format="tabular" /> + </inputs> + <outputs> + <data name="output1" label="corrected measurements data file" format="csv" /> + <data name="output2" label="processing log file" format="txt" /> + </outputs> + <tests> + <test> + <param name="tracer" value="13C"/> + <param name="input1" value="Metabolites.dat"/> + <param name="input2" value="Derivatives.dat"/> + <param name="input3" value="Isotopes.dat"/> + <param name="input4" value="Data_example.tsv"/> + <output name="output1"> + <assert_contents> + <has_n_columns n="9" /> + </assert_contents> + </output> + <output name="output2"> + <assert_contents> + <has_text text="- root - INFO - errors: 0" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +.. class:: warningmark + + We strongly encourage you to read the `Tutorials <https://isocor.readthedocs.io/en/latest/tutorials.html#tutorials>`_ before using IsoCor. + +---- + +usage: + isocorcli [-h] [-M M] [-D D] [-I I] -t TRACER [-r RESOLUTION] [-m MZ_OF_RESOLUTION] [-f {orbitrap,ft-icr,constant,datafile}] [-p TRACER_PURITY] [-n] [-v] inputdata + + correction of MS data for naturally occurring isotopes + +positional arguments: + inputdata measurements file to process + +optional arguments: + -h, --help show this help message and exit + -M M path to metabolites database + -D D path to derivatives database + -I I path to isotopes database + -t TRACER, --tracer TRACER the isotopic tracer (e.g. "13C") + + -r RESOLUTION, --resolution RESOLUTION HR only: resolution of the mass spectrometer (e.g. 1e4) + + -m MZ_OF_RESOLUTION, --mz_of_resolution MZ_OF_RESOLUTION HR only: mz at which resolution is given (e.g. "400") + + -f FORMULA_ORIGIN, --resolution_formula_code FORMULA_ORIGIN + HR only: spectrometer formula code + + -p TRACER_PURITY, --tracer_purity TRACER_PURITY purity vector of the tracer + -n, --correct_NA_tracer flag to correct tracer natural abundance + -v, --verbose flag to enable verbose logs + ]]></help> + <citations> + <citation type="bibtex"> +@article{10.1093/bioinformatics/btz209, + author = {Delépine, Baudoin and Létisse, Fabien and Millard, Pierre and Bellvert, Floriant and Guionnet, Matthieu and Heuillet, Maud}, + title = "{IsoCor: isotope correction for high-resolution MS labeling experiments}", + year = {2019}, + month = {03}, + abstract = "{Mass spectrometry (MS) is widely used for isotopic studies of metabolism and other (bio)chemical processes. Quantitative applications in systems and synthetic biology require to correct the raw MS data for the contribution of naturally occurring isotopes. Several tools are available to correct low-resolution MS data, and recent developments made substantial improvements by introducing resolution-dependent correction methods, hence opening the way to the correction of high-resolution MS (HRMS) data. Nevertheless, current HRMS correction methods partly fail to determine which isotopic species are resolved from the tracer isotopologues and should thus be corrected. We present an updated version of our isotope correction software (IsoCor) with a novel correction algorithm which ensures to accurately exploit any chemical species with any isotopic tracer, at any MS resolution. IsoCor v2 also includes a novel graphical user interface for intuitive use by end-users and a command-line interface to streamline integration into existing pipelines.IsoCor v2 is implemented in Python 3 and was tested on Windows, Unix and MacOS platforms. The source code and the documentation are freely distributed under GPL3 license at https://github.com/MetaSys-LISBP/IsoCor/ and https://isocor.readthedocs.io/.Supplementary data are available at Bioinformatics online.}", + doi = {10.1093/bioinformatics/btz209}, + url = {https://doi.org/10.1093/bioinformatics/btz209}, + eprint = {http://oup.prod.sis.lan/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btz209/28212636/btz209.pdf}, +}</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Data_example.tsv Mon May 27 03:33:36 2019 -0400 @@ -0,0 +1,88 @@ +sample metabolite derivative isotopologue area resolution +Sample_1 Fum 0 376000 70000 +Sample_1 Fum 1 235000 70000 +Sample_1 Fum 2 127000 70000 +Sample_1 Fum 3 143000 70000 +Sample_1 Fum 4 40000 70000 +Sample_1 OA 0 0 80000 +Sample_1 OA 1 0 80000 +Sample_1 OA 2 0 80000 +Sample_1 OA 3 0 80000 +Sample_1 OA 4 0 80000 +Sample_1 aKG 0 761000 70000 +Sample_1 aKG 1 95100 70000 +Sample_1 aKG 2 391000 70000 +Sample_1 aKG 3 39300 70000 +Sample_1 aKG 4 0 70000 +Sample_1 aKG 5 0 70000 +Sample_1 G3P 0 715000 100000 +Sample_1 G3P 1 557000 100000 +Sample_1 G3P 2 24800 100000 +Sample_1 G3P 3 133000 100000 +Sample_1 2/3PG 0 1430000 70000 +Sample_1 2/3PG 1 2920000 70000 +Sample_1 2/3PG 2 226000 70000 +Sample_1 2/3PG 3 765000 70000 +Sample_1 E4P 0 854 70000 +Sample_1 E4P 1 10200 70000 +Sample_1 E4P 2 7760 70000 +Sample_1 E4P 3 1730 70000 +Sample_1 E4P 4 320 70000 +Sample_2 Fum 0 376000 70000 +Sample_2 Fum 1 235000 70000 +Sample_2 Fum 2 127000 70000 +Sample_2 Fum 3 143000 70000 +Sample_2 Fum 4 40000 70000 +Sample_2 OA 0 0 70000 +Sample_2 OA 1 0 70000 +Sample_2 OA 2 0 70000 +Sample_2 OA 3 0 70000 +Sample_2 OA 4 0 70000 +Sample_2 aKG 0 761000 70000 +Sample_2 aKG 1 95100 70000 +Sample_2 aKG 2 391000 70000 +Sample_2 aKG 3 39300 70000 +Sample_2 aKG 4 0 70000 +Sample_2 aKG 5 0 70000 +Sample_2 G3P 0 715000 70000 +Sample_2 G3P 1 557000 70000 +Sample_2 G3P 2 24800 70000 +Sample_2 G3P 3 133000 70000 +Sample_2 2/3PG 0 1430000 70000 +Sample_2 2/3PG 1 2920000 70000 +Sample_2 2/3PG 2 226000 70000 +Sample_2 2/3PG 3 765000 70000 +Sample_2 E4P 0 854 70000 +Sample_2 E4P 1 10200 70000 +Sample_2 E4P 2 7760 70000 +Sample_2 E4P 3 1730 70000 +Sample_2 E4P 4 320 70000 +Sample_3 Fum TMS 0 376000 70000 +Sample_3 Fum TMS 1 235000 70000 +Sample_3 Fum TMS 2 127000 70000 +Sample_3 Fum TMS 3 143000 70000 +Sample_3 Fum TMS 4 40000 70000 +Sample_3 OA TMS 0 0 70000 +Sample_3 OA TMS 1 0 70000 +Sample_3 OA TMS 2 0 70000 +Sample_3 OA TMS 3 0 70000 +Sample_3 OA TMS 4 0 70000 +Sample_3 aKG TMS 0 761000 70000 +Sample_3 aKG TMS 1 95100 70000 +Sample_3 aKG TMS 2 391000 70000 +Sample_3 aKG TMS 3 39300 70000 +Sample_3 aKG TMS 4 0 70000 +Sample_3 aKG TMS 5 0 70000 +Sample_3 G3P TMS 0 715000 70000 +Sample_3 G3P TMS 1 557000 70000 +Sample_3 G3P TMS 2 24800 70000 +Sample_3 G3P TMS 3 133000 70000 +Sample_3 2/3PG TMS 0 1430000 70000 +Sample_3 2/3PG TMS 1 2920000 70000 +Sample_3 2/3PG TMS 2 226000 70000 +Sample_3 2/3PG TMS 3 765000 70000 +Sample_3 E4P TMS 0 854 70000 +Sample_3 E4P TMS 1 10200 70000 +Sample_3 E4P TMS 2 7760 70000 +Sample_3 E4P TMS 3 1730 70000 +Sample_3 E4P TMS 4 320 70000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Derivatives.dat Mon May 27 03:33:36 2019 -0400 @@ -0,0 +1,2 @@ +name formula +TMS C3H9Si
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Isotopes.dat Mon May 27 03:33:36 2019 -0400 @@ -0,0 +1,19 @@ +"element","mass","abundance" +H,1.0078250322,0.999885 +H,2.0141017781,0.000115 +C,12.0,0.9893 +C,13.003354835,0.0107 +N,14.003074004,0.99636 +N,15.000108899,0.00364 +O,15.99491462,0.99757 +O,16.999131757,0.00038 +O,17.999159613,0.00205 +Si,27.976926535,0.92223 +Si,28.976494665,0.04685 +Si,29.9737701,0.03092 +P,30.973761998,1.0 +S,31.972071174,0.9499 +S,32.971458910,0.0075 +S,33.9678670,0.0425 +S,35.,0. +S,35.967081,0.0001
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Metabolites.dat Mon May 27 03:33:36 2019 -0400 @@ -0,0 +1,27 @@ +name formula charge +Suc C4H4O3 -1 +Fum C4H3O4 -1 +Mal C4H5O5 -1 +Cit C6H7O7 -1 +aKG C5H5O5 -1 +OA C4H3O5 -1 +Asp C4H6NO4 -1 +Aco C6HO3 -1 +2/3PG C3H6O3 -1 +G3P C3H7O3 -1 +PEP C3H4O3 -1 +E4P C4H8O4 -1 +R1P C5H8O4 -1 +R5P C5H8O4 -1 +G1P C6H10O5 -1 +G6P C6H10O5 -1 +F1P C6H10O5 -1 +F6P C6H10O5 -1 +M6P C6H10O5 -1 +6PG C6H10O6 -1 +S7P C7H11O6 -1 +FBP C6H11O8P -1 +AMP C10H14N5O4 -1 +ADP C10H14N5O4 -1 +ATP C10H16N5O10 -1 +CDP C9H15N3O7P -1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results.log Mon May 27 03:33:36 2019 -0400 @@ -0,0 +1,58 @@ +2019-02-20 15:46:03 - root - INFO - ------------------------------------------------ +2019-02-20 15:46:03 - root - INFO - Correction process +2019-02-20 15:46:03 - root - INFO - ------------------------------------------------ +2019-02-20 15:46:03 - root - INFO - data files +2019-02-20 15:46:03 - root - INFO - data file: Data_example.tsv +2019-02-20 15:46:03 - root - INFO - derivatives database: Derivatives.dat +2019-02-20 15:46:03 - root - INFO - metabolites database: Metabolites.dat +2019-02-20 15:46:03 - root - INFO - isotopes database: Isotopes.dat +2019-02-20 15:46:03 - root - INFO - correction parameters +2019-02-20 15:46:03 - root - INFO - isotopic tracer: 13C +2019-02-20 15:46:03 - root - INFO - correct natural abundance of the tracer element: False +2019-02-20 15:46:03 - root - INFO - isotopic purity of the tracer: None +2019-02-20 15:46:03 - root - INFO - mode: low-resolution +2019-02-20 15:46:03 - root - INFO - natural abundance of isotopes +2019-02-20 15:46:03 - root - INFO - {'C': {'mass': [Decimal('12.0'), Decimal('13.003354835')], 'abundance': [0.9893, 0.0107]}, 'H': {'mass': [Decimal('1.0078250322'), Decimal('2.0141017781')], 'abundance': [0.999885, 0.000115]}, 'N': {'mass': [Decimal('14.003074004'), Decimal('15.000108899')], 'abundance': [0.99636, 0.00364]}, 'O': {'mass': [Decimal('15.99491462'), Decimal('16.999131757'), Decimal('17.999159613')], 'abundance': [0.99757, 0.00038, 0.00205]}, 'P': {'mass': [Decimal('30.973761998')], 'abundance': [1.0]}, 'S': {'mass': [Decimal('31.972071174'), Decimal('32.971458910'), Decimal('33.9678670'), Decimal('35'), Decimal('35.967081')], 'abundance': [0.9499, 0.0075, 0.0425, 0.0, 0.0001]}, 'Si': {'mass': [Decimal('27.976926535'), Decimal('28.976494665'), Decimal('29.9737701')], 'abundance': [0.92223, 0.04685, 0.03092]}} +2019-02-20 15:46:03 - root - INFO - IsoCor version: 2.1.0 +2019-02-20 15:46:03 - root - INFO - ------------------------------------------------ +2019-02-20 15:46:03 - root - INFO - Constructing correctors for all (metabolite, derivative)... +2019-02-20 15:46:03 - root - INFO - ------------------------------------------------ +2019-02-20 15:46:03 - root - INFO - ('Fum', '') successfully constructed. +2019-02-20 15:46:03 - root - INFO - ('OA', '') successfully constructed. +2019-02-20 15:46:03 - root - INFO - ('aKG', '') successfully constructed. +2019-02-20 15:46:03 - root - INFO - ('G3P', '') successfully constructed. +2019-02-20 15:46:03 - root - INFO - ('2/3PG', '') successfully constructed. +2019-02-20 15:46:03 - root - INFO - ('E4P', '') successfully constructed. +2019-02-20 15:46:03 - root - INFO - ('Fum', 'TMS') successfully constructed. +2019-02-20 15:46:03 - root - INFO - ('OA', 'TMS') successfully constructed. +2019-02-20 15:46:03 - root - INFO - ('aKG', 'TMS') successfully constructed. +2019-02-20 15:46:03 - root - INFO - ('G3P', 'TMS') successfully constructed. +2019-02-20 15:46:03 - root - INFO - ('2/3PG', 'TMS') successfully constructed. +2019-02-20 15:46:03 - root - INFO - ('E4P', 'TMS') successfully constructed. +2019-02-20 15:46:03 - root - INFO - ------------------------------------------------ +2019-02-20 15:46:03 - root - INFO - Correcting raw MS data... +2019-02-20 15:46:03 - root - INFO - ------------------------------------------------ +2019-02-20 15:46:03 - root - INFO - Sample_1 - ('Fum', ''): processed +2019-02-20 15:46:03 - root - INFO - Sample_2 - ('Fum', ''): processed +2019-02-20 15:46:03 - root - INFO - Sample_1 - ('OA', ''): processed +2019-02-20 15:46:03 - root - INFO - Sample_2 - ('OA', ''): processed +2019-02-20 15:46:03 - root - INFO - Sample_1 - ('aKG', ''): processed +2019-02-20 15:46:03 - root - INFO - Sample_2 - ('aKG', ''): processed +2019-02-20 15:46:03 - root - INFO - Sample_1 - ('G3P', ''): processed +2019-02-20 15:46:04 - root - INFO - Sample_2 - ('G3P', ''): processed +2019-02-20 15:46:04 - root - INFO - Sample_1 - ('2/3PG', ''): processed +2019-02-20 15:46:04 - root - INFO - Sample_2 - ('2/3PG', ''): processed +2019-02-20 15:46:04 - root - INFO - Sample_1 - ('E4P', ''): processed +2019-02-20 15:46:04 - root - INFO - Sample_2 - ('E4P', ''): processed +2019-02-20 15:46:04 - root - INFO - Sample_3 - ('Fum', 'TMS'): processed +2019-02-20 15:46:04 - root - INFO - Sample_3 - ('OA', 'TMS'): processed +2019-02-20 15:46:04 - root - INFO - Sample_3 - ('aKG', 'TMS'): processed +2019-02-20 15:46:04 - root - INFO - Sample_3 - ('G3P', 'TMS'): processed +2019-02-20 15:46:04 - root - INFO - Sample_3 - ('2/3PG', 'TMS'): processed +2019-02-20 15:46:04 - root - INFO - Sample_3 - ('E4P', 'TMS'): processed +2019-02-20 15:46:04 - root - INFO - ------------------------------------------------ +2019-02-20 15:46:04 - root - INFO - Correction process summary +2019-02-20 15:46:04 - root - INFO - ------------------------------------------------ +2019-02-20 15:46:04 - root - INFO - number of samples: 3 +2019-02-20 15:46:04 - root - INFO - number of (metabolite, derivative): 12 +2019-02-20 15:46:04 - root - INFO - errors: 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results.tsv Mon May 27 03:33:36 2019 -0400 @@ -0,0 +1,89 @@ +sample metabolite derivative isotopologue area corrected_area isotopologue_fraction residuum mean_enrichment +Sample_1 Fum 0 376000.0 379808.0494972019 0.41168665351703776 0.0 0.2897659902799015 +Sample_1 Fum 1 235000.0 236670.2675765585 0.2565348221938963 0.0 0.2897659902799015 +Sample_1 Fum 2 127000.0 124721.39583086275 0.13518969421410323 1.5800125112233282e-17 0.2897659902799015 +Sample_1 Fum 3 143000.0 142264.79335165164 0.15420556980234792 -3.1600250224466564e-17 0.2897659902799015 +Sample_1 Fum 4 40000.0 39101.348751418525 0.04238326027261486 0.0 0.2897659902799015 +Sample_2 Fum 0 376000.0 379808.0494972019 0.41168665351703776 0.0 0.2897659902799015 +Sample_2 Fum 1 235000.0 236670.2675765585 0.2565348221938963 0.0 0.2897659902799015 +Sample_2 Fum 2 127000.0 124721.39583086275 0.13518969421410323 1.5800125112233282e-17 0.2897659902799015 +Sample_2 Fum 3 143000.0 142264.79335165164 0.15420556980234792 -3.1600250224466564e-17 0.2897659902799015 +Sample_2 Fum 4 40000.0 39101.348751418525 0.04238326027261486 0.0 0.2897659902799015 +Sample_1 OA 0 0.0 0.0 +Sample_1 OA 1 0.0 0.0 +Sample_1 OA 2 0.0 0.0 +Sample_1 OA 3 0.0 0.0 +Sample_1 OA 4 0.0 0.0 +Sample_2 OA 0 0.0 0.0 +Sample_2 OA 1 0.0 0.0 +Sample_2 OA 2 0.0 0.0 +Sample_2 OA 3 0.0 0.0 +Sample_2 OA 4 0.0 0.0 +Sample_1 aKG 0 761000.0 770757.2822531819 0.5971059382536738 -1.9986617443107176e-07 0.15239309254478398 +Sample_1 aKG 1 95100.0 94408.21105160222 0.07313807438059411 -1.1232997022303625e-07 0.15239309254478398 +Sample_1 aKG 2 391000.0 387815.2020768239 0.3004405737538707 3.24340113523371e-05 0.15239309254478398 +Sample_1 aKG 3 39300.0 37840.9710506128 0.029315413611861445 1.0996123584802932e-05 0.15239309254478398 +Sample_1 aKG 4 0.0 0.0 0.0 -0.003157788575981497 0.15239309254478398 +Sample_1 aKG 5 0.0 0.0 0.0 -0.00030802561931763875 0.15239309254478398 +Sample_2 aKG 0 761000.0 770757.2822531819 0.5971059382536738 -1.9986617443107176e-07 0.15239309254478398 +Sample_2 aKG 1 95100.0 94408.21105160222 0.07313807438059411 -1.1232997022303625e-07 0.15239309254478398 +Sample_2 aKG 2 391000.0 387815.2020768239 0.3004405737538707 3.24340113523371e-05 0.15239309254478398 +Sample_2 aKG 3 39300.0 37840.9710506128 0.029315413611861445 1.0996123584802932e-05 0.15239309254478398 +Sample_2 aKG 4 0.0 0.0 0.0 -0.003157788575981497 0.15239309254478398 +Sample_2 aKG 5 0.0 0.0 0.0 -0.00030802561931763875 0.15239309254478398 +Sample_1 G3P 0 715000.0 720817.843203928 0.5037179457196655 -8.142070347386684e-17 0.2307972956362909 +Sample_1 G3P 1 557000.0 560128.1627924398 0.3914256703849595 8.142070347386684e-17 0.2307972956362909 +Sample_1 G3P 2 24800.0 19465.731702013378 0.013602935162211748 -5.088793967116678e-17 0.2307972956362909 +Sample_1 G3P 3 133000.0 130583.22551280692 0.09125344873316321 1.2213105521080026e-16 0.2307972956362909 +Sample_2 G3P 0 715000.0 720817.843203928 0.5037179457196655 -8.142070347386684e-17 0.2307972956362909 +Sample_2 G3P 1 557000.0 560128.1627924398 0.3914256703849595 8.142070347386684e-17 0.2307972956362909 +Sample_2 G3P 2 24800.0 19465.731702013378 0.013602935162211748 -5.088793967116678e-17 0.2307972956362909 +Sample_2 G3P 3 133000.0 130583.22551280692 0.09125344873316321 1.2213105521080026e-16 0.2307972956362909 +Sample_1 2/3PG 0 1430000.0 1441469.8983039188 0.26951520374142846 0.0 0.350613297990272 +Sample_1 2/3PG 1 2920000.0 2940779.0438875123 0.5498447550687304 0.0 0.350613297990272 +Sample_1 2/3PG 2 226000.0 213534.01511096465 0.03992498466743767 1.0898270157923124e-17 0.350613297990272 +Sample_1 2/3PG 3 765000.0 752597.6842841837 0.1407150565224034 2.1796540315846248e-17 0.350613297990272 +Sample_2 2/3PG 0 1430000.0 1441469.8983039188 0.26951520374142846 0.0 0.350613297990272 +Sample_2 2/3PG 1 2920000.0 2940779.0438875123 0.5498447550687304 0.0 0.350613297990272 +Sample_2 2/3PG 2 226000.0 213534.01511096465 0.03992498466743767 1.0898270157923124e-17 0.350613297990272 +Sample_2 2/3PG 3 765000.0 752597.6842841837 0.1407150565224034 2.1796540315846248e-17 0.350613297990272 +Sample_1 E4P 0 854.0 863.1453281237473 0.041336917027350754 2.4329549962951284e-14 0.3817239095188967 +Sample_1 E4P 1 10200.0 10307.12055255345 0.4936185983859252 -1.0461978931437058e-14 0.3817239095188967 +Sample_1 E4P 2 7760.0 7810.814463659301 0.37406793373042024 1.508268629282176e-14 0.3817239095188967 +Sample_1 E4P 3 1730.0 1644.6719684418108 0.0787650311963941 -2.3299698911887947e-14 0.3817239095188967 +Sample_1 E4P 4 320.0 254.98554081254488 0.012211519659909676 3.423846073733581e-14 0.3817239095188967 +Sample_2 E4P 0 854.0 863.1453281237473 0.041336917027350754 2.4329549962951284e-14 0.3817239095188967 +Sample_2 E4P 1 10200.0 10307.12055255345 0.4936185983859252 -1.0461978931437058e-14 0.3817239095188967 +Sample_2 E4P 2 7760.0 7810.814463659301 0.37406793373042024 1.508268629282176e-14 0.3817239095188967 +Sample_2 E4P 3 1730.0 1644.6719684418108 0.0787650311963941 -2.3299698911887947e-14 0.3817239095188967 +Sample_2 E4P 4 320.0 254.98554081254488 0.012211519659909676 3.423846073733581e-14 0.3817239095188967 +Sample_3 Fum TMS 0 376000.0 425785.0538505561 0.45766573056460497 0.0 0.2626278340043467 +Sample_3 Fum TMS 1 235000.0 229433.5002431335 0.24661234478564592 -3.1600250224466564e-17 0.2626278340043467 +Sample_3 Fum TMS 2 127000.0 105318.33031467753 0.11320404544361702 -3.1600250224466564e-17 0.2626278340043467 +Sample_3 Fum TMS 3 143000.0 141951.9567793512 0.15258061648002147 3.1600250224466564e-17 0.2626278340043467 +Sample_3 Fum TMS 4 40000.0 27851.853810968023 0.029937262726110622 0.0 0.2626278340043467 +Sample_3 OA TMS 0 0.0 0.0 +Sample_3 OA TMS 1 0.0 0.0 +Sample_3 OA TMS 2 0.0 0.0 +Sample_3 OA TMS 3 0.0 0.0 +Sample_3 OA TMS 4 0.0 0.0 +Sample_3 aKG TMS 0 761000.0 864080.4383954712 0.6634102607174354 -1.4215099326884681e-05 0.1302868347875265 +Sample_3 aKG TMS 1 95100.0 33111.70372452174 0.02542198969516514 -7.027619573886684e-05 0.1302868347875265 +Sample_3 aKG TMS 2 391000.0 400501.8154913149 0.3074910645197312 0.0005087109208496222 0.1302868347875265 +Sample_3 aKG TMS 3 39300.0 4788.818975572151 0.003676685067668318 0.0011821047313132886 0.1302868347875265 +Sample_3 aKG TMS 4 0.0 0.0 0.0 -0.013225164964720594 0.1302868347875265 +Sample_3 aKG TMS 5 0.0 0.0 0.0 -0.000751685958158175 0.1302868347875265 +Sample_3 G3P TMS 0 715000.0 806222.8908729891 0.5421097940219233 0.0011462823123024992 0.20893939381005114 +Sample_3 G3P TMS 1 557000.0 555357.5466204376 0.37342621825203837 0.002864378095056404 0.20893939381005114 +Sample_3 G3P TMS 2 24800.0 0.0 0.0 -0.03321751751634703 0.20893939381005114 +Sample_3 G3P TMS 3 133000.0 125614.40709996362 0.08446398772603834 -2.6150701541736555e-12 0.20893939381005114 +Sample_3 2/3PG TMS 0 1430000.0 1613070.9343452677 0.2934931923774996 0.0004794245823734611 0.3239815179271314 +Sample_3 2/3PG TMS 1 2920000.0 3153601.731582657 0.5737879345430535 0.0011960645935207325 0.3239815179271314 +Sample_3 2/3PG TMS 2 226000.0 0.0 0.0 -0.01388900414166337 0.3239815179271314 +Sample_3 2/3PG TMS 3 765000.0 729437.5548178032 0.1327188730794469 1.6153633993476813e-12 0.3239815179271314 +Sample_3 E4P TMS 0 854.0 967.700772009107 0.046150526549923535 -2.9138586415226663e-06 0.3493645351728113 +Sample_3 E4P TMS 1 10200.0 11473.616488166983 0.5471871653687257 -1.4649378122356719e-05 0.3493645351728113 +Sample_3 E4P TMS 2 7760.0 7752.336450775334 0.369715948921533 0.00010602215694356356 0.3493645351728113 +Sample_3 E4P TMS 3 1730.0 774.7044932023791 0.036946359159817824 0.000251776357076686 0.3493645351728113 +Sample_3 E4P TMS 4 320.0 0.0 0.0 -0.002903094538807673 0.3493645351728113 +