# HG changeset patch
# User gmat
# Date 1558942416 14400
# Node ID 96f7617b4848d8ac4870b05a221d4c6c0d835b23

planemo upload

diff -r 000000000000 -r 96f7617b4848 isocor.xml
--- /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>
diff -r 000000000000 -r 96f7617b4848 test-data/Data_example.tsv
--- /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
diff -r 000000000000 -r 96f7617b4848 test-data/Derivatives.dat
--- /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
diff -r 000000000000 -r 96f7617b4848 test-data/Isotopes.dat
--- /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
diff -r 000000000000 -r 96f7617b4848 test-data/Metabolites.dat
--- /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
diff -r 000000000000 -r 96f7617b4848 test-data/results.log
--- /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
diff -r 000000000000 -r 96f7617b4848 test-data/results.tsv
--- /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
+