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fix-met.prop: correct metFormulas #155

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merged 7 commits into from
Dec 11, 2018
Merged

fix-met.prop: correct metFormulas #155

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b6f9eb8
fix-met.prop: correct metFormulas
wtscott31 Sep 3, 2018
275ed3e
fix-met.prop: correct metFormulas
wtscott31 Sep 14, 2018
3326a81
fix-met.prop: correct metFormula
wtscott31 Sep 28, 2018
90a9268
Merge branch 'devel' into fix/metFormulas
BenjaSanchez Oct 26, 2018
9451f05
fix-data: empty rows
BenjaSanchez Dec 6, 2018
5c4f58d
fix-data: carbohydrate formulas
BenjaSanchez Dec 6, 2018
763a9fd
feat-met.prop: chemical formulas
BenjaSanchez Dec 6, 2018
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19 changes: 19 additions & 0 deletions ComplementaryData/modelCuration/Missingmetaboliteformulas.tsv
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Original file line number Diff line number Diff line change
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Met ID Met Name Met Formula Source
s_0709[m] ferricytochrome c [mitochondrion] C42H44FeN8O8S2R4 https://www.genome.jp/dbget-bin/www_bget?cpd:C00125
s_0710[m] ferrocytochrome c [mitochondrion] C42H44FeN8O8S2R4 https://www.genome.jp/dbget-bin/www_bget?cpd:C00126
s_0773[c] glycogen [cytoplasm] C6H12O6 Monomeric form = glucose
s_0774[v] glycogen [vacuole] C6H12O6 Monomeric form = glucose
s_1107[c] mannan [cytoplasm] C6H12O6 Monomeric form = mannose
s_1108[er] mannan [endoplasmic reticulum] C6H12O6 Monomeric form = mannose
s_2775[m] 3-hydroxybutanoyl-ACP [mitochondrion] C4H7O2SR https://www.genome.jp/dbget-bin/www_bget?C04618
s_2778[m] trans-but-2-enoyl-ACP [mitochondrion] C4H5OS https://www.ebi.ac.uk/chebi/searchId.do?chebiId=132146
s_2779[m] trans-hex-2-enoyl-ACP [mitochondrion] C6H9OSR https://www.genome.jp/dbget-bin/www_bget?C05748
s_2780[m] trans-oct-2-enoyl-ACP [mitochondrion] C8H13OSR https://www.genome.jp/dbget-bin/www_bget?C05751
s_2812[erm] trans-icos-2-enoyl-CoA [endoplasmic reticulum membrane] C41H72N7O17P3S http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:75061
s_2889[p] trans-icos-2-enoyl-CoA [peroxisome] C41H72N7O17P3S http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:75061
s_2896[p] trans-2,cis-5-dodecadienoyl-CoA [peroxisome] C35H54N7O17P3S http://mousecyc.jax.org/META/NEW-IMAGE?type=COMPOUND&object=CPD0-1162
s_2904[p] (R)-3-hydroxyoctanoyl-CoA [peroxisome] C29H50N7O18P3S https://www.genome.jp/dbget-bin/www_bget?cpd:C05278
s_3479[ce] 1-acylglycerophosphoserine (16:0) [cell envelope] C22H44NP10 Found by elemental balance
s_3481[ce] 1-acylglycerophosphoserine (16:1) [cell envelope] C22H42NP10 Found by elemental balance
s_3483[ce] 1-acylglycerophosphoserine (18:0) [cell envelope] C24H48NP10 Found by elemental balance
s_3485[ce] 1-acylglycerophosphoserine (18:1) [cell envelope] C24H46NP10 Found by elemental balance
32 changes: 32 additions & 0 deletions ComplementaryScripts/modelCuration/updateMetaboliteFormula.m
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% model = updateMetaboliteFormula(model)
%
% Reads the data file and updates the metabolite formula information in the model
%
% William T. Scott, Jr.
% Last Update: 2018-08-23
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Load model
cd ..
model = loadYeastModel;

%Load data:
fid = fopen('../ComplementaryData/modelCuration/Missingmetaboliteformulas.tsv','r');
metaboliteData = textscan(fid,'%s %s %s %s %f32 %s','Delimiter','\t','HeaderLines',1);
fclose(fid);

%Update formulas:
for i = 1:length(metaboliteData{1})
for j = 1:length(model.mets)
if strcmp(model.metNames{j},metaboliteData{2}{i})
model.metFormulas{j} = metaboliteData{3}{i};
end
end
end

% Save model
saveYeastModel(model)
cd modelCuration

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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