Merge pull request #155 from wtscott31/fix/metFormulas

fix-met.prop: correct metFormulas

ComplementaryData/modelCuration/Missingmetaboliteformulas.tsv

@@ -0,0 +1,19 @@
+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

ComplementaryScripts/modelCuration/updateMetaboliteFormula.m

@@ -0,0 +1,32 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% 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
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%