yeast 8.1.2

ComplementaryData/modelCuration/databasenewGPR.tsv

@@ -0,0 +1,46 @@
+rxnID_yeast_model	genes_yeast_model	final_GPR
+r_0308	YGL184C	( YFR055W or YGL184C )
+r_0148	YDR226W	( YDL166C or YDR226W )
+r_1729	NAN	YDL166C
+r_1077	YNR012W	( YDR020C or YNR012W )
+r_1078	YNR012W	( YDR020C or YNR012W )
+r_0226	(( Q0080 and Q0085 and Q0130 and YBL099W and YBR039W and YDL004W and YDR298C and YDR322C-A and YDR377W and YJR121W and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W ) or ( Q0080 and Q0085 and Q0130 and YBL099W and YBR039W and YDL004W and YDR298C and YDR377W and YJR121W and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W and YPR020W ))	(( Q0080 and Q0085 and Q0130 and YBL099W and YBR039W and YDL004W and YDR298C and YDR322C-A and YDR377W and YJR121W and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W ) or ( Q0080 and Q0085 and Q0130 and YBL099W and YBR039W and YDL004W and YDR298C and YDR377W and YJR121W and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W and YPR020W ) or ( Q0080 and Q0085 and Q0130 and YBL099W and YBR039W and YDL004W and YDR298C and YDR322C-A and YDR377W and YJR121W and YKL016C and YLR295C and YML081C-A and YPL078C and YPL271W and YJL180C and YLR393W and YNL315C and YOL077W-A and YCL005W-A))
+r_0364	YBR252W	( YJR069C or YBR252W )
+r_0815	YAL012W	( YLL058W or YML082W or YAL012W )
+r_0448	YJL155C	( YLR345W or YJL155C )
+r_0534	( YCL040W or YFR053C or YGL253W )	( YLR446W or YCL040W or YFR053C or YGL253W )
+r_0533	( YFR053C or YGL253W )	( YLR446W or YFR053C or YGL253W )
+r_0535	( YFR053C or YGL253W )	( YLR446W or YFR053C or YGL253W )
+r_0477	YKL104C	( YMR084W or YKL104C )
+r_2116	( YMR170C or YER073W or YOR374W )	( YMR110C or YMR170C or YER073W or YOR374W  )
+r_0172	( YMR169C or YMR170C )	( YMR110C or YMR169C or YMR170C )
+r_0483	( YBR244W or YCL035C or YDR513W or YIR037W or YKL026C )	( YNL229C or YBR244W or YCL035C or YDR513W or YIR037W or YKL026C )
+r_2025	NAN	YNR027W
+r_1185	YBR293W	( YOL092W or YBR293W )
+r_1200	( YBR293W or YCL069W or YMR088C )	( YOL092W or YBR293W or YCL069W or YMR088C )
+r_1212	( YBR293W or YCL069W or YMR088C )	( YOL092W or YBR293W or YCL069W or YMR088C )
+r_0366	( YGR254W or YHR174W ) 	( YPL281C or YGR254W or YHR174W or YMR323W or YOR393W)
+r_1805	NAN	( YBR241C or YGL104C )
+r_0783	YLR328W	( YCL047C or YLR328W )
+r_0530	( YDR376W and YPL252C )	( YER141W or (YDR376W and YPL252C) )
+r_1084	YKL035W	( YHL012W or YKL035W )
+r_0475	NAN	YFL060C
+r_4049	NAN	( YBL035C or YBR278W or YCR014C or YIR008C or YKL045W or YDL102W or YDL164C or YDR121W or YDR419W or YJR006W or YJR043C or YNL102W or YNL262W or YOR330C or YPL167C or YPR175W or YKR002W )
+r_4050	NAN	( YBR154C or YHR143W-A or YIL021W or YKL144C or YKR025W or YFL036W or YDL140C or YDL150W or YDR045C or YDR156W or YDR404C or YGL070C or YJL011C or YJL140W or YJL148W or YJR063W or YNL113W or YNL151C or YNL248C or YNR003C or YOL005C or YOR116C or YOR151C or YOR207C or YOR210W or YOR224C or YOR340C or YOR341W or YPR010C or YPR110C or YPR187W or YPR190C )
+r_0438	(( Q0045 and Q0250 and Q0275 and YDL067C and YEL039C and YGL187C and YGL191W and YHR051W and YIL111W and YLR038C and YLR395C and YMR256C ) or ( Q0045 and Q0250 and Q0275 and YDL067C and YEL039C and YGL187C and YGL191W and YHR051W and YLR038C and YLR395C and YMR256C and YNL052W ) or ( Q0045 and Q0250 and Q0275 and YDL067C and YGL187C and YGL191W and YHR051W and YIL111W and YJR048W and YLR038C and YLR395C and YMR256C ) or ( Q0045 and Q0250 and Q0275 and YDL067C and YGL187C and YGL191W and YHR051W and YJR048W and YLR038C and YLR395C and YMR256C and YNL052W ))	(( Q0045 and Q0250 and Q0275 and YDL067C and YEL039C and YGL187C and YGL191W and YHR051W and YIL111W and YLR038C and YLR395C and YMR256C ) or ( Q0045 and Q0250 and Q0275 and YDL067C and YEL039C and YGL187C and YGL191W and YHR051W and YLR038C and YLR395C and YMR256C and YNL052W ) or ( Q0045 and Q0250 and Q0275 and YDL067C and YGL187C and YGL191W and YHR051W and YIL111W and YJR048W and YLR038C and YLR395C and YMR256C ) or ( Q0045 and Q0250 and Q0275 and YDL067C and YGL187C and YGL191W and YHR051W and YJR048W and YLR038C and YLR395C and YMR256C and YNL052W ) or (Q0045 and Q0250 and Q0275 and YDL067C and YHR116W and YDR231C and YGR062C and YJL003W and YPL132W and YLL018C-A))
+r_1166	( YDL245C or YDL247W or YDR342C or YDR343C or YDR345C or YDR536W or YEL069C or YFL011W or YHR092C or YHR094C or YHR096C or YJL214W or YJL219W or YJR158W or YJR160C or YLR081W or YMR011W or YNR072W or YOL156W )	( YDL245C or YDL247W or YDR342C or YDR343C or YDR345C or YDR536W or YEL069C or YFL011W or YHR092C or YHR094C or YHR096C or YJL214W or YJL219W or YJR158W or YJR160C or YLR081W or YMR011W or YNR072W or YOL156W  or YDR387C )
+r_3264	( YBR204C or YKR089C or YMR313C or YOR081C )	( YBR204C or YKR089C or YMR313C or YOR081C or YCR068W )
+r_3297	YMR313C	( YCR068W or YMR313C )
+r_0804	YER005W	( YAL035W or YLL001W or YER005W )
+r_1667	NAN	YNL036W
+r_0005	( YGR032W or ( YLR342W and YCR034W ))	( YGR032W or YMR306W or ( YLR342W and YCR034W ))
+r_1172	YLL043W	( YFL054C or YLL043W )
+r_1217	YDR105C	( YCL025C  or YDR508C or YFL055W or YKR039W or YPL265W or YDR105C )
+r_1258	YLR138W	( YDR456W or YLR138W)
+r_1249	YJL129C	( YDR456W or YJL129C )
+r_0193	YPR026W	( YPR026W or YBR001C )
+r_2064	NAN	YDL024C
+r_0323	YJR159W	( YDL246C or YJR159W )
+r_0199	YMR293C	( YDR242W or YMR293C )
+r_0139	YML022W	( YDR441C or YML022W)
+r_0542	YDR234W	( YJL200C or YDR234W )

ComplementaryScripts/increaseVersion.m

@@ -46,8 +46,8 @@ function increaseVersion(bumpType)
 model = readCbModel('../ModelFiles/xml/yeastGEM.xml');
 
 %Include tag and save model:
-model.description = ['yeastGEM_v' newVersion];
-saveYeastModel(model)
+model.modelID = ['yeastGEM_v' newVersion];
+saveYeastModel(model,false)
 
 %Allow .mat & .xls storage:
 copyfile('../.gitignore','backup')

ComplementaryScripts/modelCuration/addDBNewGeneAnnotation.m

@@ -0,0 +1,52 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% addDBNewGeneAnnotation
+% Add changes from the database new anootation for new genes + manual curation on those changes
+% Input: model, databasenewGPR.tsv,SGDgeneNames.tsv.
+% As for the reference of new GPR, please find detailed information in:
+% ComplementaryData/databases/DBnewGeneAnnotation.tsv
+% NOTE: changeGeneAssociation.m is a function from cobra
+%
+% Feiran Li & Hongzhong Lu
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+% Load model
+cd ..
+model = loadYeastModel;
+
+% Change GPR relations
+fid           = fopen('../ComplementaryData/modelCuration/databasenewGPR.tsv');
+changegpr     = textscan(fid,'%s %s %s','Delimiter','\t','HeaderLines',1);
+newGPR.ID     = changegpr{1};
+newGPR.oldGPR = changegpr{2};
+newGPR.GPR    = changegpr{3};
+fclose(fid);
+for i = 1:length(newGPR.ID)
+    rxnIndex = find(strcmp(model.rxns, newGPR.ID(i)));
+    model    = changeGeneAssociation(model, model.rxns{rxnIndex}, newGPR.GPR{i});
+end
+
+% Delete unused genes (if any)
+model = removeUnusedGenes(model);
+
+% Add gene standard name for new genes
+fid = fopen('../ComplementaryData/databases/SGDgeneNames.tsv');
+yeast_gene_annotation = textscan(fid,'%s %s','Delimiter','\t','HeaderLines',1);
+fclose(fid);
+for i = 1: length(model.genes)
+    geneIndex = strcmp(yeast_gene_annotation{1}, model.genes{i});
+    if sum(geneIndex) == 1 && ~isempty(yeast_gene_annotation{2}{geneIndex})
+        model.geneNames{i} = yeast_gene_annotation{2}{geneIndex};
+    else
+        model.geneNames{i} = model.genes{i};
+    end
+end
+
+% Add protein name for genes
+for i = 1:length(model.genes)
+    model.proteins{i} = strcat('COBRAProtein',num2str(i));
+end
+
+% Save model:
+model = rmfield(model,'grRules');
+saveYeastModel(model)
+cd modelCuration

ComplementaryScripts/saveYeastModel.m

@@ -1,12 +1,16 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% saveYeastModel(model)
+% saveYeastModel(model,upDATE)
 % Saves model as a .xml, .txt and .yml file. Also updates complementary
-% files (boundaryMets.txt and dependencies.txt).
+% files (boundaryMets.txt, README.md and dependencies.txt).
 %
 % Benjamín J. Sánchez
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-function saveYeastModel(model)
+function saveYeastModel(model,upDATE)
+
+if nargin < 2
+    upDATE = true;
+end
 
 %Remove any space in rxnECNumbers:
 model.rxnECNumbers = strrep(model.rxnECNumbers,' ','');
@@ -16,8 +20,17 @@ function saveYeastModel(model)
 scriptFolder = fileparts(which(mfilename));
 currentDir = cd(scriptFolder);
 
-%Save changes to current model:
-writeCbModel(model,'sbml','../ModelFiles/xml/yeastGEM.xml');
+%Check if model is a valid SBML structure:
+writeCbModel(model,'sbml','tempModel.xml');
+[~,errors] = TranslateSBML('tempModel.xml');
+if ~isempty(errors)
+    delete('tempModel.xml');
+    error('Model should be a valid SBML structure. Please fix all errors before saving.')
+end
+
+%Update .xml, .txt and .yml models:
+copyfile('tempModel.xml','../ModelFiles/xml/yeastGEM.xml')
+delete('tempModel.xml');
 writeCbModel(model,'text','../ModelFiles/txt/yeastGEM.txt');
 exportForGit(model,'yeastGEM','..',{'yml'});
 
@@ -31,6 +44,31 @@ function saveYeastModel(model)
 end
 fclose(fid);
 
+%Update README file: date + size of model
+copyfile('../README.md','backup.md')
+fin  = fopen('backup.md','r');
+fout = fopen('../README.md','w');
+still_reading = true;
+while still_reading
+    inline = fgets(fin);
+    if ~ischar(inline)
+        still_reading = false;
+    else
+        if startsWith(inline,'* Last update: ') && upDATE
+            inline = ['* Last update: ' datestr(datetime,'yyyy-mm-dd') newline];
+        elseif startsWith(inline,'|_Saccharomyces cerevisiae_|')
+            inline = ['|_Saccharomyces cerevisiae_|[Yeast 7.6]' ...
+                '(https://sourceforge.net/projects/yeast/)|' ...
+                num2str(length(model.rxns)) '|' ...
+                num2str(length(model.mets)) '|' ...
+                num2str(length(model.genes)) '|' newline];
+        end
+        fwrite(fout,inline);
+    end
+end
+fclose('all');
+delete('backup.md');
+
 %Convert notation "e-005" to "e-05 " in stoich. coeffs. to avoid
 %inconsistencies between Windows and MAC:
 copyfile('../ModelFiles/xml/yeastGEM.xml','backup.xml')

ModelFiles/dependencies.txt

@@ -1,7 +1,7 @@
 MATLAB	9.4.0.813654 (R2018a)
 libSBML	5.17.0
 RAVEN_toolbox	2.0.0
-COBRA_toolbox	commit 4bfe8b3
+COBRA_toolbox	commit c72a7bd
 SBML_level	3
 SBML_version	1
 fbc_version	2