fix: use readYAMLmodel and writeYAMLmodel in funcs

SysBioChalmers · Dec 23, 2024 · 91a6e78 · 91a6e78
1 parent 1a562ce
commit 91a6e78
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Showing 8 changed files with 12 additions and 12 deletions.
diff --git a/code/DepMapGeneEss/PrepDepMapData.m b/code/DepMapGeneEss/PrepDepMapData.m
@@ -37,7 +37,7 @@
 save('data/arrayDataDepMap.mat','arrayDataDepMap');
 
 %Generate ftINIT prepData - only needs to be done once. Can take up to an hour to run
-model = importYaml('../../model/Human-GEM.yml');
+model = readYAMLmodel('../../model/Human-GEM.yml');
 [model.grRules, skipped] = simplifyGrRules(model.grRules, true);%takes a few minutes to run
 prepData = prepHumanModelForftINIT(model, true, '../../data/metabolicTasks/metabolicTasks_Essential.txt', '../../model/reactions.tsv');
 save('data/prepDataGeneSymbols.mat', 'prepData')
diff --git a/code/modelCuration/GlycolysisCuration.m b/code/modelCuration/GlycolysisCuration.m
@@ -2,7 +2,7 @@
 rxnStruct = importTsvFile('../../data/modelCuration/addRxnGly_20230414.tsv');
 MetStruct = importTsvFile('../../data/modelCuration/addMetGly_20230414.tsv');
 
-model = importYaml('Human-GEM.yml');
+model = readYAMLmodel('Human-GEM.yml');
 
 rxnsToAdd.rxns = rxnStruct.rxnID;
 rxnsToAdd.eccodes = rxnStruct.ECNumber;

diff --git a/code/modelCuration/addAAnewRxn20230518.m b/code/modelCuration/addAAnewRxn20230518.m
@@ -2,7 +2,7 @@
 rxnStruct = importTsvFile('../../data/modelCuration/addRxnAA_20230518.tsv');
 MetStruct = importTsvFile('../../data/modelCuration/addMetAA_20230518.tsv');
 
-model = importYaml('Human-GEM.yml');
+model = readYAMLmodel('Human-GEM.yml');
 
 rxnsToAdd.rxns = rxnStruct.rxnID;
 rxnsToAdd.eccodes = rxnStruct.ECNumber;
@@ -91,4 +91,4 @@
 structure.rxnRetired = [structure.rxnRetired;rxnStruct.emptyID(idx,1) ];
 
 exportTsvFile(structure, '../../model/reactions.tsv')
-exportYaml(newModel, 'Human-GEM.yml');
+writeYAMLmodel(newModel, 'Human-GEM.yml');
diff --git a/code/modelCuration/addRxnACOD1_20221102.m b/code/modelCuration/addRxnACOD1_20221102.m
@@ -1,5 +1,5 @@
 % load model and new reaction info
-ihuman = importYaml('../../model/Human-GEM.yml');
+ihuman = readYAMLmodel('../../model/Human-GEM.yml');
 rxnsToAdd = importTsvFile('../../data/modelCuration/addRxnACOD1_20221102.tsv');
 
 % add new genes to Human-GEM
@@ -28,6 +28,6 @@
 end
 
 % update yaml model and reaction association file
-exportYaml(newGEM, '../../model/Human-GEM.yml');
+writeYAMLmodel(newGEM, '../../model/Human-GEM.yml');
 exportTsvFile(rxnAssoc,'../../model/reactions.tsv');
 
diff --git a/code/modelCuration/changeCompAbbrevs.m b/code/modelCuration/changeCompAbbrevs.m
@@ -7,7 +7,7 @@
 modelname = 'Human-GEM';
 
 % load model and other data files
-model = importYaml(fullfile('..', '..', 'model', [modelname '.yml']));
+model = readYAMLmodel(fullfile('..', '..', 'model', [modelname '.yml']));
 metAssoc = importTsvFile(fullfile('..', '..', 'model', 'metabolites.tsv'));
 metAssoc_table = struct2table(metAssoc);
 metsDep = importTsvFile(fullfile('..', '..', 'data', 'deprecatedIdentifiers', 'deprecatedMetabolites.tsv'));
@@ -30,7 +30,7 @@
 metAssoc.mets = regexprep(metAssoc.mets, 'p$', 'x');
 
 % export the new model and files
-exportYaml(model, fullfile('..', '..', 'model', [modelname '.yml']));
+writeYAMLmodel(model, fullfile('..', '..', 'model', [modelname '.yml']));
 exportTsvFile(metAssoc, fullfile('..', '..', 'model', 'metabolites.tsv'));
 exportTsvFile(metsDep_table, fullfile('..', '..', 'data', 'deprecatedIdentifiers', 'deprecatedMetabolites.tsv'));
 

diff --git a/code/modelCuration/removeDuplicateRxns_issue345.m b/code/modelCuration/removeDuplicateRxns_issue345.m
@@ -1,7 +1,7 @@
 
 
 % load Human-GEM
-model = importYaml('../../model/Human-GEM.yml');
+model = readYAMLmodel('../../model/Human-GEM.yml');
 
 
 % specify pairs of duplicate reactions, where reactions in first column are
@@ -107,7 +107,7 @@
 
 % delete reactions from model and annotation file
 model = removeReactions(model, rxns(:,2));
-exportYaml(model, '../../model/Human-GEM.yml');
+writeYAMLmodel(model, '../../model/Human-GEM.yml');
 rxnAssocTable(rxn_indx(:,2), :) = [];
 exportTsvFile(rxnAssocTable, rxnAssocFile);
 

diff --git a/code/test/testMetabolicTasks.m b/code/test/testMetabolicTasks.m
@@ -20,7 +20,7 @@
 
 % Import yaml model
 ymlFile=fullfile(modelPath,'model','Human-GEM.yml');
-ihuman = importYaml(ymlFile, true);
+ihuman = readYAMLmodel(ymlFile);
 
 % parse metabolic tasks
 model = addBoundaryMets(ihuman);

diff --git a/code/updateAnimalGEM.m b/code/updateAnimalGEM.m
@@ -58,7 +58,7 @@
     load(matFile);
 elseif isfile(ymlFile)
     % Load Human-GEM Yaml file
-    ihuman = importYaml(ymlFile);
+    ihuman = readYAMLmodel(ymlFile);
 else
     error('ERROR: No model file is found!');
 end