Human 1.17

.github/workflows/check-metabolictasks.yml

@@ -10,10 +10,9 @@ jobs:
       matrix:
         task-type: [essential, verification]
     steps:
+      - name: Checkout
+        uses: actions/checkout@v3
 
-    - name: Checkout
-      uses: actions/checkout@v3
-
-    - name: Check ${{ matrix.task-type }} metabolic tasks
-      run: |
-        /usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r "addpath(genpath('.')); testMetabolicTasks('${{ matrix.task-type }}'); exit;"
+      - name: Check ${{ matrix.task-type }} metabolic tasks
+        run: |
+          /usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r "addpath(genpath('.')); testMetabolicTasks('${{ matrix.task-type }}');"

.github/workflows/yaml-conversion.yml

@@ -8,10 +8,9 @@ jobs:
     timeout-minutes: 60
 
     steps:
+      - name: Checkout
+        uses: actions/checkout@v3
 
-    - name: Checkout
-      uses: actions/checkout@v3
-
-    - name: Run conversion script
-      run: |
-        /usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r "addpath(genpath('.')); run('code/test/testYamlConversion.m'); exit;" 
+      - name: Run conversion script
+        run: |
+          /usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r "addpath(genpath('.')); testYamlConversion"

.github/workflows/yaml-validation.yml

@@ -25,5 +25,8 @@ jobs:
           ## Return non-zero exit code on warnings as well as errors
           # strict: # optional, default is false
 
+      - name: Basic MEMOTE tests
+        run: python code/test/memoteTest.py
+
       - name: Test import with cobrapy and consistency with annotation files
-        run: python code/test/sanityCheck.py
+        run: python code/test/sanityCheck.py

code/GPRs/simplifyGrRules.m

@@ -176,7 +176,7 @@
 eqn = str2sym(eqn_str);
 
 % separate equation into terms/pieces ("children")
-eqn_pieces = arrayfun(@char,children(eqn),'UniformOutput',false);
+eqn_pieces = cellfun(@char,children(eqn),'UniformOutput',false);
 
 % find pieces that are further separable, and recursively separate until
 % all pieces are single genes
@@ -202,12 +202,14 @@
 %% Functions to test whether an equation is a collection of ORs or ANDs
 function res = is_or(eqn)
 % check if outermost operations contain ORs
-res = length(regexp(char(eqn),'\|')) > length(regexp(char(children(eqn)),'\|'));
+res = length(regexp(char(eqn),'\|')) > ...
+    sum(cell2mat(cellfun(@(x) length(regexp(char(x), '\|')), children(eqn), 'UniformOutput', false)));
 end
 
 function res = is_and(eqn)
 % check if outermost operations contain ANDs
-res = length(regexp(char(eqn),'&')) > length(regexp(char(children(eqn)),'&'));
+res = length(regexp(char(eqn),'&')) > ...
+    sum(cell2mat(cellfun(@(x) length(regexp(char(x), '\&')), children(eqn), 'UniformOutput', false)));
 end
 
 

code/addMetabolicNetwork.m

@@ -144,8 +144,11 @@
     newGenes = setdiff(newGenes, newModel.genes);
 end
 
-% append new genes to list of model genes
+% append new genes and their names to model
 newModel.genes = [newModel.genes; newGenes];
+emptyGeneNames = newGenes;
+emptyGeneNames(:) = {''};
+newModel.geneShortNames = [newModel.geneShortNames; emptyGeneNames];
 
 % add new columns to rxnGeneMat will be updated after the new reactions are added below.
 newModel.rxnGeneMat(:, end+1:end+numel(newGenes)) = 0;

code/test/memoteTest.py

@@ -0,0 +1,18 @@
+import cobra
+import memote.support.basic
+
+if __name__ == "__main__":
+    try:
+        model = cobra.io.load_yaml_model("model/Human-GEM.yml")
+
+        # Use the MEMOTE way of testing
+        # https://github.com/opencobra/memote/blob/c8bd3fe75e2d955deaec824d1e93ebe60e754710/tests/test_for_support/test_for_basic.py#L908-L909
+        rxns, num = memote.support.basic.find_duplicate_reactions(model)
+        assert num == 0, "Duplicate reactions found: {}".format(rxns)
+
+        # Make sure all reactions have at least one metabolite
+        for r in model.reactions:
+            assert len(r.metabolites) > 0, "Reaction with no metabolite found: {}".format(r.id)
+    except AssertionError as e:
+        print(e)
+        exit(1)

code/test/sanityCheck.py

@@ -38,8 +38,12 @@ def checkRxnAnnotation(rxns):
     rxnList = get_column_from_tsv("model/reactions.tsv", "rxns")
     spontaneous = get_column_from_tsv("model/reactions.tsv", "spontaneous", False)
     rxnDeprecated = get_column_from_tsv("data/deprecatedIdentifiers/deprecatedReactions.tsv", "rxns")
-    assert set(rxnList).isdisjoint(set(rxnDeprecated)), "Deprecated reaction reused!"
-    assert rxnList == rxns, "Reaction annotation mismatch!"
+    rxnMisused = set(rxns).intersection(set(rxnDeprecated))
+    assert len(rxnMisused) == 0, "Deprecated reaction(s) used: {}".format(rxnMisused)
+    rxnMisused = set(rxns).difference(set(rxnList))
+    assert len(rxnMisused) == 0, "Reaction(s) not annotated in reactions.tsv: {}".format(rxnMisused)
+    rxnMisused = set(rxnList).difference(set(rxns))
+    assert len(rxnMisused) == 0, "Annotated reactions are missing from the model: {}".format(rxnMisused)  
     assert pd.api.types.is_numeric_dtype(spontaneous), "Spontaneous column should be in numeric!"
 
 
@@ -49,16 +53,22 @@ def checkMetAnnotation(mets):
     """
     metList = get_column_from_tsv("model/metabolites.tsv", "mets")
     metDeprecated = get_column_from_tsv("data/deprecatedIdentifiers/deprecatedMetabolites.tsv", "mets")
-    assert set(metList).isdisjoint(set(metDeprecated)), "Deprecated metabolite reused!"
-    assert metList == mets, "Metabolite annotation mismatch!"
-
+    metMisused = set(mets).intersection(set(metDeprecated))
+    assert len(metMisused) == 0, "Deprecated metabolite(s) used: {}".format(metMisused)
+    metMisused = set(mets).difference(set(metList))
+    assert len(metMisused) == 0, "Metabolite(s) not annotated in metabolites.tsv: {}".format(metMisused)
+    metMisused = set(metList).difference(set(mets))
+    assert len(metMisused) == 0, "Annotated metabolite(s) are missing from the model: {}".format(metMisused)  
 
 def checkGeneAnnotation(genes):
     """
     check consistency of gene lists between model and annotation file
     """
     geneList = get_column_from_tsv("model/genes.tsv", "genes")
-    assert geneList == genes, "Gene annotation mismatch!"
+    geneMisused = set(genes).difference(set(geneList))
+    assert len(geneMisused) == 0, "Gene(s) not annotated in genes.tsv: {}".format(geneMisused)
+    geneMisused = set(geneList).difference(set(genes))
+    assert len(geneMisused) == 0, "Annotated gene(s) are missing from the model: {}".format(geneMisused)  
 
 
 def find_unused_entities(model, entity_type):
@@ -93,7 +103,7 @@ def checkUnusedEntities(model, entity_type):
 
     # collect unused entites
     unused_entities = find_unused_entities(model, entity_type)
-    assert len(unused_entities) == 0, f"Found unused {{entity_type}}!"
+    assert len(unused_entities) == 0, f"Found unused {entity_type}: {unused_entities}"
 
 
 if __name__ == "__main__":

code/test/testMetabolicTasks.m

@@ -10,7 +10,8 @@
 %
 
 if nargin < 1
-    error('Task type is missing!');
+    disp('::error::Task type is missing!');
+    exit(1)
 end
 
 % Get model path
@@ -28,7 +29,8 @@
 elseif taskType == "verification"
     taskFile=fullfile(modelPath,'data','metabolicTasks','metabolicTasks_VerifyModel.txt');
 else
-    error('Unknown task type is provided.');
+    warning('::error::Unknown task type is provided.');
+    exit(1)
 end
 verificationTasks = parseTaskList(taskFile);
 
@@ -38,6 +40,6 @@
     fprintf('Suceeded with %s tasks.\n', taskType)
     status = 1;
 else
-    error('Failed in %s tasks.', taskType);
+    warning('::error::Failed in %s tasks.', taskType);
+    exit(1)
 end
-

code/test/testYamlConversion.m

@@ -2,42 +2,40 @@
 % test the functions for yaml import/export see if the conversion process
 % changes the model content
 %
-% Usage: status = testYamlConversion
-%
-
 
 % Get model path
 [ST, I]=dbstack('-completenames');
 modelPath=fileparts(fileparts(fileparts(ST(I).file)));
 
-% Import yaml model
-ymlFile=fullfile(modelPath,'model','Human-GEM.yml');
-model = importYaml(ymlFile, true);
+% export to yml and then import back
+try
 
-% make sure there is no intermediate Yaml file under the current folder
-warning('off', 'MATLAB:DELETE:FileNotFound')
-if exist('testYamlConversion.yml','file')
-    delete testYamlConversion.yml;
-end
+    % Import yaml model
+    ymlFile=fullfile(modelPath,'model','Human-GEM.yml');
+    model = importYaml(ymlFile, true);
 
+    % make sure there is no intermediate Yaml file under the current folder
+    warning('off', 'MATLAB:DELETE:FileNotFound')
+    if exist('testYamlConversion.yml','file')
+        delete testYamlConversion.yml;
+    end
 
-% export to yml and then import back
-try
     exportYaml(model,'testYamlConversion.yml');
     importedHumanGEM = importYaml('testYamlConversion.yml', true);
-catch
-    error('There are problems during the conversion import and export');
-end
 
-% remove intermediate Yaml file
-delete testYamlConversion.yml;
+    % remove intermediate Yaml file
+    delete testYamlConversion.yml;
 
-% compare the imported model from yaml with the original one
-if isequal(model, importedHumanGEM)
-    % model conversion between Matlab and Yaml files is successful
-    disp('The conversion was successful.')
-    status = 1;
-else
-    error('There are problems during the conversion between Matlab and Yaml files');
+    % compare the imported model from yaml with the original one
+    if ~isequal(model, importedHumanGEM)
+        warning('::error::Re-imported model is diffrent from export');
+        exit(1);
+    end
+catch
+    warning('::error::There are problems during the conversion import and export');
+    exit(1)
 end
 
+% model conversion between Matlab and Yaml files is successful
+disp('The conversion was successful.')
+exit(0)

code/updateAnimalGEM.m

@@ -1,4 +1,4 @@
-function [animalGEM, speciesSpecNetwork, gapfillNetwork]=updateAnimalGEM(orthologPairs,rxnsToAdd,metsToAdd,modelId)
+function [animalGEM, speciesSpecNetwork, gapfillNetwork]=updateAnimalGEM(orthologPairs,rxnsToAdd,metsToAdd,modelId,resetBiomass)
 % updateAnimalGEM
 %   Generate a model by using the Human-GEM as a template and taking into
 %   account species-specific pathways/reactions
@@ -11,7 +11,9 @@
 %   rxnsToAdd            the structure of species-specific reactions
 %   metsToAdd            the structure of species-specific metabolites
 %   modelId              model id
-%
+%   resetBiomass         reset biomass objective function to "biomass_components"
+%                        which is constituted by generic componenets that
+%                        suppose to occur in a eukaryotic cell (opt, default TRUE)
 %
 %   Output:
 %   animalGEM            an updated animal GEM
@@ -81,7 +83,8 @@
 
 
 %% Gap-filling
-[animalGEM, gapfillNetwork]=gapfill4EssentialTasks(animalGEM,ihuman);
+[animalGEM, gapfillNetwork]=gapfill4EssentialTasks(animalGEM,ihuman,resetBiomass);
+animalGEM.b = animalGEM.b(:,1);   % ensure b field in single column
 
 
 %% post-gapfilling procedures

data/deprecatedIdentifiers/deprecatedMetabolites.tsv

@@ -2203,4 +2203,47 @@ mets	metsNoComp	metBiGGID	metKEGGID	metHMDBID	metChEBIID	metPubChemID	metLipidMa
 "MAM03573m"	"MAM03573"	"etfox"	""	""	""	""	""	""	""	"etfox"	"MNXM11479"	""	"etfox_m"
 "MAM03574m"	"MAM03574"	"etfrd"	""	""	""	""	""	""	""	"etfrd"	"MNXM11480"	""	"etfrd_m"
 "MAM03494c"	"MAM03494"	"c3dc"	""	""	""	"22833583"	""	""	""	"c3dc"	""	""	"c3dc_c"
-"MAM03494e"	"MAM03494"	"c3dc"	""	""	""	"22833583"	""	""	""	"c3dc"	""	""	"c3dc_s"
+"MAM03494e"	"MAM03494"	"c3dc"	""	""	""	"22833583"	""	""	""	"c3dc"	""	""	"c3dc_s"
+"MAM03318e"	"MAM03318"	"C02528"	"C02528"	"HMDB0000518"	"CHEBI:16755"	"10133"	""	""	""	"C02528"	"MNXM1183"	""	"C02528_s"
+"MAM03318c"	"MAM03318"	"C02528"	"C02528"	"HMDB0000518"	"CHEBI:16755"	"10133"	""	""	""	"C02528"	"MNXM1183"	""	"C02528_c"
+"MAM03318r"	"MAM03318"	"C02528"	"C02528"	"HMDB0000518"	"CHEBI:16755"	"10133"	""	""	""	"C02528"	"MNXM1183"	""	"C02528_r"
+"MAM03318m"	"MAM03318"	"C02528"	"C02528"	"HMDB0000518"	"CHEBI:16755"	"10133"	""	""	""	"C02528"	"MNXM1183"	""	"C02528_m"
+"MAM03325c"	"MAM03325"	"C08276"	"C08276"	"HMDB0001527"	"CHEBI:1438"	"563"	""	""	""	"C08276"	"MNXM2782"	""	"C08276_c"
+"MAM00591c"	"MAM00591"	""	"C14748"	""	"CHEBI:34306"	""	""	""	"HC02179"	""	"MNXM6760"	"m00591c"	"m00591c"
+"MAM00591e"	"MAM00591"	""	"C14748"	""	"CHEBI:34306"	""	""	""	"HC02179"	""	"MNXM6760"	"m00591s"	"m00591s"
+"MAM03162c"	"MAM03162"	""	"C05578"	""	"CHEBI:27404"	""	""	""	""	"M03162"	"MNXM2336"	"m03162c"	"m03162c"
+"MAM03231c"	"MAM03231"	""	""	""	"CHEBI:57277"	""	""	""	""	"3hppa"	""	""	"3hppa_c"
+"MAM03540c"	"MAM03540"	"ddeccrn"	""	""	""	"168381"	""	""	""	"ddeccrn"	""	""	"ddeccrn_c"
+"MAM03540e"	"MAM03540"	"ddeccrn"	""	""	""	"168381"	""	""	""	"ddeccrn"	""	""	"ddeccrn_s"
+"MAM03226m"	"MAM03226"	"3hibutcoa"	"C04047"	""	"CHEBI:15481"	""	""	""	""	"3hibutcoa"	"MNXM446"	""	"3hibutcoa_m"
+"MAM03884c"	"MAM03884"	"phyt"	"C01607"	"HMDB0000801"	"CHEBI:16285"	"26840"	""	""	""	"phyt"	"MNXM91275"	""	"phyt_c"
+"MAM03884e"	"MAM03884"	"phyt"	"C01607"	"HMDB0000801"	"CHEBI:16285"	"26840"	""	""	""	"phyt"	"MNXM91275"	""	"phyt_s"
+"MAM03554c"	"MAM03554"	"dmnoncoa"	""	""	""	""	""	""	""	"dmnoncoa"	"MNXM6100"	""	"dmnoncoa_c"
+"MAM03884x"	"MAM03884"	"phyt"	"C01607"	"HMDB0000801"	"CHEBI:16285"	"26840"	""	""	""	"phyt"	"MNXM91275"	""	"phyt_p"
+"MAM03354c"	"MAM03354"	"CE4837"	"C16171"	"HMDB0006516"	"CHEBI:63548"	"53477846"	""	"CE4837"	""	"CE4837"	"MNXM165171"	""	"CE4837_c"
+"MAM03332c"	"MAM03332"	"CE2516"	"C03242"	"HMDB0002925"	"CHEBI:53486"	"5280581"	""	"CE2516"	""	"CE2516"	"MNXM5607"	""	"CE2516_c"
+"MAM03332e"	"MAM03332"	""	"C03242"	"HMDB0002925"	"CHEBI:53486"	"5280581"	""	"CE2516"	""	"CE2516"	""	""	"CE2516_s"
+"MAM03354r"	"MAM03354"	"CE4837"	"C16171"	"HMDB0006516"	"CHEBI:63548"	"53477846"	""	"CE4837"	""	"CE4837"	"MNXM165171"	""	"CE4837_r"
+"MAM00029c"	"MAM00029"	""	""	""	"CHEBI:81563"	"16061126"	"LMFA03070025"	"CE7090"	""	"CE7090"	"MNXM33782"	"m00029c"	"m00029c"
+"MAM03368m"	"MAM03368"	""	"C05467"	"HMDB0006891"	"CHEBI:27379"	"440690"	""	"CE5169"	""	"CE5169"	""	""	"CE5169_m"
+"MAM03368x"	"MAM03368"	""	"C05467"	"HMDB0006891"	"CHEBI:27379"	"440690"	""	"CE5169"	""	"CE5169"	""	""	"CE5169_p"
+"MAM00902c"	"MAM00902"	""	""	""	""	""	""	"CE4820"	""	"CE4820"	"MNXM164259"	"m00902c"	"m00902c"
+"MAM00616m"	"MAM00616"	"cholcoar"	"C15613"	""	"CHEBI:37642"	"15942889"	"LMST01010218"	"CE5165"	"HC01348"	"cholcoar"	"MNXM549;MNXM90922;MNXM91096"	"m00616p"	"m00616p"
+"MAM00749m"	"MAM00749"	"cholcoads"	"C05460"	"HMDB0006889"	"CHEBI:27505"	"5280797"	"LMST01010217"	""	"HC01466"	"cholcoads"	"MNXM162945;MNXM2747"	"m00749m"	"m00749m"
+"MAM00036m"	"MAM00036"	""	"C05450"	""	"CHEBI:52050"	"46224537"	""	"CE5168"	""	"HC01459"	"MNXM732;MNXM827"	"m00036m"	"m00036m"
+"MAM00748m"	"MAM00748"	"cholcoaone"	"C05467"	"HMDB0006891"	"CHEBI:27379"	"440690"	"LMST01010216"	"CE5169"	"HC01473"	"cholcoaone"	"MNXM162946;MNXM873"	"m00748m"	"m00748m"
+"MAM03367m"	"MAM03367"	""	""	""	""	""	""	"CE5168"	""	"CE5168"	""	""	"CE5168_m"
+"MAM00618m"	"MAM00618"	"cholcoas"	"C17343"	""	"CHEBI:37643"	"15942888"	""	"CE5166"	""	"CE5166;cholcoas"	"MNXM1201;MNXM8131"	"m00618m"	"m00618m"
+"MAM01445m"	"MAM01445"	"cholate"	"C00695"	"HMDB0000619"	"CHEBI:16359"	"221493"	"LMST04010001"	""	"HC00502"	"cholate"	"MNXM450"	"m01445m"	"m01445m"
+"MAM01514m"	"MAM01514"	"cholcoa"	"C01794"	"HMDB0001374"	"CHEBI:15519"	"439573"	""	""	"HC00844"	"cholcoa"	"MNXM162468;MNXM431"	"m01514m"	"m01514m"
+"MAM00759c"	"MAM00759"	""	"C13712"	""	""	""	"LMST02030130"	""	""	"M00759"	"MNXM3494"	"m00759c"	"m00759c"
+"MAM01268c"	"MAM01268"	""	""	""	""	""	"PROTEIN"	""	""	"M01268"	""	"m01268c"	"m01268c"
+"MAM01268m"	"MAM01268"	""	""	""	""	""	"PROTEIN"	""	""	"M01268"	""	"m01268m"	"m01268m"
+"MAM01268n"	"MAM01268"	""	""	""	""	""	"PROTEIN"	""	""	"M01268"	""	"m01268n"	"m01268n"
+"MAM01268x"	"MAM01268"	""	""	""	""	""	"PROTEIN"	""	""	"M01268"	""	"m01268p"	"m01268p"
+"MAM01268r"	"MAM01268"	""	""	""	""	""	"PROTEIN"	""	""	"M01268"	""	"m01268r"	"m01268r"
+"MAM01268e"	"MAM01268"	""	""	""	""	""	"PROTEIN"	""	""	"M01268"	""	"m01268s"	"m01268s"
+"MAM02757c"	"MAM02757"	""	""	""	""	""	""	""	""	"M02757"	""	"m02757c"	"m02757c"
+"MAM02757l"	"MAM02757"	""	""	""	""	""	""	""	""	"M02757"	""	"m02757l"	"m02757l"
+"MAM02757n"	"MAM02757"	""	""	""	""	""	""	""	""	"M02757"	""	"m02757n"	"m02757n"
+"MAM01816n"	"MAM01816"	""	""	""	""	""	"PROTEIN"	""	""	"M01816"	""	"m01816n"	"m01816n"