added distributed models for testCreatePanModels

opencobra · Nov 6, 2024 · 15b8766 · 15b8766
1 parent a369b99
commit 15b8766
Show file tree

Hide file tree

Showing 5 changed files with 37 additions and 21 deletions.
diff --git a/src/analysis/multiSpecies/microbiomeModelingToolbox/mgPipe/retrieveModelStats.m b/src/analysis/multiSpecies/microbiomeModelingToolbox/mgPipe/retrieveModelStats.m
@@ -101,18 +101,18 @@
 % create violin plot of model stats
 if nargin <5
     % have reactions and metabolites in one plot
-    figure
-    subplot(1,2,1)
-    violinplot(data(:,1:2),{'Reactions','Metabolites'});
-    set(gca, 'FontSize', 12)
     % does not work if all data points are the same
-    if ~numel(unique(data(:,3)))==1
+    if ~numel(unique(data(:,1)))==1 && ~numel(unique(data(:,2)))==1 && ~numel(unique(data(:,3)))==1
+        figure
+        subplot(1,2,1)
+        violinplot(data(:,1:2),{'Reactions','Metabolites'});
+        set(gca, 'FontSize', 12)
         subplot(1,2,2)
         violinplot(data(:,3),{'Microbes'});
+        set(gca, 'FontSize', 12)
+        sgtitle('Reaction, metabolite and microbe numbers in microbiome models')
+        print('MicrobiomeModel_Sizes','-dpng','-r300')
     end
-    set(gca, 'FontSize', 12)
-    sgtitle('Reaction, metabolite and microbe numbers in microbiome models')
-    print('MicrobiomeModel_Sizes','-dpng','-r300')
 
 else
     % perform statistical analysis if file with stratification is provided

diff --git a/src/reconstruction/demeter/src/refinement/createPeriplasmaticSpace.m b/src/reconstruction/demeter/src/refinement/createPeriplasmaticSpace.m
@@ -71,6 +71,9 @@
                 transpRxns = findRxnsFromMets(model,exMets{i});
                 % remove exchange reactions
                 transpRxns(find(strncmp(transpRxns,'EX_',3)))=[];
+                % remove reactions that are already periplasmatic
+                forms = printRxnFormula(model,transpRxns);
+                transpRxns(find(contains(forms,'[p]')))=[];
                 for j=1:length(transpRxns)
                     rxnsToAdd{end+1} = [transpRxns{j} 'pp'];
                     rxnNames{end+1} = [model.rxnNames{find(strcmp(model.rxns,transpRxns{j}))} ', periplasmatic'];

diff --git a/test/verifiedTests/analysis/testMultiSpeciesModelling/testCreatePanModels.m b/test/verifiedTests/analysis/testMultiSpeciesModelling/testCreatePanModels.m
@@ -14,20 +14,33 @@
 fileDir = fileparts(which('testCreatePanModels'));
 cd(fileDir);
 
-% load the AGORA models
-websave('AGORA-master.zip','https://github.com/VirtualMetabolicHuman/AGORA/archive/master.zip')
-try
-    unzip('AGORA-master')
-end
-modPath = [pwd filesep 'AGORA-master' filesep 'CurrentVersion' filesep 'AGORA_1_03' filesep' 'AGORA_1_03_mat'];
-
+modelList={
+        'Abiotrophia_defectiva_ATCC_49176'
+        'Acidaminococcus_fermentans_DSM_20731'
+        'Acidaminococcus_intestini_RyC_MR95'
+        'Acidaminococcus_sp_D21'
+        'Acinetobacter_baumannii_AB0057'
+        'Acinetobacter_calcoaceticus_PHEA_2'
+        'Acinetobacter_haemolyticus_NIPH_261'
+        'Acinetobacter_johnsonii_SH046'
+        'Acinetobacter_junii_SH205'
+        'Acinetobacter_lwoffii_WJ10621'
+        'Acinetobacter_pittii_ANC_4052'
+        'Acinetobacter_radioresistens_NIPH_2130'
+        };
+    for i=1:length(modelList)
+        model = getDistributedModel([modelList{i} '.mat']);
+        % Save all the models into the modelFolder
+        save(fullfile(fileDir, modelList{i}), 'model');
+    end
+
 numWorkers=4;
 
 % create the pan-models on species level
 panPath=[pwd filesep 'panSpeciesModels'];
 
-builtTaxa = {'Acinetobacter junii','Bacteroides ovatus','Enterobacter cloacae','Megasphaera elsdenii','Ruminococcus flavefaciens'};
-createPanModels(modPath,panPath,'Species','AGORA_infoFile.xlsx',numWorkers,builtTaxa)
+builtTaxa = {'Abiotrophia defectiva','Acidaminococcus fermentans','Acidaminococcus intestini','Acidaminococcus sp. D21','Acinetobacter_baumannii','Acinetobacter haemolyticus','Acinetobacter johnsonii','Acinetobacter junii','Acinetobacter lwoffii','Acinetobacter pittii','Acinetobacter radioresistens'};
+createPanModels(fileDir,panPath,'Species','AGORA_infoFile.xlsx',numWorkers,builtTaxa)
 
 % test that pan-models can grow
 [notGrowing,Biomass_fluxes] = plotBiomassTestResults(panPath, 'pan-models','numWorkers',numWorkers);
@@ -41,8 +54,8 @@
 % create the pan-models on genus level
 panPath=[pwd filesep 'panGenusModels'];
 
-builtTaxa = {'Acinetobacter','Butyricimonas','Megasphaera','Ruminococcus'};
-createPanModels(modPath,panPath,'Genus','AGORA_infoFile.xlsx',numWorkers,builtTaxa);
+builtTaxa = {'Abiotrophia','Acidaminococcus','Acinetobacter'};
+createPanModels(fileDir,panPath,'Genus','AGORA_infoFile.xlsx',numWorkers,builtTaxa);
 
 % test that pan-models can grow
 [notGrowing,Biomass_fluxes] = plotBiomassTestResults(panPath, 'pan-models','numWorkers',numWorkers);

diff --git a/test/verifiedTests/analysis/testMultiSpeciesModelling/testJoinModelsPairwiseFromList.m b/test/verifiedTests/analysis/testMultiSpeciesModelling/testJoinModelsPairwiseFromList.m
@@ -28,8 +28,8 @@
         'Abiotrophia_defectiva_ATCC_49176'
         'Acidaminococcus_fermentans_DSM_20731'
         'Acidaminococcus_intestini_RyC_MR95'
-        'Acidaminococcus_sp_D21'
         'Acinetobacter_calcoaceticus_PHEA_2'
+        'Acinetobacter_baumannii_AB0057'
         };
     for i=1:length(modelList)
         model = getDistributedModel([modelList{i} '.mat']);

diff --git a/test/verifiedTests/analysis/testMultiSpeciesModelling/testSimulatePairwiseInteractions.m b/test/verifiedTests/analysis/testMultiSpeciesModelling/testSimulatePairwiseInteractions.m
@@ -30,8 +30,8 @@
         'Abiotrophia_defectiva_ATCC_49176'
         'Acidaminococcus_fermentans_DSM_20731'
         'Acidaminococcus_intestini_RyC_MR95'
-        'Acidaminococcus_sp_D21'
         'Acinetobacter_calcoaceticus_PHEA_2'
+        'Acinetobacter_baumannii_AB0057'
         };
     for i=1:length(modelList)
         model = getDistributedModel([modelList{i} '.mat']);