Fixed some bugs in DEMETER/mgPipe

src/analysis/multiSpecies/microbiomeModelingToolbox/additionalAnalysis/analyzeMgPipeResults.m

@@ -112,9 +112,9 @@ function analyzeMgPipeResults(infoFilePath,resPath,varargin)
             % Print the results as a text file
             filename = strrep(fileList{i},'.csv','');
             filename = strrep(filename,'.txt','');
-            writetable(cell2table(Statistics),[statPath filesep filename '_' sampleGroupHeaders{j} '_Statistics'],'FileType','text','WriteVariableNames',false,'Delimiter','tab');
+            writetable(cell2table(Statistics),[statPath filesep filename '_' sampleGroupHeaders{j} '_Statistics.csv'],'WriteVariableNames',false);
             if size(significantFeatures,2)>1
-                writetable(cell2table(significantFeatures),[statPath filesep filename '_' sampleGroupHeaders{j} '_SignificantFeatures'],'FileType','text','WriteVariableNames',false,'Delimiter','tab');
+                writetable(cell2table(significantFeatures),[statPath filesep filename '_' sampleGroupHeaders{j} '_SignificantFeatures.csv'],'WriteVariableNames',false);
             end
 
             % create plots
@@ -133,9 +133,9 @@ function analyzeMgPipeResults(infoFilePath,resPath,varargin)
         % Print the results as a text file
         filename = strrep(fileList{i},'.csv','');
         filename = strrep(filename,'.txt','');
-        writetable(cell2table(Statistics),[statPath filesep filename '_Statistics'],'FileType','text','WriteVariableNames',false,'Delimiter','tab');
+        writetable(cell2table(Statistics),[statPath filesep filename '_Statistics.csv'],'WriteVariableNames',false);
         if size(significantFeatures,2)>1
-            writetable(cell2table(significantFeatures),[statPath filesep filename '_SignificantFeatures'],'FileType','text','WriteVariableNames',false,'Delimiter','tab');
+            writetable(cell2table(significantFeatures),[statPath filesep filename '_SignificantFeatures.csv'],'WriteVariableNames',false);
         end
 
         % create violin plots

src/analysis/multiSpecies/microbiomeModelingToolbox/additionalAnalysis/makeViolinPlots.m

@@ -54,9 +54,16 @@ function makeViolinPlots(sampleData, sampleInformation, varargin)
 cnt=1;
 delArray=[];
 for i=2:size(sampleData,1)
-    if sum(str2double(sampleData(i,2:end)))<0.0001
-        delArray(cnt,1)=i;
-        cnt=cnt+1;
+    if contains(version,'R202') % for MATLAB 2020a or newer
+        if sum(cell2mat(sampleData(i,2:end)))<0.0001
+            delArray(cnt,1)=i;
+            cnt=cnt+1;
+        end
+    else
+        if sum(str2double(sampleData(i,2:end)))<0.0001
+            delArray(cnt,1)=i;
+            cnt=cnt+1;
+        end
     end
 end
 sampleData(delArray,:)=[];

src/analysis/multiSpecies/microbiomeModelingToolbox/mgPipe/createPanModels.m

@@ -1,4 +1,4 @@
-function createPanModels(agoraPath, panPath, taxonLevel, agoraVersion, numWorkers)
+function createPanModels(agoraPath, panPath, taxonLevel, agoraVersion, numWorkers, builtTaxa)
 % This function creates pan-models for all unique taxa (e.g., species)
 % included in the AGORA resource. If reconstructions of multiple strains
 % in a given taxon are present, the reactions in these reconstructions will
@@ -23,16 +23,22 @@ function createPanModels(agoraPath, panPath, taxonLevel, agoraVersion, numWorker
 %                  created pan-models will be stored in. Must end with a file separator.
 %    taxonLevel    String with desired taxonomical level of the pan-models.
 %                  Allowed inputs are 'Species','Genus','Family','Order', 'Class','Phylum'.
-%    agoraVersion  Version of AGORA that will be used (allowed inputs: 'AGORA', 'AGORA2')
+%    agoraVersion  Version of AGORA that will be used (allowed inputs: 'AGORA', 'AGORA2', 
+%                  alternatively: path to custom table with reconstruction information)
 %
 % OPTIONAL INPUTS
 %    numWorkers    Number of workers for parallel pool (default: no pool)
+%    builtTaxa     Names of taxa in table that will be built (default:
+%                  all). Need to be entered as a cell array of strings with names written
+%                  exactly as in the corresponding column in the table.
 %
 % .. Authors
 %       - Stefania Magnusdottir, 2016
 %       - Almut Heinken, 06/2018: adapted to function.
 %       - Almut Heinken, 03/2021: enabled parallelization
 %       - Almut Heinken, 05/2024: enforced specifying AGORA version
+%       - Almut Heinken, 10/2024: allowed specifying input table and taxa
+%                                 to create
 
 tol = 1e-5;
 
@@ -58,13 +64,13 @@ function createPanModels(agoraPath, panPath, taxonLevel, agoraVersion, numWorker
 solver = CBT_LP_SOLVER;
 environment = getEnvironment();
 
-% load the file with information on AGORA/AGORA2
+% load the file with information on AGORA/AGORA2 or custom table
 if strcmp(agoraVersion,'AGORA')
     infoFile = readInputTableForPipeline('AGORA_infoFile.xlsx');
 elseif strcmp(agoraVersion,'AGORA2')
     infoFile = readInputTableForPipeline('AGORA2_infoFile.xlsx');
 else
-    error('Incorrect input for agoraVersion! Allowed inputs: AGORA, AGORA2')
+    infoFile = readInputTableForPipeline(agoraVersion);
 end
 
 % get the reaction and metabolite database
@@ -78,6 +84,12 @@ function createPanModels(agoraPath, panPath, taxonLevel, agoraVersion, numWorker
 allTaxa(strncmp(allTaxa, 'unclassified',  12)) = [];
 allTaxa(strcmp(allTaxa, '')) = [];
 
+% reduce to specified list of taxa to build if entered
+if nargin >5
+    [~,I] = setdiff(allTaxa,builtTaxa);
+    allTaxa(I,:) = [];
+end
+
 % Remove models that have already been assembled from the list of models to create
 dInfo = dir(panPath);
 dInfo = dInfo(~[dInfo.isdir]);

test/verifiedTests/analysis/testMultiSpeciesModelling/testCreatePanModels.m

@@ -26,7 +26,8 @@
 % create the pan-models on species level
 panPath=[pwd filesep 'panSpeciesModels'];
 
-createPanModels(modPath,panPath,'Species','AGORA',numWorkers);
+builtTaxa = {'Acinetobacter junii','Bacteroides ovatus','Enterobacter cloacae','Megasphaera elsdenii','Ruminococcus flavefaciens'};
+createPanModels(modPath,panPath,'Species','AGORA_infoFile.xlsx',numWorkers,builtTaxa)
 
 % test that pan-models can grow
 [notGrowing,Biomass_fluxes] = plotBiomassTestResults(panPath, 'pan-models','numWorkers',numWorkers);
@@ -40,7 +41,8 @@
 % create the pan-models on genus level
 panPath=[pwd filesep 'panGenusModels'];
 
-createPanModels(modPath,panPath,'Genus','AGORA',numWorkers);
+builtTaxa = {'Acinetobacter','Bacteroides','Megasphaera','Ruminococcus'};
+createPanModels(modPath,panPath,'Genus','AGORA_infoFile.xlsx',numWorkers,builtTaxa);
 
 % test that pan-models can grow
 [notGrowing,Biomass_fluxes] = plotBiomassTestResults(panPath, 'pan-models','numWorkers',numWorkers);