Merge pull request #440 from SysBioChalmers/addCompartmentPrediction

feat: add compartment info from deeploc2 prediction

code/modelCuration/getCompFromDeepLoc2.m

@@ -0,0 +1,60 @@
+% This function is to extract the compartment prediction from DeepLoc2 tool
+% to expand the gene.tsv file.
+% Only when there is not such info from cellAtlas or SwissPort, we use the
+% compartment prediction from the DeepLoc2.
+% DeepLoc2 is used for the localization prediction, the protein fasta file
+% for all metabolic proteins in the model was used as the input file, the
+% default parameter was used in the prediction, output file is stored as
+% DeepLoc2_compartment.tsv in ../../data/modelCuration
+
+% Read the predicted compartment info
+fileName = '../../data/modelCuration/DeepLoc2_compartment.csv';
+fid  = fopen(fileName);
+DeeplocData = textscan(fid,[repmat('%s ',[1,12]) '%s'],'Delimiter',',');
+DeeplocData = [DeeplocData{1:end}];
+DeeplocData = DeeplocData(2:end,:);
+DeeplocData(:,[1,14]) = split(DeeplocData(:,1),';');
+fclose(fid);
+
+% Read gene.tsv
+fileName = '../../model/genes.tsv';
+fid  = fopen(fileName);
+geneData = textscan(fid,[repmat('%s ',[1,9]) '%s'],'Delimiter','\t');
+geneData = [geneData{1:end}];
+fclose(fid);
+geneData = strrep(geneData,'"','');
+
+% index the DeeplocDdata by geneData order
+DeeplocDdata_sorted(1:length(geneData(:,1)),1:length(DeeplocData(1,:))) = {''};
+[~,idx] = ismember(geneData(:,1),DeeplocData(:,1));
+DeeplocDdata_sorted(idx~=0,:) = DeeplocData(idx(idx~=0),:);
+
+
+% build a dict for key word mapping of compartment assignment
+DeepLoc_keywords = {'Cytoplasm','Cytosol';
+'Nucleus','Nucleus';
+'Extracellular','Extracellular';
+'Cell membrane','Cell membrane';
+'Mitochondrion','Mitochondria';
+'Plastid','';
+'Endoplasmic reticulum','Endoplasmic reticulum';
+'Lysosome/Vacuole','Lysosome';
+'Golgi apparatus','Golgi apparatus';
+'Peroxisome','Peroxisome'
+'|',';'};
+for i = 1:length(DeepLoc_keywords(:,1))
+    DeeplocDdata_sorted(:,2) = strrep(DeeplocDdata_sorted(:,2),DeepLoc_keywords{i,1},DeepLoc_keywords{i,2});
+end
+% fill the compartment for protein without localization info from CellAtlas
+%and SwissPort
+idx = cellfun(@isempty,geneData(:,9)) & ~(cellfun(@isempty,DeeplocDdata_sorted(:,1)));
+geneData(idx,9) = DeeplocDdata_sorted(idx,2);
+geneData(idx,10) = {'DeepLoc2'};
+
+% write out gene.tsv
+out = geneData';
+fID = fopen('../../model/genes.tsv','w');
+fprintf(fID,[repmat('%s\t',[1,9]) '%s\n'],out{1:10});
+fprintf(fID,[repmat('"%s"\t',[1,9]) '"%s"\n'],out{11:end});
+fclose(fID);
+