diff --git a/.gitattributes b/.gitattributes index 7f4d5667..3e0ca4ab 100644 --- a/.gitattributes +++ b/.gitattributes @@ -10,4 +10,3 @@ mafft binary .gitattributes export-ignore .gitignore export-ignore .github export-ignore -*.mat filter=lfs diff=lfs merge=lfs -text diff --git a/doc/external/kegg/getGenesFromKEGG.html b/doc/external/kegg/getGenesFromKEGG.html index 2035078a..cba93c72 100644 --- a/doc/external/kegg/getGenesFromKEGG.html +++ b/doc/external/kegg/getGenesFromKEGG.html @@ -102,7 +102,7 @@

CROSS-REFERENCE INFORMATION ^ <h2><a name=SUBFUNCTIONS ^

+
  • function allKOs=getAllKOs(keggPath)
  • function downloadKEGGgenes()

    • SOURCE CODE ^

    0001 function model=getGenesFromKEGG(keggPath,koList)
@@ -178,273 +178,339 @@ 
    SOURCE CODE ^'external','kegg','keggGenes.mat');
-0074 if exist(genesFile, 'file')
-0075     fprintf(['Importing KEGG genes from ' strrep(genesFile,'\','/') '... ']);
-0076     load(genesFile);
-0077 else
-0078     fprintf(['NOTE: Cannot locate ' strrep(genesFile,'\','/') ', it will therefore be generated from the local KEGG database\n']);
-0079     if ~isfile(fullfile(keggPath,'ko')) || ~isfile(fullfile(keggPath,'reaction'))
-0080         EM=fprintf(['The files ''ko'' and ''reaction'' cannot be located at ' strrep(keggPath,'\','/') '/ and should be downloaded from the KEGG FTP\n']);
-0081         dispEM(EM);
-0082     else
-0083         fprintf('Generating keggGenes.mat file...\n');
-0084         %Get all KOs that are associated to reactions
-0085         allKOs=getAllKOs(keggPath);
-0086         
-0087         %Since the list of genes will be accessed many times the hash table
-0088         %is established
-0089         geneMap=containers.Map('KeyType','char','ValueType','int32');
-0090         
-0091         %Add new functionality in the order specified in models
-0092         model.id='KEGG';
-0093         model.name='Automatically generated from KEGG database';
-0094         
-0095         %Preallocate memory
-0096         model.rxns=cell(numel(allKOs),1);
-0097         model.rxnNames=cell(numel(allKOs),1);
-0098         
-0099         %Reserve space for 500000 genes
-0100         model.genes=cell(500000,1);
+0074 if ~exist(genesFile, 'file')
+0075     try
+0076         downloadKEGGgenes();
+0077     catch
+0078         %Download failed; fall through to local regeneration below
+0079     end
+0080 end
+0081 if exist(genesFile, 'file')
+0082     fprintf(['Importing KEGG genes from ' strrep(genesFile,'\','/') '... ']);
+0083     load(genesFile);
+0084 else
+0085     fprintf(['NOTE: Cannot locate ' strrep(genesFile,'\','/') ', it will therefore be generated from the local KEGG database\n']);
+0086     if ~isfile(fullfile(keggPath,'ko')) || ~isfile(fullfile(keggPath,'reaction'))
+0087         EM=fprintf(['The files ''ko'' and ''reaction'' cannot be located at ' strrep(keggPath,'\','/') '/ and should be downloaded from the KEGG FTP\n']);
+0088         dispEM(EM);
+0089     else
+0090         fprintf('Generating keggGenes.mat file...\n');
+0091         %Get all KOs that are associated to reactions
+0092         allKOs=getAllKOs(keggPath);
+0093         
+0094         %Since the list of genes will be accessed many times the hash table
+0095         %is established
+0096         geneMap=containers.Map('KeyType','char','ValueType','int32');
+0097         
+0098         %Add new functionality in the order specified in models
+0099         model.id='KEGG';
+0100         model.name='Automatically generated from KEGG database';
 0101         
-0102         %Load information on KO ID, name, and associated genes
-0103         fid = fopen(fullfile(keggPath,'ko'), 'r');
-0104         
-0105         %Keeps track of how many KOs that have been added
-0106         koCounter=0;
-0107         nGenes=0;
-0108         addingGenes=false;
-0109         
-0110         %These contain the mapping between KOs and genes and are used to
-0111         %generate the model.rxnGeneMat in the end
-0112         koIndex=zeros(5000000,1);
-0113         geneIndex=koIndex;
-0114         nMappings=0;
-0115         
-0116         skipRead=false;
-0117         
-0118         %Loop through the file
-0119         while 1
-0120             %Get the next line
-0121             if skipRead==false
-0122                 tline = fgetl(fid);
-0123             else
-0124                 skipRead=false;
-0125             end
-0126             
-0127             %Abort at end of file
-0128             if ~ischar(tline)
-0129                 break;
-0130             end
-0131             
-0132             %Skip '///'
-0133             if numel(tline)<12
-0134                 addingGenes=false;
-0135                 continue;
-0136             end
-0137             
-0138             %Check if it's a new reaction
-0139             if strcmp(tline(1:12),'ENTRY       ')
-0140                 %Check if it should be added
-0141                 koID=tline(13:18);
-0142                 
-0143                 if ismember(koID,allKOs)
-0144                     addMe=true;
-0145                     koCounter=koCounter+1;
-0146                 else
-0147                     addMe=false;
-0148                     continue;
-0149                 end
-0150                 
-0151                 %Add reaction ID (always 6 characters)
-0152                 model.rxns{koCounter}=koID;
-0153                 
-0154                 model.rxnNames{koCounter}='';
-0155                 %Will be overwritten if it exists
-0156             end
-0157             
-0158             %To get here we must be in a KO that should be added
-0159             if addMe==true
-0160                 %Add name
-0161                 if strcmp(tline(1:12),'DEFINITION  ')
-0162                     model.rxnNames{koCounter}=tline(13:end);
-0163                 end
-0164                 
-0165                 %Check if it's time to start adding genes
-0166                 if strcmp(tline(1:12),'GENES       ')
-0167                     addingGenes=true;
-0168                 end
-0169                 
-0170                 %Add genes
-0171                 if addingGenes==true
-0172                     %We are now adding genes for the current KO. All gene
-0173                     %rows start with 12 spaces. If this is not true it
-0174                     %means that there is additional annotation such as
-0175                     %AUTHORS. This is not common but it exists
-0176                     if strcmp(tline(1:12),'            ') || strcmp(tline(1:12),'GENES       ')
-0177                         geneLine=tline(13:end);
-0178                         
-0179                         %Check if the line is from a new organism of from
-0180                         %the same as before
-0181                         if strcmp(geneLine(4),':')
-0182                             %If organism id contains 3 letters;
-0183                             currentOrganism=geneLine(1:3);
-0184                             %Parse the string
-0185                             genes=regexp(geneLine(6:end),' ','split');
-0186                             genes=strcat(currentOrganism,':',genes(:));
-0187                         elseif strcmp(geneLine(5),':')
-0188                             %If organism id contains 4 letters;
-0189                             currentOrganism=geneLine(1:4);
-0190                             %Parse the string
-0191                             genes=regexp(geneLine(7:end),' ','split');
-0192                             genes=strcat(currentOrganism,':',genes(:));
-0193                         end
-0194                         
-0195                         %Add the genes to the gene list
-0196                         for i=1:numel(genes)
-0197                             geneString=genes{i};
-0198                             if geneMap.isKey(geneString)
-0199                                 index=geneMap(geneString);
-0200                             else
-0201                                 nGenes=nGenes+1;
-0202                                 model.genes{nGenes}=geneString;
-0203                                 index=nGenes;
-0204                                 geneMap(geneString)=index;
-0205                             end
-0206                             
-0207                             %Add the connection to the KO
-0208                             nMappings=nMappings+1;
-0209                             koIndex(nMappings)=koCounter;
-0210                             geneIndex(nMappings)=index;
-0211                         end
-0212                     else
-0213                         %Now we want to throw away everything until the
-0214                         %next entry
-0215                         while 1
-0216                             tline = fgetl(fid);
-0217                             if strcmp(tline,'///')
-0218                                 %When the new entry is found, skip reading
-0219                                 %one line to fit with the rest of the code
-0220                                 skipRead=true;
-0221                                 break;
-0222                             end
-0223                         end
-0224                     end
-0225                 end
-0226             end
-0227         end
-0228         %Close the file
-0229         fclose(fid);
-0230         
-0231         %If too much space was allocated, shrink the model
-0232         model.rxns=model.rxns(1:koCounter);
-0233         model.rxnNames=model.rxnNames(1:koCounter);
-0234         model.genes=model.genes(1:nGenes);
-0235         
-0236         %Retrieve and add the gene associations
-0237         model.rxnGeneMat=sparse(koIndex(1:nMappings),geneIndex(1:nMappings),ones(nMappings,1));
-0238         
-0239         %To make sure the size is correct if the last KOs don't have genes
-0240         if size(model.rxnGeneMat,1)~=koCounter
-0241             model.rxnGeneMat(koCounter,1)=0;
-0242         end
-0243         
-0244         %Trim the genes so that they only contain information that can be
-0245         %matched to the KEGG file of protein sequences (remove all
-0246         %information after first parenthesis)
-0247         %NOTE: For some reason the organism abbreviation should be in lower
-0248         %case in this database. Fix this here
-0249         for i=1:numel(model.genes)
-0250             parIndex=strfind(model.genes{i},'(');
-0251             if any(parIndex)
-0252                 model.genes{i}=model.genes{i}(1:parIndex-1);
-0253             end
-0254             colIndex=strfind(model.genes{i},':');
-0255             model.genes{i}=[lower(model.genes{i}(1:colIndex-1)) model.genes{i}(colIndex:end)];
-0256         end
-0257         
-0258         %Save the model structure
-0259         save(genesFile,'model');
-0260     end
-0261 end
-0262 
-0263 %Only get the KOs in koList
-0264 if nargin>1
-0265     I=~ismember(model.rxns,koList);
-0266     model=removeReactions(model,I,true,true);
-0267 end
-0268 fprintf('COMPLETE\n');
-0269 end
-0270 
-0271 function allKOs=getAllKOs(keggPath)
-0272 %Retrieves all KOs that are associated to reactions. This is because the
-0273 %number of genes in KEGG is very large so without this parsing it would
-0274 %take many hours
-0275 
-0276 allKOs={};
+0102         %Preallocate memory
+0103         model.rxns=cell(numel(allKOs),1);
+0104         model.rxnNames=cell(numel(allKOs),1);
+0105         
+0106         %Reserve space for 500000 genes
+0107         model.genes=cell(500000,1);
+0108         
+0109         %Load information on KO ID, name, and associated genes
+0110         fid = fopen(fullfile(keggPath,'ko'), 'r');
+0111         
+0112         %Keeps track of how many KOs that have been added
+0113         koCounter=0;
+0114         nGenes=0;
+0115         addingGenes=false;
+0116         
+0117         %These contain the mapping between KOs and genes and are used to
+0118         %generate the model.rxnGeneMat in the end
+0119         koIndex=zeros(5000000,1);
+0120         geneIndex=koIndex;
+0121         nMappings=0;
+0122         
+0123         skipRead=false;
+0124         
+0125         %Loop through the file
+0126         while 1
+0127             %Get the next line
+0128             if skipRead==false
+0129                 tline = fgetl(fid);
+0130             else
+0131                 skipRead=false;
+0132             end
+0133             
+0134             %Abort at end of file
+0135             if ~ischar(tline)
+0136                 break;
+0137             end
+0138             
+0139             %Skip '///'
+0140             if numel(tline)<12
+0141                 addingGenes=false;
+0142                 continue;
+0143             end
+0144             
+0145             %Check if it's a new reaction
+0146             if strcmp(tline(1:12),'ENTRY       ')
+0147                 %Check if it should be added
+0148                 koID=tline(13:18);
+0149                 
+0150                 if ismember(koID,allKOs)
+0151                     addMe=true;
+0152                     koCounter=koCounter+1;
+0153                 else
+0154                     addMe=false;
+0155                     continue;
+0156                 end
+0157                 
+0158                 %Add reaction ID (always 6 characters)
+0159                 model.rxns{koCounter}=koID;
+0160                 
+0161                 model.rxnNames{koCounter}='';
+0162                 %Will be overwritten if it exists
+0163             end
+0164             
+0165             %To get here we must be in a KO that should be added
+0166             if addMe==true
+0167                 %Add name
+0168                 if strcmp(tline(1:12),'DEFINITION  ')
+0169                     model.rxnNames{koCounter}=tline(13:end);
+0170                 end
+0171                 
+0172                 %Check if it's time to start adding genes
+0173                 if strcmp(tline(1:12),'GENES       ')
+0174                     addingGenes=true;
+0175                 end
+0176                 
+0177                 %Add genes
+0178                 if addingGenes==true
+0179                     %We are now adding genes for the current KO. All gene
+0180                     %rows start with 12 spaces. If this is not true it
+0181                     %means that there is additional annotation such as
+0182                     %AUTHORS. This is not common but it exists
+0183                     if strcmp(tline(1:12),'            ') || strcmp(tline(1:12),'GENES       ')
+0184                         geneLine=tline(13:end);
+0185                         
+0186                         %Check if the line is from a new organism of from
+0187                         %the same as before
+0188                         if strcmp(geneLine(4),':')
+0189                             %If organism id contains 3 letters;
+0190                             currentOrganism=geneLine(1:3);
+0191                             %Parse the string
+0192                             genes=regexp(geneLine(6:end),' ','split');
+0193                             genes=strcat(currentOrganism,':',genes(:));
+0194                         elseif strcmp(geneLine(5),':')
+0195                             %If organism id contains 4 letters;
+0196                             currentOrganism=geneLine(1:4);
+0197                             %Parse the string
+0198                             genes=regexp(geneLine(7:end),' ','split');
+0199                             genes=strcat(currentOrganism,':',genes(:));
+0200                         end
+0201                         
+0202                         %Add the genes to the gene list
+0203                         for i=1:numel(genes)
+0204                             geneString=genes{i};
+0205                             if geneMap.isKey(geneString)
+0206                                 index=geneMap(geneString);
+0207                             else
+0208                                 nGenes=nGenes+1;
+0209                                 model.genes{nGenes}=geneString;
+0210                                 index=nGenes;
+0211                                 geneMap(geneString)=index;
+0212                             end
+0213                             
+0214                             %Add the connection to the KO
+0215                             nMappings=nMappings+1;
+0216                             koIndex(nMappings)=koCounter;
+0217                             geneIndex(nMappings)=index;
+0218                         end
+0219                     else
+0220                         %Now we want to throw away everything until the
+0221                         %next entry
+0222                         while 1
+0223                             tline = fgetl(fid);
+0224                             if strcmp(tline,'///')
+0225                                 %When the new entry is found, skip reading
+0226                                 %one line to fit with the rest of the code
+0227                                 skipRead=true;
+0228                                 break;
+0229                             end
+0230                         end
+0231                     end
+0232                 end
+0233             end
+0234         end
+0235         %Close the file
+0236         fclose(fid);
+0237         
+0238         %If too much space was allocated, shrink the model
+0239         model.rxns=model.rxns(1:koCounter);
+0240         model.rxnNames=model.rxnNames(1:koCounter);
+0241         model.genes=model.genes(1:nGenes);
+0242         
+0243         %Retrieve and add the gene associations
+0244         model.rxnGeneMat=sparse(koIndex(1:nMappings),geneIndex(1:nMappings),ones(nMappings,1));
+0245         
+0246         %To make sure the size is correct if the last KOs don't have genes
+0247         if size(model.rxnGeneMat,1)~=koCounter
+0248             model.rxnGeneMat(koCounter,1)=0;
+0249         end
+0250         
+0251         %Trim the genes so that they only contain information that can be
+0252         %matched to the KEGG file of protein sequences (remove all
+0253         %information after first parenthesis)
+0254         %NOTE: For some reason the organism abbreviation should be in lower
+0255         %case in this database. Fix this here
+0256         for i=1:numel(model.genes)
+0257             parIndex=strfind(model.genes{i},'(');
+0258             if any(parIndex)
+0259                 model.genes{i}=model.genes{i}(1:parIndex-1);
+0260             end
+0261             colIndex=strfind(model.genes{i},':');
+0262             model.genes{i}=[lower(model.genes{i}(1:colIndex-1)) model.genes{i}(colIndex:end)];
+0263         end
+0264         
+0265         %Save the model structure
+0266         save(genesFile,'model');
+0267     end
+0268 end
+0269 
+0270 %Only get the KOs in koList
+0271 if nargin>1
+0272     I=~ismember(model.rxns,koList);
+0273     model=removeReactions(model,I,true,true);
+0274 end
+0275 fprintf('COMPLETE\n');
+0276 end
 0277 
-0278 %First check if the reactions have already been parsed
-0279 ravenPath=findRAVENroot;
-0280 rxnsFile=fullfile(ravenPath,'external','kegg','keggRxns.mat');
-0281 if exist(rxnsFile, 'file')
-0282     fprintf(['NOTE: Importing KEGG ORTHOLOGY list from ' strrep(rxnsFile,'\','/') '.\n']);
-0283     load(rxnsFile,'model');
-0284     
-0285     %Loop through the reactions and add the corresponding genes
-0286     for i=1:numel(model.rxns)
-0287         if isstruct(model.rxnMiriams{i})
-0288             %Get all KOs
-0289             allKOs=[allKOs;model.rxnMiriams{i}.value(strcmpi(model.rxnMiriams{i}.name,'kegg.orthology'))];
-0290         end
-0291     end
-0292 else
-0293     %Parse the reaction file instead First load information on reaction ID,
-0294     %reaction name, KO, pathway and ec-number
-0295     fid = fopen(fullfile(keggPath,'reaction'), 'r');
-0296     orthology=false;
-0297     while 1
-0298         %Get the next line
-0299         tline = fgetl(fid);
-0300         
-0301         %Abort at end of file
-0302         if ~ischar(tline)
-0303             break;
-0304         end
-0305         
-0306         %Skip '///'
-0307         if numel(tline)<12
-0308             continue;
-0309         end
-0310         
-0311         %Check if it's a new reaction
-0312         if strcmp(tline(1:12),'ENTRY       ')
-0313             orthology=false;
-0314         end
-0315         
-0316         if strcmp(tline(1:9),'REFERENCE')
-0317             orthology=false;
-0318         end
-0319         
-0320         %Add KO-ids
-0321         if numel(tline)>16
-0322             if strcmp(tline(1:16),'ORTHOLOGY   KO: ') || strcmp(tline(1:16),'            KO: ') || strcmp(tline(1:12),'ORTHOLOGY   ') || orthology==true
-0323                 if strcmp(tline(13:16),'KO:')
-0324                     %This is in the old version
-0325                     allKOs=[allKOs;tline(17:22)];
-0326                 elseif strcmp(tline(1:12),'ORTHOLOGY   ')
-0327                     %This means that it found one KO in the new format and
-0328                     %that subsequent lines might be other KOs
-0329                     orthology=true;
-0330                     allKOs=[allKOs;tline(13:18)];
-0331                 end
-0332             end
-0333         end
-0334     end
-0335     
-0336     %Close the file
-0337     fclose(fid);
-0338 end
-0339 allKOs=unique(allKOs);
-0340 end
    +0278 function allKOs=getAllKOs(keggPath) +0279 %Retrieves all KOs that are associated to reactions. This is because the +0280 %number of genes in KEGG is very large so without this parsing it would +0281 %take many hours +0282 +0283 allKOs={}; +0284 +0285 %First check if the reactions have already been parsed +0286 ravenPath=findRAVENroot; +0287 rxnsFile=fullfile(ravenPath,'external','kegg','keggRxns.mat'); +0288 if exist(rxnsFile, 'file') +0289 fprintf(['NOTE: Importing KEGG ORTHOLOGY list from ' strrep(rxnsFile,'\','/') '.\n']); +0290 load(rxnsFile,'model'); +0291 +0292 %Loop through the reactions and add the corresponding genes +0293 for i=1:numel(model.rxns) +0294 if isstruct(model.rxnMiriams{i}) +0295 %Get all KOs +0296 allKOs=[allKOs;model.rxnMiriams{i}.value(strcmpi(model.rxnMiriams{i}.name,'kegg.orthology'))]; +0297 end +0298 end +0299 else +0300 %Parse the reaction file instead First load information on reaction ID, +0301 %reaction name, KO, pathway and ec-number +0302 fid = fopen(fullfile(keggPath,'reaction'), 'r'); +0303 orthology=false; +0304 while 1 +0305 %Get the next line +0306 tline = fgetl(fid); +0307 +0308 %Abort at end of file +0309 if ~ischar(tline) +0310 break; +0311 end +0312 +0313 %Skip '///' +0314 if numel(tline)<12 +0315 continue; +0316 end +0317 +0318 %Check if it's a new reaction +0319 if strcmp(tline(1:12),'ENTRY ') +0320 orthology=false; +0321 end +0322 +0323 if strcmp(tline(1:9),'REFERENCE') +0324 orthology=false; +0325 end +0326 +0327 %Add KO-ids +0328 if numel(tline)>16 +0329 if strcmp(tline(1:16),'ORTHOLOGY KO: ') || strcmp(tline(1:16),' KO: ') || strcmp(tline(1:12),'ORTHOLOGY ') || orthology==true +0330 if strcmp(tline(13:16),'KO:') +0331 %This is in the old version +0332 allKOs=[allKOs;tline(17:22)]; +0333 elseif strcmp(tline(1:12),'ORTHOLOGY ') +0334 %This means that it found one KO in the new format and +0335 %that subsequent lines might be other KOs +0336 orthology=true; +0337 allKOs=[allKOs;tline(13:18)]; +0338 end +0339 end +0340 end +0341 end +0342 +0343 %Close the file +0344 fclose(fid); +0345 end +0346 allKOs=unique(allKOs); +0347 end +0348 +0349 function downloadKEGGgenes() +0350 % downloadKEGGgenes +0351 % Downloads keggGenes.mat from the RAVEN GitHub release into +0352 % external/kegg/. This file is distributed as a release asset rather +0353 % than shipped in the repository because it exceeds GitHub's 100 MB +0354 % file-size limit. +0355 % +0356 % The following asset is expected on the release tag defined below: +0357 % keggGenes.zip containing keggGenes.mat +0358 % +0359 % To force a refresh (for example, after a new KEGG snapshot has been +0360 % published with a new RAVEN release), delete +0361 % external/kegg/keggGenes.mat and call getGenesFromKEGG again. +0362 % +0363 % Usage: downloadKEGGgenes() +0364 +0365 % Release tag that hosts the data archive. Bump this for any RAVEN +0366 % release that ships an updated keggGenes.mat. +0367 releaseTag = 'v2.11.1'; +0368 +0369 archiveName = 'keggGenes.zip'; +0370 targetDir = fullfile(findRAVENroot(),'external','kegg'); +0371 targetFile = fullfile(targetDir,'keggGenes.mat'); +0372 url = ['https://github.com/SysBioChalmers/RAVEN/releases/download/',... +0373 releaseTag,'/',archiveName]; +0374 zipPath = fullfile(targetDir,archiveName); +0375 +0376 fprintf(['Downloading ' archiveName ' from RAVEN ' releaseTag ' release... ']); +0377 try +0378 websave(zipPath,url); +0379 catch ME +0380 if strcmp(ME.identifier,'MATLAB:webservices:HTTP404StatusCodeError') +0381 error(['Failed to download ' archiveName ': the server returned ' ... +0382 'a 404 error. If this persists, please report it at ' ... +0383 'https://github.com/SysBioChalmers/RAVEN/issues']); +0384 else +0385 rethrow(ME); +0386 end +0387 end +0388 fprintf('COMPLETE\n'); +0389 +0390 fprintf(['Extracting ' archiveName ' to ' strrep(targetDir,'\','/') '... ']); +0391 try +0392 unzip(zipPath,targetDir); +0393 catch ME +0394 if isfile(zipPath); delete(zipPath); end +0395 error(['Failed to extract ' archiveName '. The downloaded archive ' ... +0396 'may be corrupted.\nOriginal error: %s'],ME.message); +0397 end +0398 fprintf('COMPLETE\n'); +0399 +0400 if isfile(zipPath); delete(zipPath); end +0401 +0402 if ~isfile(targetFile) +0403 error(['keggGenes.mat was not found in ' archiveName ... +0404 '. Please verify the release asset contents.']); +0405 end +0406 end
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/external/kegg/index.html b/doc/external/kegg/index.html index 6bb246fa..ee196128 100644 --- a/doc/external/kegg/index.html +++ b/doc/external/kegg/index.html @@ -23,7 +23,7 @@

    Matlab files in this directory:

    Other Matlab-specific files in this directory:

    +
  • keggMets.mat
  • keggPhylDist.mat
  • keggRxns.mat
    • Generated by m2html © 2005
    diff --git a/external/kegg/getGenesFromKEGG.m b/external/kegg/getGenesFromKEGG.m index 12d267ca..0f29305a 100755 --- a/external/kegg/getGenesFromKEGG.m +++ b/external/kegg/getGenesFromKEGG.m @@ -71,6 +71,13 @@ ravenPath=findRAVENroot(); genesFile=fullfile(ravenPath,'external','kegg','keggGenes.mat'); +if ~exist(genesFile, 'file') + try + downloadKEGGgenes(); + catch + %Download failed; fall through to local regeneration below + end +end if exist(genesFile, 'file') fprintf(['Importing KEGG genes from ' strrep(genesFile,'\','/') '... ']); load(genesFile); @@ -338,3 +345,62 @@ end allKOs=unique(allKOs); end + +function downloadKEGGgenes() +% downloadKEGGgenes +% Downloads keggGenes.mat from the RAVEN GitHub release into +% external/kegg/. This file is distributed as a release asset rather +% than shipped in the repository because it exceeds GitHub's 100 MB +% file-size limit. +% +% The following asset is expected on the release tag defined below: +% keggGenes.zip containing keggGenes.mat +% +% To force a refresh (for example, after a new KEGG snapshot has been +% published with a new RAVEN release), delete +% external/kegg/keggGenes.mat and call getGenesFromKEGG again. +% +% Usage: downloadKEGGgenes() + +% Release tag that hosts the data archive. Bump this for any RAVEN +% release that ships an updated keggGenes.mat. +releaseTag = 'v2.11.1'; + +archiveName = 'keggGenes.zip'; +targetDir = fullfile(findRAVENroot(),'external','kegg'); +targetFile = fullfile(targetDir,'keggGenes.mat'); +url = ['https://github.com/SysBioChalmers/RAVEN/releases/download/',... + releaseTag,'/',archiveName]; +zipPath = fullfile(targetDir,archiveName); + +fprintf(['Downloading ' archiveName ' from RAVEN ' releaseTag ' release... ']); +try + websave(zipPath,url); +catch ME + if strcmp(ME.identifier,'MATLAB:webservices:HTTP404StatusCodeError') + error(['Failed to download ' archiveName ': the server returned ' ... + 'a 404 error. If this persists, please report it at ' ... + 'https://github.com/SysBioChalmers/RAVEN/issues']); + else + rethrow(ME); + end +end +fprintf('COMPLETE\n'); + +fprintf(['Extracting ' archiveName ' to ' strrep(targetDir,'\','/') '... ']); +try + unzip(zipPath,targetDir); +catch ME + if isfile(zipPath); delete(zipPath); end + error(['Failed to extract ' archiveName '. The downloaded archive ' ... + 'may be corrupted.\nOriginal error: %s'],ME.message); +end +fprintf('COMPLETE\n'); + +if isfile(zipPath); delete(zipPath); end + +if ~isfile(targetFile) + error(['keggGenes.mat was not found in ' archiveName ... + '. Please verify the release asset contents.']); +end +end diff --git a/external/kegg/keggGenes.mat b/external/kegg/keggGenes.mat deleted file mode 100644 index 2494cbe9..00000000 --- a/external/kegg/keggGenes.mat +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:d19545a9ec9bc2c0fc69dbfd80e26ffad18f5c7144a8dbc149f8702a1c895061 -size 117040308 diff --git a/external/kegg/keggMets.mat b/external/kegg/keggMets.mat index 784901c0..f0b11b9b 100644 Binary files a/external/kegg/keggMets.mat and b/external/kegg/keggMets.mat differ diff --git a/external/kegg/keggPhylDist.mat b/external/kegg/keggPhylDist.mat index 0f05bf94..16c9cb98 100644 Binary files a/external/kegg/keggPhylDist.mat and b/external/kegg/keggPhylDist.mat differ diff --git a/external/kegg/keggRxns.mat b/external/kegg/keggRxns.mat index f5a62f8d..b1c512e4 100644 Binary files a/external/kegg/keggRxns.mat and b/external/kegg/keggRxns.mat differ diff --git a/external/metacyc/metaCycEnzymes.mat b/external/metacyc/metaCycEnzymes.mat index 7b03db05..1caf660f 100644 Binary files a/external/metacyc/metaCycEnzymes.mat and b/external/metacyc/metaCycEnzymes.mat differ diff --git a/external/metacyc/metaCycMets.mat b/external/metacyc/metaCycMets.mat index 26707d6a..cb86ac0c 100644 Binary files a/external/metacyc/metaCycMets.mat and b/external/metacyc/metaCycMets.mat differ diff --git a/external/metacyc/metaCycRxns.mat b/external/metacyc/metaCycRxns.mat index e5c680ce..97a069a1 100644 Binary files a/external/metacyc/metaCycRxns.mat and b/external/metacyc/metaCycRxns.mat differ diff --git a/software/m2html/private/m2htmltoolbarimages.mat b/software/m2html/private/m2htmltoolbarimages.mat index 19e9f16b..2fd358ee 100644 Binary files a/software/m2html/private/m2htmltoolbarimages.mat and b/software/m2html/private/m2htmltoolbarimages.mat differ diff --git a/testing/unit_tests/test_data/ecoli_textbook.mat b/testing/unit_tests/test_data/ecoli_textbook.mat index 67e344ad..ac202963 100644 Binary files a/testing/unit_tests/test_data/ecoli_textbook.mat and b/testing/unit_tests/test_data/ecoli_textbook.mat differ diff --git a/testing/unit_tests/test_data/expBlastResults.mat b/testing/unit_tests/test_data/expBlastResults.mat index 7b81eac8..051bfa72 100644 Binary files a/testing/unit_tests/test_data/expBlastResults.mat and b/testing/unit_tests/test_data/expBlastResults.mat differ diff --git a/testing/unit_tests/test_data/expCdhitMafftOutput.mat b/testing/unit_tests/test_data/expCdhitMafftOutput.mat index d13059f6..6d80662d 100644 Binary files a/testing/unit_tests/test_data/expCdhitMafftOutput.mat and b/testing/unit_tests/test_data/expCdhitMafftOutput.mat differ diff --git a/testing/unit_tests/test_data/expDiamondResults.mat b/testing/unit_tests/test_data/expDiamondResults.mat index c242a16a..d064d42c 100644 Binary files a/testing/unit_tests/test_data/expDiamondResults.mat and b/testing/unit_tests/test_data/expDiamondResults.mat differ diff --git a/testing/unit_tests/test_data/importExportResults.mat b/testing/unit_tests/test_data/importExportResults.mat index 4a3f9c35..83f86ac8 100644 Binary files a/testing/unit_tests/test_data/importExportResults.mat and b/testing/unit_tests/test_data/importExportResults.mat differ diff --git a/testing/unit_tests/test_data/miriamTestOutput.mat b/testing/unit_tests/test_data/miriamTestOutput.mat index 8035ad4e..d5fc3b09 100644 Binary files a/testing/unit_tests/test_data/miriamTestOutput.mat and b/testing/unit_tests/test_data/miriamTestOutput.mat differ diff --git a/testing/unit_tests/test_data/solverTestOutput.mat b/testing/unit_tests/test_data/solverTestOutput.mat index aaec2fc2..a0e8dd76 100644 Binary files a/testing/unit_tests/test_data/solverTestOutput.mat and b/testing/unit_tests/test_data/solverTestOutput.mat differ diff --git a/tutorial/empty.mat b/tutorial/empty.mat index 7e05da08..936aead1 100644 Binary files a/tutorial/empty.mat and b/tutorial/empty.mat differ diff --git a/tutorial/iMK1208+suppInfo.mat b/tutorial/iMK1208+suppInfo.mat index 86a5fc7c..9aa45a08 100644 Binary files a/tutorial/iMK1208+suppInfo.mat and b/tutorial/iMK1208+suppInfo.mat differ diff --git a/tutorial/pathway.mat b/tutorial/pathway.mat index 5ffd49bc..bc01714f 100644 Binary files a/tutorial/pathway.mat and b/tutorial/pathway.mat differ diff --git a/tutorial/pcPathway.mat b/tutorial/pcPathway.mat index d696b633..acfa80b5 100644 Binary files a/tutorial/pcPathway.mat and b/tutorial/pcPathway.mat differ