getWoLFScores Calls WoLF PSort to predict the sub-cellular localization of proteins. The output can be used as input to predictLocalization. This function is currently only available for Linux and requires PERL to be installed. If you want to use another predictor, see parseScores. inputFile a FASTA file with protein sequences kingdom the kingdom of the organism, 'animal', 'fungi' or 'plant'. The function normalizes the scores so that the best score for each gene is 1.0. geneScoreStructure a structure to be used in predictLocalization Usage: geneScoreStruct=getWoLFScores(inputFile,kingdom) Rasmus Agren, 2012-03-27
0001 function geneScoreStruct=getWoLFScores(inputFile,kingdom) 0002 % getWoLFScores 0003 % Calls WoLF PSort to predict the sub-cellular localization of proteins. 0004 % The output can be used as input to predictLocalization. This function 0005 % is currently only available for Linux and requires PERL to be 0006 % installed. If you want to use another predictor, see parseScores. 0007 % 0008 % inputFile a FASTA file with protein sequences 0009 % kingdom the kingdom of the organism, 'animal', 'fungi' or 'plant'. 0010 % 0011 % The function normalizes the scores so that the best score for each gene 0012 % is 1.0. 0013 % 0014 % geneScoreStructure a structure to be used in predictLocalization 0015 % 0016 % Usage: geneScoreStruct=getWoLFScores(inputFile,kingdom) 0017 % 0018 % Rasmus Agren, 2012-03-27 0019 0020 if ~strcmp(kingdom,'animal') && ~strcmp(kingdom,'fungi') && ~strcmp(kingdom,'plant') 0021 dispEM('Allowed kingdoms are "animal", "fungi", and "plant"'); 0022 end 0023 0024 if ispc==true 0025 dispEM('This function currently runs only on Linux. Use parseScores if you want to use another predictor'); 0026 end 0027 0028 %Get the directory for RAVEN Toolbox. This may not be the easiest or best 0029 %way to do this 0030 [ST I]=dbstack('-completenames'); 0031 ravenPath=fileparts(ST(I).file); 0032 0033 %Temporary output name 0034 outFile=tempname; 0035 fid=fopen(outFile,'w'); 0036 0037 %Do the prediction 0038 [crap output]=unix(['perl ' ravenPath '/software/WoLFPSORT_package_v0.2/bin/runWolfPsortSummary ' kingdom ' < ' inputFile]); 0039 0040 %Save output and call the general parser 0041 fprintf(fid,output); 0042 fclose(fid); 0043 geneScoreStruct=parseScores(outFile,'wolf'); 0044 0045 %Clean up 0046 delete(outFile);