Reads an output of the NeMo and construct a new output file which has been added the name of the related SBML metabolites or reactions %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% The "PostProcess" Functions in this toolbox do some changes on some useful structural plugins in the Cytoscape software. This function reads an output of the NeMo (a Cytoscape plugin), and construct a new output file which has been added the name of the related SBML metabolites or reactions. http://apps.cytoscape.org/apps/nemo Note: COBRA Toolbox must be installed in MATLAB before running this function Note: This function is applicable for MCODE analysis on Bipartite, Metabolite-Metabolite, and Enzyme-Enzyme networks (both Directed and Undirected). [Output] = postprocess_NeMo(fileName1,fileName2) INPUTS fileName1 text file includes NeMo results for network clustering fileName2 The metabolic Network in the SBML format OUTPUTS *_fileName_fileName2_NeMo_clusters.dat The output file which includes the name of the related SBML metabolites or reactions. *_fileName_fileName2_NeMo.dat This output file saves some data which will be used for the main output file in this program Yazdan Asgari 12/07/2012 http://lbb.ut.ac.ir %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0001 function [Output] = postprocess_NeMo(fileName1,fileName2) 0002 % Reads an output of the NeMo and construct a new output file which has been added the name of the related SBML metabolites or reactions 0003 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0004 % The "PostProcess" Functions in this toolbox do some changes on some useful structural plugins in the Cytoscape software. 0005 % This function reads an output of the NeMo (a Cytoscape plugin), 0006 % and construct a new output file which has been added the name of the related SBML metabolites or reactions. 0007 % http://apps.cytoscape.org/apps/nemo 0008 % Note: COBRA Toolbox must be installed in MATLAB before running this function 0009 % Note: This function is applicable for MCODE analysis on Bipartite, Metabolite-Metabolite, and Enzyme-Enzyme networks (both Directed and Undirected). 0010 % 0011 % [Output] = postprocess_NeMo(fileName1,fileName2) 0012 % 0013 %INPUTS 0014 % fileName1 text file includes NeMo results for network clustering 0015 % fileName2 The metabolic Network in the SBML format 0016 % 0017 %OUTPUTS 0018 % *_fileName_fileName2_NeMo_clusters.dat The output file which includes the name of the related SBML metabolites or reactions. 0019 % *_fileName_fileName2_NeMo.dat This output file saves some data which will be used for the main output file in this program 0020 % 0021 % Yazdan Asgari 12/07/2012 http://lbb.ut.ac.ir 0022 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0023 0024 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0025 % check validity of input files format 0026 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0027 check=regexp(fileName2,'.xml'); 0028 assert(~isempty(check),'Error in the second input: The fileName2 must contain .xml at its end') 0029 0030 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0031 % start time evaluation of program 0032 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0033 tic; 0034 0035 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0036 % reading the SBML file using COBRA Toolbox Command 0037 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0038 model=readCbModel(fileName2); 0039 0040 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0041 % reading an output of the MCODE and write first 10 lines to the new output file. 0042 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0043 fid = fopen(fileName1); 0044 outname1=strrep(fileName2,'.xml','_'); 0045 outname2=strcat(outname1,fileName1); 0046 outname3=strcat(outname2,'_NeMo_clusters.dat') 0047 fout = fopen(outname3, 'w+'); 0048 B={}; 0049 for i=1:10 0050 B{i}=fgetl(fid); 0051 fprintf(fout,'%s\n',B{i}); 0052 end 0053 0054 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0055 % reading the rest of the NeMo output file and construct a new output file, 0056 % which has been added the name of the related SBML metabolites or reactions. 0057 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0058 i=1; 0059 A={}; 0060 line={}; 0061 while ~feof(fid) 0062 A{i} = fscanf(fid,'%d %f %d %d'); 0063 line{i} = fgetl(fid); 0064 i=i+1; 0065 end 0066 0067 M={}; 0068 for j=1:i-1 0069 M{1,j}=regexp(line{1,j},',','split'); 0070 end 0071 fclose(fid); 0072 0073 outname4=strrep(fileName2,'.xml','_'); 0074 outname5=strcat(outname4,fileName1); 0075 outname6=strcat(outname5,'_NeMo.dat') 0076 fout2 = fopen(outname6, 'w+'); 0077 [h,hh]=size(model.mets); 0078 [r,rr]=size(model.rxns); 0079 for k=1:i-1 0080 k; 0081 [ee,e]=size(M{1,k}); 0082 g=1; 0083 while g<e+1 0084 M{1,k}{1,g}; 0085 if g==1 0086 p=0; 0087 if strncmp(M{1,k}{1,g},'E_',2)==1 0088 fprintf(fout2,'%s\t\t',M{1,k}{1,g}); 0089 p=p+1; 0090 end 0091 if p==0 0092 for jj=1:r 0093 Raddition=strcat('R_',model.rxns{jj}); 0094 if strcmp(M{1,k}{1,g},Raddition)==1 0095 fprintf(fout2,'%s\t\t',model.rxnNames{jj}); 0096 p=p+1; 0097 break; 0098 end 0099 end 0100 end 0101 if p==0 0102 for jj=1:h 0103 Maddition=strcat('M_',model.mets{jj}); 0104 if strcmp(M{1,k}{1,g},Maddition)==1 0105 fprintf(fout2,'%s\t\t',model.metNames{jj}); 0106 p=p+1; 0107 break; 0108 end 0109 end 0110 end 0111 if p==0 0112 fprintf(fout2,'%s\t\t',M{1,k}{1,g}); 0113 end 0114 g=g+1; 0115 elseif g~=1 0116 p=0; 0117 if strncmp(M{1,k}{1,g},' E_',2)==1 0118 fprintf(fout2,'%s\t\t',M{1,k}{1,g}); 0119 p=p+1; 0120 end 0121 if p==0 0122 for jj=1:r 0123 Raddition=strcat(' R_',model.rxns{jj}); 0124 if strcmp(M{1,k}{1,g},Raddition)==1 0125 fprintf(fout2,'%s\t\t',model.rxnNames{jj}); 0126 p=p+1; 0127 break; 0128 end 0129 end 0130 end 0131 if p==0 0132 for jj=1:h 0133 Maddition=strcat(' M_',model.mets{jj}); 0134 if strcmp(M{1,k}{1,g},Maddition)==1 0135 fprintf(fout2,'%s\t\t',model.metNames{jj}); 0136 p=p+1; 0137 break; 0138 end 0139 end 0140 end 0141 if p==0 0142 fprintf(fout2,'%s\t\t',M{1,k}{1,g}); 0143 end 0144 g=g+1; 0145 end 0146 end 0147 fprintf(fout2,'\n'); 0148 end 0149 fclose(fout2); 0150 0151 fid2 = fopen(outname6); 0152 y=1; 0153 while ~feof(fid2) 0154 E{y}=fgetl(fid2); 0155 y=y+1; 0156 end 0157 fclose(fid2); 0158 0159 for i=1:i-1 0160 C=A{1,i}; 0161 fprintf(fout,'%d\t%f\t%d\t%d\t%s\n',C(1),C(2),C(3),C(4),line{1,i}); 0162 fprintf(fout,'%s\n\n',E{i}); 0163 end 0164 fclose(fout); 0165 0166 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0167 % End of time evaluation of program 0168 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0169 toc;