corrAnalyzer

 corrAnalyzer
 compares the reconciled reactions in BiGG and KEGG databases
 taken from MetaNetX repository and BiKEGG (specifically, Bigg2Kegg
 function). 
 WARNING: To execute this function, you need to include all BiGG models
 in a folder named "BiGG Models".

0001 function corr = corrAnalyzer
0002 % corrAnalyzer
0003 % compares the reconciled reactions in BiGG and KEGG databases
0004 % taken from MetaNetX repository and BiKEGG (specifically, Bigg2Kegg
0005 % function).
0006 % WARNING: To execute this function, you need to include all BiGG models
0007 % in a folder named "BiGG Models".
0008 
0009 % O. Jamialahmadi
0010 % TMU, Chem. Eng. Dept., Biotech. Group
0011 % Apr. 2016
0012 
0013 
0014 clc
0015 Pth1 = which ('Bigg2Kegg.m');
0016 tind = find(Pth1=='\',1,'last');
0017 Pth = Pth1(1:tind-1);
0018 Pth2 = fullfile(Pth,'BiGG2KEGG\*.mat');
0019 Pth3 = fullfile(Pth,'BiGG2KEGG');
0020 Pth22 = fullfile(Pth,'BiGG Models\*.xml');
0021 Pth33 = fullfile(Pth,'BiGG Models');
0022 
0023 % Read MetaNetX data
0024 Fileid = fopen(fullfile(Pth,'MetaNetX.txt'),'r');
0025 rawmetanet = textscan(Fileid,'%s %[^\n]');
0026 fclose(Fileid);
0027 metaid = rawmetanet{2}; metaref = rawmetanet{1};
0028 metabigg = regexp(metaref,'bigg:\w*');
0029 metabigg = ~cellfun('isempty',metabigg);
0030 metabigg1 = metaid(metabigg);
0031 for ct = 1:numel(metabigg1)
0032     metabigg11(ct) = cellstr(metabigg1{ct});
0033 end
0034 clear metabigg1
0035 metabigg1 = metabigg11;
0036 metabigg = metaref(metabigg); metabigg = strrep(metabigg,'bigg:','');
0037 metakegg = regexp(metaref,'kegg:\w*');
0038 metakegg = ~cellfun('isempty',metakegg);
0039 metakegg1 = metaid(metakegg);
0040 for ct = 1:numel(metakegg1)
0041     metakegg11(ct) = cellstr(metakegg1{ct});
0042 end
0043 clear metakegg1
0044 metakegg1 = metakegg11;
0045 metakegg = metaref(metakegg); metakegg = strrep(metakegg,'kegg:','');
0046 clear metaref metaid rawmetanet metakegg11 metabigg11
0047 netbigg = metabigg(ismember(metabigg1,metakegg1));
0048 ct2 = 1; netkegg = ({});
0049 for ct = 1:numel(metabigg1)
0050     netloci = find(ismember(metakegg1,metabigg1{ct}));
0051     if ~isempty(netloci)
0052         for ct1 = 1:numel(netloci)
0053             netkegg{ct2}{ct1} = metakegg{netloci(ct1)};
0054         end
0055         ct2 = ct2 + 1;
0056     end
0057 end
0058 
0059 % Read data from bigg2kegg
0060 BMatfiles = dir(Pth2);
0061 BMatfiles1 = dir(Pth22);
0062 xmlname1 = struct2cell(BMatfiles1);
0063 xmlname = xmlname1(1,:);
0064 xmlname = strrep(xmlname,'.xml','');
0065 ct1 = 1;
0066 for ct = 1:numel(BMatfiles)
0067     if ~strcmp(BMatfiles(ct).name,'BiGG2KEGG_HMRbased-RECON1.mat') && ...
0068             ~strcmp(BMatfiles(ct).name,'Multirxns.mat') && ...
0069             ~strcmp(BMatfiles(ct).name,'UniModelKEGG.mat')
0070         BNames = BMatfiles(ct).name;
0071         btempname = BNames(1:end-8);
0072         load(fullfile(Pth3,BNames))
0073         B=B2Kegg.B;K=B2Kegg.K;
0074         modelname = xmlname(ismember(xmlname,btempname));
0075         model = readCbModel(fullfile(Pth33,[modelname{1},'.xml']));
0076         modelrxn = model.rxns;
0077         currnetkegg = netkegg(ismember(netbigg,modelrxn));
0078         metxn = numel(currnetkegg);
0079         bikegg = sum(ismember(modelrxn,B));
0080         corr(ct1).m = metxn; corr(ct1).bi = bikegg;
0081         corr(ct1).mRxns = netbigg(ismember(netbigg,modelrxn)); corr(ct1).biRxns = modelrxn(ismember(modelrxn,B));
0082         corr(ct1).bRxns = currnetkegg;
0083         names{ct1} = modelname{1};
0084         clear B2Kegg
0085         ct1 = ct1 + 1;
0086     end
0087 end