UniModel

 UiModel
 generates one unified model containing all shared reaction among
 all BiGG models in Bigg2Kegg folder. This model is of use in cases where
 user wants not to use a special BiGG model, or a new model is in hand.
 
 O. Jamialahmadi
 TMU, Chem. Eng. Dept., Biotech. Group 
 Jan. 2015

0001 function UniModel
0002 % UiModel
0003 % generates one unified model containing all shared reaction among
0004 % all BiGG models in Bigg2Kegg folder. This model is of use in cases where
0005 % user wants not to use a special BiGG model, or a new model is in hand.
0006 %
0007 % O. Jamialahmadi
0008 % TMU, Chem. Eng. Dept., Biotech. Group
0009 % Jan. 2015
0010 
0011 Pth1 = which ('Bigg2Kegg.m');
0012 tind = find(Pth1=='\',1,'last');
0013 Pth = Pth1(1:tind-1);
0014 Pth2 = fullfile(Pth,'BiGG2KEGG\*.mat');
0015 Pth3 = fullfile(Pth,'BiGG2KEGG');
0016 BMatfiles = dir(Pth2);
0017 BNames = cell(numel(BMatfiles)-2,1);
0018 ct1 = 1; NewB = ({}); NewK = ({});
0019 for ct = 1:numel(BMatfiles)
0020     if ~strcmp(BMatfiles(ct).name,'BiGG2KEGG_HMRbased-RECON1.mat') && ...
0021             ~strcmp(BMatfiles(ct).name,'Multirxns.mat')
0022         BNames{ct1} = BMatfiles(ct).name;
0023         load(fullfile(Pth3,BNames{ct1}))
0024         B=B2Kegg.B;K=B2Kegg.K;
0025         Mlt = find(ismember(B,'MULTIR'));
0026         if ~isempty(Mlt)
0027             TB = B(1:Mlt-1); TK = K(1:Mlt-1);
0028         end
0029         if isempty(NewB)
0030             NewB = TB; NewK = TK;
0031         else
0032             NotB = TB(~ismember(TB,NewB));
0033             NotK = TK(~ismember(TB,NewB));
0034             NewLen = numel(NewB)+1:numel(NotB)+numel(NewB);
0035             NewB(NewLen) = NotB; NewK(NewLen) = NotK;
0036         end
0037         clear B2Kegg
0038         ct1 = ct1 + 1;
0039     end
0040 end
0041 Len1 = numel(NewB);
0042 NewB{Len1+1} = 'MULTIR';
0043 NewK{Len1+1} = 'MULTIR';
0044 load(fullfile(Pth3,'Multirxns.mat'))
0045 Pr = Multirxns.P; Cr = Multirxns.C;
0046 clear Multirxns
0047 for c1 = 1:numel(Pr)
0048     TempN = NewB(ismember(NewK,Pr{c1}));
0049     TempC = Cr{c1};
0050     Len = numel(TempC);
0051     for c2 = 1:numel(TempN)
0052         Len1 = numel(NewB);
0053         Len2 = Len1 + 1: Len1 + Len;
0054         NewB(Len2) = TempN(c2);
0055         NewK(Len2) = TempC;
0056     end
0057 end
0058 B2Kegg.B = NewB; B2Kegg.K = NewK;
0059 fname = fullfile(Pth3,'UniModelKEGG.mat');
0060 save (fname,'B2Kegg')