AllKEGG2BiGGmet

 AllKEGG2BiGGmet
 Extracts all KEGG metabolites from BIGG API and save them
 as a mat file (AllKEGG2BiGGmet.mat), which is used in MapAdjuster for
 displaying compound details on created customized maps by NetDraw.

0001 function AllKEGG2BiGGmet
0002 % AllKEGG2BiGGmet
0003 % Extracts all KEGG metabolites from BIGG API and save them
0004 % as a mat file (AllKEGG2BiGGmet.mat), which is used in MapAdjuster for
0005 % displaying compound details on created customized maps by NetDraw.
0006 
0007 % O. Jamialahmadi
0008 % TMU, Chem. Eng. Dept., Biotech. Group
0009 % July 2016
0010 %--------------------------------------------------------------------------
0011 
0012 Pth1 = which ('Bigg2Kegg.m');
0013 tind = find(Pth1=='\',1,'last');
0014 Pth = Pth1(1:tind-1);
0015 Fileid3 = fopen(fullfile(Pth,'bigg_models_metabolites.txt'),'r');
0016 biggmets = textscan(Fileid3,'%s %s %[^\n]');
0017 fclose(Fileid3);
0018 biggmetid = biggmets{1}; biggmetdes = biggmets{3}; clear biggmets
0019 Metkegg = ({}); Metbigg = ({});
0020 ct3 = 1;
0021 for ct1 = 2:numel(biggmetid)
0022     temploci = regexp(biggmetdes{ct1},...
0023         'http://identifiers.org/kegg.compound/C\S{5}','match');
0024     if isempty(temploci)
0025         continue
0026     end
0027     if iscell(temploci{1})
0028         temploci = temploci{1};
0029     end
0030     if isempty(temploci)
0031         continue
0032     else
0033         for ct2 = 1:numel(temploci)
0034             regtemp = regexp(temploci{ct2},'C\S{5}','match');
0035             Metkegg{ct3}{ct2} = regtemp{1};
0036             Metbigg{ct3}{ct2} = biggmetid{ct1};
0037         end
0038         ct3 = ct3 + 1;
0039     end
0040 end
0041 for ct1 = 2:numel(biggmetid) % KEGG glycan
0042     temploci = regexp(biggmetdes{ct1},...
0043         'http://identifiers.org/kegg.compound/G\S{5}','match');
0044     if isempty(temploci)
0045         continue
0046     end
0047     if iscell(temploci{1})
0048         temploci = temploci{1};
0049     end
0050     if isempty(temploci)
0051         continue
0052     else
0053         for ct2 = 1:numel(temploci)
0054             regtemp = regexp(temploci{ct2},'G\S{5}','match');
0055             Metkegg{ct3}{ct2} = regtemp{1};
0056             Metbigg{ct3}{ct2} = biggmetid{ct1};
0057         end
0058         ct3 = ct3 + 1;
0059     end
0060 end
0061 AllKEGG2BiGGmet.Metkegg = Metkegg; AllKEGG2BiGGmet.Metbigg = Metbigg;
0062 save('AllKEGG2BiGGmet.mat','AllKEGG2BiGGmet')