readGeneRules.m

function [term,ng,nt,nr,nko,reactionKO,reactionKO2term] = readGeneRules(model)
% readGeneRules is a function of gDel_minRN that reads
% gene-protein-reaction relations and outputs the necessary
% information for the MILP formalization 
%
%function [term,ng,nt,nr,nko,reactionKO,reactionKO2term] = readGeneRules(model)
%
%INPUT
% model     COBRA model structure containing the following required fields to perform GridProd.
%   rxns                    Rxns in the model
%   mets                    Metabolites in the model
%   S                       Stoichiometric matrix (sparse)
%   b                       RHS of Sv = b (usually zeros)
%   c                       Objective coefficients
%   lb                      Lower bounds for fluxes
%   ub                      Upper bounds for fluxes
%   rev                     Reversibility of fluxes
%
%OUTPUTS
% term    the list of Boolean functions extracted from the gene-protein-reaction relations
% ng  the number of genes
% nt  the number of internal terms
% nr  the number of reactions
% nko the number of repressible reactions
% 
% Apr. 22 2021   Takeyuki TAMURA
%
model.grRules;
x=1;y=1;reactionKO=0;qq=0;ww=0;
for i=1:size(model.grRules)
    %i
    GRrelation=model.grRules{i};
    empty=0;
    if isempty(GRrelation)==0
        if (isempty(strfind(GRrelation,'or'))==0)||(isempty(strfind(GRrelation,'and'))==0)
            GRrelation=strcat('(',GRrelation,')');
        else
            GRrelation=strtrim(GRrelation);
            term(x).output=sprintf('reactionKO_%d',i);
            term(x).function='equal';
            term(x).input{1,1}=GRrelation;
            reactionKO2term(i,1)=x;
            x=x+1;
            reactionKO=reactionKO+1;
            qq=qq+1;
        end
    else
        empty=1;
    end
    flag=1;
    while isempty(strfind(GRrelation,')'))==0
        size(GRrelation,2);
        p_tail_list=strfind(GRrelation,')');
        p_tail=p_tail_list(1);
        j=p_tail;
        flag=1;
        while flag==1
            j=j-1;
            if  GRrelation(j)=='('
                p_head=j;
                flag=0;
            end
        end
        extract=GRrelation(p_head+1:p_tail-1);
        extract2=strtrim(extract);
        term(x).output=sprintf('term_%d',y);
        term(x).output;
        y=y+1;
        unit=strsplit(extract2);
        for k=1:floor(size(unit,2)/2)
            if strcmp(unit(2),unit(2*k))==0
                save('readGeneRules.mat');
                error('Boolean functions are inappropriate.')
            end
        end
        
        term(x).function=unit(2);
        for k=1:ceil(size(unit,2)/2)
            term(x).input{k,1}=unit(2*k-1);
        end
        str=sprintf('(%s)',extract);
        GRrelation=strrep(GRrelation,str,term(x).output);
        x=x+1;
    end
    if (empty==0 && strcmp(term(x-1).function,'equal')==0)
        term(x-1).output=sprintf('reactionKO_%d',i);
        reactionKO2term(i,1)=x-1;
        reactionKO=reactionKO+1;
        ww=ww+1;
    end
end
ng=size(model.genes,1);
nr=size(model.rxns,1);
nko=ww+qq;
nt=y-ww-1;
j=1;
for i=1:nt+nko
    if contains(term(i).output,'term')==1
        term2(j)=term(i);
        j=j+1;
    end
end
for i=1:nt+nko
    if contains(term(i).output,'reaction')==1
        term2(j)=term(i);
        j=j+1;
    end
end
term=term2;
save('readGeneRules.mat');

end