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FVA.m
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FVA.m
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function [Vmin,Vmax,Val]=FVA(GEM,L,solver,split,Blocked,eps)
%Calculates the Vmin, Vmax and flux range per each reaction of the model
%Inputs:
%GEM: a model in cobra structure format (at least S and rev fields)
%L: the maximum absolute value used as boudary condition, default is 1
%solver: string displaying either 'glpk' or 'gurobi'
%split: if TRUE, FVA returns the ranges of the extended matrix S',
%constructed by splitting reversible reactions, i.e. S'=[S,-S(:,RevRxns)]
%Blocked: an index vector indicating reactions that should be blocked, i.e. zero
%flux
%Tasks: an index vector indicating reactions that should be always
%operative, i.e. non-zero flux
%Semidán, December 2014
%**************************************************************************
if nargin<2,
L=1;
end
if isempty(L),
L=1;
end
if nargin<3,
solver='gurobi';
end
if isempty(solver),
solver='gurobi';
end
if nargin<4,
split='F';
end
if isempty(split),
split='F';
end
if nargin<5,
Blocked=[];
end
if isempty(Blocked),
Blocked=[];
end
if nargin<6,
eps=1e-6*L;
end
if isempty(eps),
eps=1e-6*L;
end
RevRxns=find(GEM.rev==1);
if split=='F',
S=full(GEM.S);
Rxns=size(S,2);
Mets=size(S,1);
lb=zeros(Rxns,1);lb(RevRxns)=-L;
ub=L*ones(Rxns,1);
% if ~isempty(Blocked),
% lb(Blocked)=0;
% ub(Blocked)=0;
% end
elseif split=='T',
S=[full(GEM.S),-full(GEM.S(:,RevRxns))];
Rxns=size(S,2);
Mets=size(S,1);
end
if strcmpi('gurobi',solver),
n=1;m=1;
%main loop: gurobi
for i=1:Rxns,
c=zeros(Rxns,1);c(i)=1;
if split=='T',
lb=zeros(Rxns,1);
ub=L*ones(Rxns,1);
if ismember(i,RevRxns)
ub(size(GEM.S,2)+n)=0;
n=n+1;
elseif i>size(GEM.S,2),
ub(RevRxns(m))=0;
m=m+1;
end
end
model.A=sparse(S);
model.modelsense='min';
model.obj=c;
model.sense=repmat('=',Mets,1);
model.rhs=zeros(Mets,1);
model.lb=lb;
model.ub=ub;
params.OutputFlag=0;
gur=gurobi(model,params);
Vmin(i)=gur.objval;
model.A=sparse(S);
model.modelsense='max';
model.obj=c;
model.sense=repmat('=',Mets,1);
model.rhs=zeros(Mets,1);
model.lb=lb;
model.ub=ub;
params.OutputFlag=0;
gur=gurobi(model,params);
Vmax(i)=gur.objval;
end
end
if strcmpi('glpk',solver),
n=1;
%main loop: glpk
for i=1:Rxns,
c=zeros(Rxns,1);c(i)=1;
if split=='T',
lb=zeros(Rxns,1);
ub=L*ones(Rxns,1);
if ismember(i,RevRxns),
ub(size(GEM.S,2)+n)=0;
n=n+1;
elseif i>size(GEM.S,2),
ub(RevRxns(i-size(GEM.S,2)))=0;
end
end
a=sparse(S);
sense=1;
ctype=repmat('S',Mets,1);
vartype=repmat('C',Rxns,1);
b=zeros(Mets,1);
[~,fopt,~,~]=glpk(c,a,b,lb,ub,ctype,vartype,sense);
Vmin(i)=fopt;
a=sparse(S);
sense=-1;
ctype=repmat('S',Mets,1);
vartype=repmat('C',Rxns,1);
b=zeros(Mets,1);
[~,fopt,~,~]=glpk(c,a,b,lb,ub,ctype,vartype,sense);
Vmax(i)=fopt;
end
end
Val.blocked=find(abs(Vmin)<=eps & abs(Vmax)<=eps);
Val.VminMax(:,1)=Vmin';
Val.VminMax(:,2)=Vmax';
Val.RevRxns=RevRxns;
Val.Rxns=Rxns;
if split=='T',
VminMaxSplit=[Vmin(1:length(GEM.rxns))',Vmax(1:length(GEM.rxns))'];
VminMaxSplit(GEM.rev==1,3:4)=[Vmin(length(GEM.rxns)+1:end)',Vmax(length(GEM.rxns)+1:end)'];
VminMaxSplit=round(1e4*VminMaxSplit)/1e4;
Val.VminMaxSplit=VminMaxSplit;
end
end