Merge pull request #1414 from opencobra/develop

Regular merge of develop

Author: artenobot

docs/source/modules/analysis/index.rst

@@ -40,6 +40,7 @@ Analysis
    parsimoniousFBA/index
    relaxedFBA/index
    rFBA/index
+   rMTA/index
    robustnessAnalysis/index
    rumba/index
    sampling/index

docs/source/modules/analysis/rMTA/index.rst

@@ -0,0 +1,9 @@
+
+.. _rMTA:
+
+
+rMTA
+----
+
+.. automodule:: src.analysis.rMTA
+   :members:

papers

@@ -436,11 +436,11 @@
         solution.s = solution.slack;
     end
     fieldOrder = {'full';'obj';'rcost';'dual';'slack';'solver';'algorithm';'stat';'origStat';'time';'basis';'vars_v';'vars_w';'ctrs_y';'ctrs_s';'f';'x';'v';'w';'y';'s'};
-    % reorder fields for better reradability
+    % reorder fields for better readability
     currentfields = fieldnames(solution);
     presentfields = ismember(fieldOrder,currentfields);
     absentfields = ~ismember(currentfields,fieldOrder);
-    solution = orderfields(solution,[currentfields(absentfields),fieldOrder(presentfields)]);
+    solution = orderfields(solution,[currentfields(absentfields);fieldOrder(presentfields)]);
 else
     %some sort of error occured.
     if printLevel>0

src/analysis/FBA/optimizeCbModel.m

@@ -0,0 +1,37 @@
+function [nMets, nRxns, nCtrs, nVars, nGenes, nComps] = getModelSizes(model)
+% Get the sizes of the basic fields of the model structure
+%
+% USAGE:
+%    [nMets, nRxns, nCtrs, nVars, nGenes, nComps] = getModelSizes(model)
+%
+% INPUT:
+%    model:     A COBRA model structure
+%
+% OUTPUTS:
+%    nMets:     The number of metabolites in the model
+%    nRxns:     The number of reactions in the model
+%    nCtrs:     The number of constraints in the model
+%    nVars:     The number of variables in the model
+%    nGenes:    The number of genes in the model
+%    nComps:    The number of compartments in the model
+
+[nMets,nRxns] = size(model.S);
+
+nCtrs = 0;
+nVars = 0;
+nComps = 0;
+nGenes = 0;
+if isfield(model,'C')
+    nCtrs = size(model.C,1);
+end
+if isfield(model,'E')
+    nVars = size(model.E,2);
+end
+
+if isfield(model,'comps')
+    nComps = size(model.comps,1);
+end
+
+if isfield(model,'genes')
+    nGenes = size(model.genes,1);
+end

src/analysis/exploration/getModelSizes.m

@@ -118,7 +118,7 @@
 showprogress(0,'Dynamic regulatory FBA analysis in progress ...');
 for stepNo = 1:nSteps
     % Run FBA
-    sol = optimizeCbModel(modelDR,'max',true);
+    sol = optimizeCbModel(modelDR,'max'); % Maximize the constraint model.
     mu = sol.f;
 
     if (sol.stat ~= 1 | mu == 0) % end if no growth for 10 steps

src/analysis/rFBA/dynamicRFBA.m

@@ -44,7 +44,7 @@
 end
 drGenes = intersect(model.genes,drGenes); % remove genes not associated with rxns
 modelDR = deleteModelGenes(model,drGenes); % set rxns to 0
-fbasolDR = optimizeCbModel(modelDR,'max',true);
+fbasolDR = optimizeCbModel(modelDR,'max'); % maximize under the constraints set by the deleted genes.
 
 % if rxn flux = 0, set state to false
 finalInputs2States = [];

src/analysis/rFBA/solveBooleanRegModel.m

@@ -0,0 +1,213 @@
+function [TSscore, deletedGenes, Vres] = MTA(model, rxnFBS, Vref, varargin)
+% Calculate Metabolic Transformation Analysis (MTA) using the the
+% solver CPLEX.
+% Code was prepared to be able to be stopped and be launched again by using
+% a temporary file called 'temp_MTA.mat'.
+% Outputs are cell array for each alpha (one simulation by alpha). It
+% there is only one alpha, content of cell will be returned
+% The code here has been based on:
+%   Yizhak, K., Gabay, O., Cohen, H., & Ruppin, E. (2013).
+%   'Model-based identification of drug targets that revert disrupted
+%   metabolism and its application to ageing'. Nature communications, 4.
+%   http://www.nature.com/ncomms/2013/131024/ncomms3632/full/ncomms3632.html
+%
+% USAGE:
+%
+%    [TSscore,deletedGenes,Vout] = MTA(model, rxnFBS, Vref, alpha, epsilon, varargin)
+%
+% INPUTS:
+%    model:               Metabolic model structure (COBRA Toolbox format).
+%    rxnFBS:              Array that contains the desired change: Forward,
+%                         Backward and Unchanged (+1;0;-1). This is calculated
+%                         from the rules and differential expression analysis.
+%    Vref:                Reference flux of the source state.
+%
+% OPTIONAL INPUTS:
+%    alpha:               Numeric value or array. Parameter of the quadratic
+%                         problem (default = 0.66)
+%    epsilon:             Numeric value or array. Minimun perturbation for each
+%                         reaction (default = 0)
+%    rxnKO:               Binary value. Calculate knock outs at reaction level
+%                         instead of gene level. (default = false)
+%    timelimit:           Time limit for the calculation of each knockout.
+%                         (default = inf)
+%    SeparateTranscript:  Character used to separate different transcripts of a gene. (default = '').
+%                         Examples:
+%                             - SeparateTranscript = ''
+%                                   - gene 10005.1    ==>    gene 10005.1
+%                                   - gene 10005.2    ==>    gene 10005.2
+%                                   - gene 10005.3    ==>    gene 10005.3
+%                             - SeparateTranscript = '.'
+%                                   - gene 10005.1
+%                                   - gene 10005.2    ==>    gene 10005
+%                                   - gene 10005.3
+%    numWorkers:          Integer: is the maximun number of workers
+%                         used by the solver. 0 = automatic, 1 = sequential,
+%                         > 1 = parallel. (default = 0)
+%    printLevel:          Integer. 1 if the process is wanted to be shown
+%                         on the screen, 0 otherwise. (default = 1)
+%
+% OUTPUTS:
+%    TSscore:             Transformation score by each transformation
+%    deletedGenes:        The list of genes/reactions removed in each knock-out
+%    Vres:                Matrix of resulting fluxes
+%
+% .. Authors:
+%       - Luis V. Valcarcel, 03/06/2015, University of Navarra, CIMA & TECNUN School of Engineering.
+%       - Luis V. Valcarcel, 26/10/2018, University of Navarra, CIMA & TECNUN School of Engineering.
+%       - Francisco J. Planes, 26/10/2018, University of Navarra, TECNUN School of Engineering.
+
+p = inputParser; % check the input information
+
+% check required arguments
+addRequired(p, 'model');
+addRequired(p, 'rxnFBS', @isnumeric);
+addRequired(p, 'Vref', @isnumeric);
+% Check optional arguments
+addOptional(p, 'alpha', 0.66, @isnumeric);
+addOptional(p, 'epsilon', 0, @isnumeric);
+% Add optional name-value pair argument
+addParameter(p, 'rxnKO', false);
+addParameter(p, 'timelimit', inf, @(x)isnumeric(x)&&isscalar(x));
+addParameter(p, 'SeparateTranscript', '', @(x)ischar(x));
+addParameter(p, 'numWorkers', 0, @(x)isnumeric(x)&&isscalar(x));
+addParameter(p, 'printLevel', 1, @(x)isnumeric(x)&&isscalar(x));
+% extract variables from parser
+parse(p, model, rxnFBS, Vref, varargin{:});
+alpha = p.Results.alpha;
+epsilon = p.Results.epsilon;
+rxnKO = p.Results.rxnKO;
+timelimit = p.Results.timelimit;
+SeparateTranscript = p.Results.SeparateTranscript;
+numWorkers = p.Results.numWorkers;
+printLevel = p.Results.printLevel;
+
+if printLevel >0
+    fprintf('===================================\n');
+    fprintf('=========  MTA algorithm  =========\n');
+    fprintf('===================================\n');
+    fprintf('Step 0: preprocessing: \n');
+end
+
+%% Initialize variables or load previously ones
+%  Check if there are any temporary files with the MTA information
+
+num_alphas = numel(alpha);
+
+% Calculate perturbation matrix
+if rxnKO
+    geneKO.genes = model.rxns;
+    geneKO.rxns = model.rxns;
+    geneKO.rxns = speye(numel(model.rxns));
+else
+    geneKO = calculateGeneKOMatrix(model, SeparateTranscript, printLevel);
+end
+
+% Reduce the size of the problem;
+geneKO2 = geneKO;
+[geneKO.matrix,geneKO.IA,geneKO.IC ] = unique(geneKO.matrix','rows');
+geneKO.matrix = geneKO.matrix';
+geneKO.genes = num2cell((1:length(geneKO.IA))');
+
+if ~exist('temp_MTA.mat','file')
+    % counters
+    i = 0;          % counter
+    i_alpha = 0;    % counter for lphas
+    % scores
+    TSscore = zeros(numel(geneKO.genes),num_alphas);
+    Vres = cell(num_alphas,1);
+    Vres(:) = {zeros(numel(model.rxns),numel(geneKO.genes))};
+else
+    load('temp_MTA.mat');
+    i_alpha = max(i_alpha-1,0);
+    i = max(i-100,0);
+end
+
+if printLevel >0
+    fprintf('-------------------\n');
+end
+
+%% ---- STEP 1 : MTA ----
+
+timerVal = tic;
+
+% treat rxnFBS to remove impossible changes
+rxnFBS_best = rxnFBS;
+rxnFBS_best(rxnFBS_best==-1 & abs(Vref)<1e-6 & model.lb==0) = 0;
+clear v_res
+
+
+while i_alpha < num_alphas
+    i_alpha = i_alpha + 1;
+    if printLevel >0
+        fprintf('\tStart MTA best scenario case for alpha = %1.2f \n',alpha(i_alpha));
+    end
+
+    % Create the CPLEX model
+    CplexModelBest = buildMTAproblemFromModel(model, rxnFBS_best, Vref, alpha(i_alpha), epsilon);
+    if printLevel >0
+        fprintf('\tcplex model for MTA built\n');
+    end
+
+    % perform the MIQP problem for each rxn's knock-out
+    if printLevel >0
+        showprogress(0, '    MIQP Iterations for MTA');
+    end
+    while i < length(geneKO.genes)
+        for w = 1:100
+            i = i+1;
+            KOrxn = find(geneKO.matrix(:,i));
+            v_res = MTA_MIQP (CplexModelBest, KOrxn, 'numWorkers', numWorkers, 'timelimit', timelimit, 'printLevel', printLevel);
+            Vres{i_alpha}(:,i) = v_res;
+            if ~isempty(KOrxn) && norm(v_res)>1
+                TSscore(i,i_alpha) = MTA_TS(v_res,Vref,rxnFBS_best);
+            else
+                % if we knock off the system, invalid solution
+                % remove perturbations with no effect score
+                TSscore(i,i_alpha) = -Inf;
+            end
+            if printLevel >0
+                showprogress(i/length(geneKO.genes), '    MIQP Iterations for MTA');
+            end
+            % Condition to exit the for loop
+            if i == length(geneKO.genes)
+                break;
+            end
+        end
+        try save('temp_MTA.mat', 'i','i_alpha','TSscore','Vres'); end
+    end
+    clear cplex_model
+    if printLevel >0
+        fprintf('\tAll MIQP problems performed\n');
+    end
+    i = 0;
+end
+
+
+time = toc(timerVal);
+if printLevel >0
+    fprintf('\tTime: %4.2f seconds = %4.2f minutes\n',time,time/60);
+end
+try save('temp_MTA.mat', 'i','i_alpha','TSscore','Vres'); end
+fprintf('-------------------\n');
+
+%% ---- STEP 2 : Return to gene size ----
+
+aux = geneKO;
+geneKO = geneKO2;
+
+% scores
+TSscore = TSscore(aux.IC,:);
+% fluxes
+for i=1:num_alphas
+    Vres{i} = Vres{i}(:,aux.IC);
+end
+
+% Define one of the outputs
+deletedGenes = geneKO.genes;
+
+
+delete('temp_MTA.mat')
+
+end
+