Merge pull request #2446 from bramnap/develop

Develop

docs/modules/analysis/multiSpecies/microbiomeModelingToolbox/mgPipe/index.html

@@ -757,7 +757,7 @@ <h1>The COBRA Toolbox</h1>
 
 <dl class="mat function">
 <dt class="sig sig-object mat" id="src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe.mgPipe">
-<span class="sig-name descname"><span class="pre">mgPipe</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">modPath</span></em>, <em class="sig-param"><span class="pre">abunFilePath</span></em>, <em class="sig-param"><span class="pre">computeProfiles</span></em>, <em class="sig-param"><span class="pre">resPath</span></em>, <em class="sig-param"><span class="pre">dietFilePath</span></em>, <em class="sig-param"><span class="pre">infoFilePath</span></em>, <em class="sig-param"><span class="pre">biomasses</span></em>, <em class="sig-param"><span class="pre">hostPath</span></em>, <em class="sig-param"><span class="pre">hostBiomassRxn</span></em>, <em class="sig-param"><span class="pre">hostBiomassRxnFlux</span></em>, <em class="sig-param"><span class="pre">figForm</span></em>, <em class="sig-param"><span class="pre">numWorkers</span></em>, <em class="sig-param"><span class="pre">rDiet</span></em>, <em class="sig-param"><span class="pre">pDiet</span></em>, <em class="sig-param"><span class="pre">lowerBMBound</span></em>, <em class="sig-param"><span class="pre">upperBMBound</span></em>, <em class="sig-param"><span class="pre">includeHumanMets</span></em>, <em class="sig-param"><span class="pre">adaptMedium</span></em>, <em class="sig-param"><span class="pre">pruneModels</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/opencobra/cobratoolbox/blob/master/src/analysis/multiSpecies/microbiomeModelingToolbox/mgPipe/mgPipe.m"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe.mgPipe" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">mgPipe</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">modPath</span></em>, <em class="sig-param"><span class="pre">abunFilePath</span></em>, <em class="sig-param"><span class="pre">computeProfiles</span></em>, <em class="sig-param"><span class="pre">resPath</span></em>, <em class="sig-param"><span class="pre">dietFilePath</span></em>, <em class="sig-param"><span class="pre">infoFilePath</span></em>, <em class="sig-param"><span class="pre">biomasses</span></em>, <em class="sig-param"><span class="pre">hostPath</span></em>, <em class="sig-param"><span class="pre">hostBiomassRxn</span></em>, <em class="sig-param"><span class="pre">hostBiomassRxnFlux</span></em>, <em class="sig-param"><span class="pre">figForm</span></em>, <em class="sig-param"><span class="pre">numWorkers</span></em>, <em class="sig-param"><span class="pre">rDiet</span></em>, <em class="sig-param"><span class="pre">pDiet</span></em>, <em class="sig-param"><span class="pre">lowerBMBound</span></em>, <em class="sig-param"><span class="pre">upperBMBound</span></em>, <em class="sig-param"><span class="pre">includeHumanMets</span></em>, <em class="sig-param"><span class="pre">adaptMedium</span></em>, <em class="sig-param"><span class="pre">pruneModels</span></em>, <em class="sig-param"><span class="pre">solver</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/opencobra/cobratoolbox/blob/master/src/analysis/multiSpecies/microbiomeModelingToolbox/mgPipe/mgPipe.m"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#src.analysis.multiSpecies.microbiomeModelingToolbox.mgPipe.mgPipe" title="Permalink to this definition">¶</a></dt>
 <dd><p>mgPipe is a MATLAB based pipeline to integrate microbial abundances
 (coming from metagenomic data) with constraint based modeling, creating
 individuals’ personalized models.
@@ -770,7 +770,7 @@ <h1>The COBRA Toolbox</h1>
 [PART 3] Simulations under different diet regimes.</p>
 <dl class="field-list simple">
 <dt class="field-odd">USAGE</dt>
-<dd class="field-odd"><p><strong>[netSecretionFluxes, netUptakeFluxes, Y, modelStats, summary, statistics, modelsOK] = mgPipe</strong> (<em>modPath, abunFilePath, computeProfiles, resPath, dietFilePath, infoFilePath, biomasses, hostPath, hostBiomassRxn, hostBiomassRxnFlux, figForm, numWorkers, rDiet, pDiet, lowerBMBound, upperBMBound, includeHumanMets, adaptMedium, pruneModels</em>)</p>
+<dd class="field-odd"><p><strong>[netSecretionFluxes, netUptakeFluxes, Y, modelStats, summary, statistics, modelsOK] = mgPipe</strong> (<em>modPath, abunFilePath, computeProfiles, resPath, dietFilePath, infoFilePath, biomasses, hostPath, hostBiomassRxn, hostBiomassRxnFlux, figForm, numWorkers, rDiet, pDiet, lowerBMBound, upperBMBound, includeHumanMets, adaptMedium, pruneModels, solver</em>)</p>
 </dd>
 <dt class="field-even">INPUTS</dt>
 <dd class="field-even"><ul class="simple">
@@ -801,6 +801,8 @@ <h1>The COBRA Toolbox</h1>
 <li><p><strong>pruneModels</strong> – boolean indicating whether reactions that do not carry flux on the
 input diet should be removed from the microbe models.
 Recommended for large datasets (default: false)</p></li>
+<li><p><strong>solver</strong> – char with the solver that will be used in microbiotamodelsimulator
+If glpk, it will increase to model solve time to hours instead of seconds (default ‘’)</p></li>
 </ul>
 </dd>
 <dt class="field-odd">OUTPUTS</dt>
@@ -875,7 +877,7 @@ <h1>The COBRA Toolbox</h1>
 checkpoints are present.</p>
 <dl class="field-list simple">
 <dt class="field-odd">USAGE</dt>
-<dd class="field-odd"><p><strong>[exchanges, netProduction, netUptake, growthRates, infeasModels] = microbiotaModelSimulator</strong> (<em>resPath, exMets, sampNames, dietFilePath, hostPath, hostBiomassRxn, hostBiomassRxnFlux, numWorkers, rDiet, pDiet, computeProfiles, lowerBMBound, upperBMBound, includeHumanMets, adaptMedium</em>)</p>
+<dd class="field-odd"><p><strong>[exchanges, netProduction, netUptake, growthRates, infeasModels] = microbiotaModelSimulator</strong> (<em>resPath, exMets, sampNames, dietFilePath, hostPath, hostBiomassRxn, hostBiomassRxnFlux, numWorkers, rDiet, pDiet, computeProfiles, lowerBMBound, upperBMBound, includeHumanMets, adaptMedium, solver</em>)</p>
 </dd>
 <dt class="field-even">INPUTS</dt>
 <dd class="field-even"><ul class="simple">
@@ -902,6 +904,8 @@ <h1>The COBRA Toolbox</h1>
 present in the gut should be provexchangesed to the models (default: true)</p></li>
 <li><p><strong>adaptMedium</strong> – boolean indicating if the medium should be adapted through the
 adaptVMHDietToAGORA function or used as is (default=true)</p></li>
+<li><p><strong>solver</strong> – char with the solver that will be used in microbiotamodelsimulator
+If glpk, it will increase to model solve time to hours instead of seconds (default ‘’)</p></li>
 </ul>
 </dd>
 <dt class="field-odd">OUTPUTS</dt>

src/analysis/multiSpecies/microbiomeModelingToolbox/mgPipe/mgPipe.m

@@ -1,4 +1,4 @@
-function [netSecretionFluxes, netUptakeFluxes, Y, modelStats, summary, statistics, modelsOK] = mgPipe(modPath, abunFilePath, computeProfiles, resPath, dietFilePath, infoFilePath, biomasses, hostPath, hostBiomassRxn, hostBiomassRxnFlux, figForm, numWorkers, rDiet, pDiet, lowerBMBound, upperBMBound, includeHumanMets, adaptMedium, pruneModels)
+function [netSecretionFluxes, netUptakeFluxes, Y, modelStats, summary, statistics, modelsOK] = mgPipe(modPath, abunFilePath, computeProfiles, resPath, dietFilePath, infoFilePath, biomasses, hostPath, hostBiomassRxn, hostBiomassRxnFlux, figForm, numWorkers, rDiet, pDiet, lowerBMBound, upperBMBound, includeHumanMets, adaptMedium, pruneModels, solver)
 % mgPipe is a MATLAB based pipeline to integrate microbial abundances
 % (coming from metagenomic data) with constraint based modeling, creating
 % individuals' personalized models.
@@ -11,7 +11,7 @@
 % [PART 3] Simulations under different diet regimes.
 %
 % USAGE:
-%       [netSecretionFluxes, netUptakeFluxes, Y, modelStats, summary, statistics, modelsOK] = mgPipe(modPath, abunFilePath, computeProfiles, resPath, dietFilePath, infoFilePath, biomasses, hostPath, hostBiomassRxn, hostBiomassRxnFlux, figForm, numWorkers, rDiet, pDiet, lowerBMBound, upperBMBound, includeHumanMets, adaptMedium, pruneModels)
+%       [netSecretionFluxes, netUptakeFluxes, Y, modelStats, summary, statistics, modelsOK] = mgPipe(modPath, abunFilePath, computeProfiles, resPath, dietFilePath, infoFilePath, biomasses, hostPath, hostBiomassRxn, hostBiomassRxnFlux, figForm, numWorkers, rDiet, pDiet, lowerBMBound, upperBMBound, includeHumanMets, adaptMedium, pruneModels, solver)
 %
 % INPUTS:
 %    modPath:                char with path of directory where models are stored
@@ -41,6 +41,8 @@
 %    pruneModels:            boolean indicating whether reactions that do not carry flux on the
 %                            input diet should be removed from the microbe models. 
 %                            Recommended for large datasets (default: false)
+%    solver:                 char with the solver that will be used in microbiotamodelsimulator
+%                            If glpk, it will increase to model solve time to hours instead of seconds (default '')
 %
 % OUTPUTS:
 %    init:                   status of initialization
@@ -306,4 +308,4 @@
     writetable(cell2table(statistics),[resPath filesep 'ModelStatsStratification.csv'], 'WriteVariableNames', false);
 end
 
-end
+end

src/analysis/multiSpecies/microbiomeModelingToolbox/mgPipe/microbiotaModelSimulator.m

@@ -8,7 +8,7 @@
 %
 % USAGE:
 %
-%   [exchanges, netProduction, netUptake, growthRates, infeasModels] = microbiotaModelSimulator(resPath, exMets, sampNames, dietFilePath, hostPath, hostBiomassRxn, hostBiomassRxnFlux, numWorkers, rDiet, pDiet, computeProfiles, lowerBMBound, upperBMBound, includeHumanMets, adaptMedium)
+%   [exchanges, netProduction, netUptake, growthRates, infeasModels] = microbiotaModelSimulator(resPath, exMets, sampNames, dietFilePath, hostPath, hostBiomassRxn, hostBiomassRxnFlux, numWorkers, rDiet, pDiet, computeProfiles, lowerBMBound, upperBMBound, includeHumanMets, adaptMedium, solver)
 %
 % INPUTS:
 %    resPath:            char with path of directory where results are saved
@@ -34,6 +34,8 @@
 %                        present in the gut should be provexchangesed to the models (default: true)
 %    adaptMedium:        boolean indicating if the medium should be adapted through the
 %                        adaptVMHDietToAGORA function or used as is (default=true)
+%    solver:             char with the solver that will be used in microbiotamodelsimulator
+%                        If glpk, it will increase to model solve time to hours instead of seconds (default '')
 %
 % OUTPUTS:
 %    exchanges:          cell array with list of all unique exchanges to diet/