Merge pull request #488 from SysBioChalmers/develop

RAVEN 2.8.1

INIT/prepINITModel.m

@@ -1,4 +1,4 @@
-function prepData = prepINITModel(origRefModel, taskStruct, spontRxnNames, convertGenes, customRxnsToIgnore, extComp)
+function prepData = prepINITModel(origRefModel, taskStruct, spontRxnNames, convertGenes, customRxnsToIgnore, extComp, skipScaling)
 % prepINITModel
 %
 % The purpose of this function is to run time-consuming calculation steps that are not
@@ -16,7 +16,19 @@
 % extComp           Name of the external compartment, typically 's' or 'e'. This
 %                   is used for identifying exch and import rxns (opt, default = 'e')
 % prepData          The resulting prepData structure which is used as input to ftINIT
-%
+% skipScaling       If true the scaling step is not run on the minimal model. The 
+%                   scaling is there to remove large differences between the 
+%                   stoichiometric coefficients within a reaction, since such
+%                   differences creates numerical issues in the ftINIT algorithm 
+%                   due to limitations in solver resolution. However,
+%                   the current scaling step is also risky and may lead to that
+%                   some reactions cannot carry flux, since it changes the stoichiometry
+%                   of the reactions with large differences. If you experience problems
+%                   where the solution is infeasible, it may be worth trying to turn off
+%                   the scaling. Note that it is only the minModel that is scaled,
+%                   the scaling will not be present in the final model.
+%                   Default: (opt, default = false)
+% 
 % Usage: prepData = prepINITModel(origRefModel, taskStruct, spontRxnNames, convertGenes, customRxnsToIgnore, extComp)
 
 
@@ -36,6 +48,9 @@
     extComp = 'e';
 end
 
+if nargin < 7
+    skipScaling = false;
+end
 disp('Step 1: Gene rules')
 [origRefModel.grRules, origRefModel.rxnGeneMat] = standardizeGrRules(origRefModel, true);
 
@@ -286,10 +301,13 @@
 %      metabolites as well (ROS => kROS, albumin => millialbumin, etc., but
 %      scaled freely with a mathematical method). It could potentially open up
 %      for using less strict margins in the MILP, and make it run faster.
-scaledMinModel = rescaleModelForINIT(minModel3);
-scaledMinModel.ub(scaledMinModel.ub > 0) = 1000;
-scaledMinModel.lb(scaledMinModel.lb < 0) = -1000;
-
+if (skipScaling)
+    scaledMinModel = minModel3;
+else
+    scaledMinModel = rescaleModelForINIT(minModel3);
+    scaledMinModel.ub(scaledMinModel.ub > 0) = 1000;
+    scaledMinModel.lb(scaledMinModel.lb < 0) = -1000;
+end
 % create data structure with pre-processing results
 prepData.taskReport = taskReport;
 prepData.essentialRxns = newEssentialRxns; %essential rxns in the minModel

core/getModelFromHomology.m

@@ -117,6 +117,15 @@
     end
 end
 
+%Check that genes do not begin with ( or end with ), as this makes problematic grRules
+for i=1:numel(blastStructure)
+    problemGenes = startsWith(blastStructure(i).fromGenes,'(') | endsWith(blastStructure(i).fromGenes,')');
+    if any(problemGenes)
+        error(['One or multiple gene identifiers from ' blastStructure(i).fromId ...
+               ' starts with ''('' and/or ends with '')'', which is not allowed'])
+    end
+end
+
 %Assume for now that all information is there and that it's correct. This
 %is important to fix since no further checks are being made!
 
@@ -509,8 +518,8 @@
 %complexes
 draftModel=mergeModels(models,'metNames');
 
-% %Remove unnecessary OLD_ genes, that were added with OR relationships
-regexStr=['OLD_(', strjoin(modelNames(:),'|'),')_\S+'];
+%Remove unnecessary OLD_ genes, that were added with OR relationships
+regexStr=['OLD_(', strjoin(modelNames(:),'|'),')_(\S^\))+'];
 draftModel.grRules=regexprep(draftModel.grRules,[' or ' regexStr],'');
 draftModel.grRules=regexprep(draftModel.grRules,[regexStr ' or '],'');
 

doc/INIT/mergeLinear.html

@@ -53,7 +53,7 @@ <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^
 </ul>
 This function is called by:
 <ul style="list-style-image:url(../matlabicon.gif)">
-<li><a href="prepINITModel.html" class="code" title="function prepData = prepINITModel(origRefModel, taskStruct, spontRxnNames, convertGenes, customRxnsToIgnore, extComp)">prepINITModel</a>	prepINITModel</li></ul>
+<li><a href="prepINITModel.html" class="code" title="function prepData = prepINITModel(origRefModel, taskStruct, spontRxnNames, convertGenes, customRxnsToIgnore, extComp, skipScaling)">prepINITModel</a>	prepINITModel</li></ul>
 <!-- crossreference -->
 
 <h2><a name="_subfunctions"></a>SUBFUNCTIONS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>