Merge pull request #543 from SysBioChalmers/develop

RAVEN 2.9.1

Author: edkerk

.github/workflows/tests.yml

@@ -8,7 +8,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Run tests
         id: matlab-test

INIT/ftINIT.m

@@ -13,11 +13,11 @@
 %                       hpaData.tissues or transcrData.tissues
 %   celltype            cell type to score for. Should exist in either
 %                       hpaData.celltypes or transcrData.celltypes for this
-%                       tissue (opt, default is to use the max values
+%                       tissue (optional, default is to use the max values
 %                       among all the cell types for the tissue.
-%   hpaData             HPA data structure from parseHPA (opt if transcrData
+%   hpaData             HPA data structure from parseHPA (optional if transcrData
 %                       is supplied, default [])
-%   transcrData         gene expression data structure (opt if hpaData is
+%   transcrData         gene expression data structure (optional if hpaData is
 %                       supplied, default []). Used to be called arrayData.
 %       genes           cell array with the unique gene names
 %       tissues         cell array with the tissue names. The list may not
@@ -29,36 +29,36 @@
 %                       used when no measurement was performed
 %       threshold       a single value or a vector of gene expression 
 %                       thresholds, above which genes are considered to be
-%                       "expressed". default = 1(opt, by default, the mean expression
+%                       "expressed". default = 1(optional, by default, the mean expression
 %                       levels of each gene across all tissues in transcrData
 %                       will be used as the threshold values)
 %       singleCells     binary value selecting whether to use the
 %                       single-cell algorithm to identify expressed genes.
 %                       If used, specify cell subpopulations in CELLTYPES
-%                       (opt, default [])
+%                       (optional, default [])
 %       plotResults     true if single cell probability distributions
-%                       should be plotted (opt, default = false)
+%                       should be plotted (optional, default = false)
 %   metabolomicsData    cell array with metabolite names that the model
-%                       should produce (opt, default [])
+%                       should produce (optional, default [])
 %   INITSteps           Specifies the steps in the algorithm. For more info,
 %                       see INITStepDesc and getINITSteps. 
-%                       (opt, default getINITSteps(), which is the standard ftINIT).
+%                       (optional, default getINITSteps(), which is the standard ftINIT).
 %   removeGenes         if true, low-abundance genes will be removed from
 %                       grRules, unless they are the only gene associated 
 %                       with a reaction, or a subunit of an enzyme complex
 %                       (see "removeLowScoreGenes" function for details).
 %                       If false, grRules will not be modified; however,
 %                       genes that were associated only with removed 
 %                       reactions will not be present in the final model.
-%                       (opt, default true).
+%                       (optional, default true).
 %   useScoresForTasks   true if the calculated reaction scored should be 
-%                       used as weights when fitting to tasks (opt, default
+%                       used as weights when fitting to tasks (optional, default
 %                       true)
 %   paramsFT            parameter structure as used by getMILPParams. This
 %                       is for the fitTasks step. For the INIT algorithm,
-%                       see params (opt, default [])
+%                       see params (optional, default [])
 %   verbose             if true, the MILP progression will be shown. 
-%                       (opt, default false)
+%                       (optional, default false)
 %
 %   model                   the resulting model structure
 %   metProduction           array that indicates which of the
@@ -86,7 +86,7 @@
 %   if any are present. Use importModel(file,false) to import a model with
 %   exchange metabolites remaining.
 %
-%   Usage: [model, metProduction, addedRxnsForTasks, deletedRxnsInINIT, ...
+% Usage: [model, metProduction, addedRxnsForTasks, deletedRxnsInINIT, ...
 %               fullMipRes] = ...
 %               ftINIT(prepData, tissue, celltype, hpaData, transcrData, ...
 %               metabolomicsData, INITSteps, removeGenes, useScoresForTasks, ...

INIT/ftINITFillGaps.m

@@ -11,13 +11,13 @@
 %                       the reactants is unavailable or because one of the
 %                       products can't be further processed. If this
 %                       parameter is true, only the first type of
-%                       unconnectivity is considered (opt, default false)
+%                       unconnectivity is considered (optional, default false)
 %   useModelConstraints true if the constraints specified in the tModel
 %                       structure should be used. If false then reactions
 %                       included from the template tModel(s) so that as many
 %                       reactions as possible in tModel can carry flux
-%                       (opt, default false)
-%   supressWarnings     false if warnings should be displayed (opt, default
+%                       (optional, default false)
+%   supressWarnings     false if warnings should be displayed (optional, default
 %                       false)
 %   rxnScores           scores for each of the reactions in the
 %                       reference tModel. 
@@ -52,7 +52,7 @@
 %   of reactions that have to be included in order for the tModel to produce
 %   biomass.
 %
-%   Usage: [newModel, exitFlag]=...
+% Usage: [newModel, exitFlag]=...
 %           fillGaps(tModel,models,allowNetProduction,...
 %           supressWarnings,rxnScores,params)
 

INIT/ftINITFillGapsForAllTasks.m

@@ -8,14 +8,14 @@
 %   model           model structure
 %   refModel        reference model from which to include reactions
 %   inputFile       a task list in Excel format. See the function
-%                   parseTaskList for details (opt if taskStructure is
+%                   parseTaskList for details (optional if taskStructure is
 %                   supplied)
 %   printOutput     true if the results of the test should be displayed
-%                   (opt, default true)
+%                   (optional, default true)
 %   rxnScores       scores for each of the reactions in the reference
 %                   model. Only negative scores are allowed. The solver will
 %                   try to maximize the sum of the scores for the included
-%                   reactions (opt, default is -1 for all reactions)
+%                   reactions (optional, default is -1 for all reactions)
 %   taskStructure   structure with the tasks, as from parseTaskList. If
 %                   this is supplied then inputFile is ignored
 %   params          parameter structure as used by getMILPParams
@@ -36,7 +36,7 @@
 %   all tasks at once. This means that the order of the tasks could influence
 %   the result.
 %
-%   Usage: [outModel, addedRxns]=fitTasks(model,refModel,inputFile,printOutput,...
+% Usage: [outModel, addedRxns]=fitTasks(model,refModel,inputFile,printOutput,...
 %           rxnScores,taskStructure,params)
 
 if isempty(rxnScores)

INIT/ftINITFillGapsMILP.m

@@ -11,13 +11,13 @@
 %   toMinimize    either a cell array of reaction IDs, a logical vector
 %                 with the same number of elements as reactions in the model,
 %                 of a vector of indexes for the reactions that should be
-%                 minimized (opt, default model.rxns)
-%   params        parameter structure as used by getMILPParams (opt)
+%                 minimized (optional, default model.rxns)
+%   params        parameter structure as used by getMILPParams (optional)
 %   scores        vector of weights for the reactions. Negative scores
 %                 should not have flux. Positive scores are not possible in this
 %                 implementation, and they are changed to max(scores(scores<0)).
 %                 Must have the same dimension as toMinimize (find(toMinimize)
-%                 if it is a logical vector) (opt, default -1 for all reactions)
+%                 if it is a logical vector) (optional, default -1 for all reactions)
 %   verbose       if true, the MILP progression will be shown. 
 %
 %   x             the corresponding fluxes for the full model
@@ -30,7 +30,7 @@
 %   NOTE: Uses 1000 mmol/gDW/h as an arbitary large flux. Could possibly
 %   cause problems if the fluxes in the model are larger than that.
 %
-%   Usage: [x,I,exitFlag]=getMinNrFluxes(model, toMinimize, params, scores)
+% Usage: [x,I,exitFlag]=getMinNrFluxes(model, toMinimize, params, scores)
 
 % glpk solver as implemented by COBRA does not work well for MILP.
 global CBT_MILP_SOLVER

INIT/ftINITInternalAlg.m

@@ -8,7 +8,7 @@
 %                   scores are reactions to exclude. Rxns set to 0 are excluded
 %                   from the problem.
 %   metData         boolean matrix with mets as rows and rxns as columns
-%                   saying which reaction produces each detected met (opt, default [])
+%                   saying which reaction produces each detected met (optional, default [])
 %   essentialRxns   cell array of reactions that are essential and that
 %                   have to be in the resulting model. This is normally
 %                   used when fitting a model to task (see fitTasks)
@@ -50,7 +50,7 @@
 %   This function is the actual implementation of the algorithm. See
 %   ftINIT for a higher-level function for model reconstruction. 
 %
-%   Usage: [deletedRxns,metProduction,res,turnedOnRxns,fluxes]=runINIT9(model,...
+% Usage: [deletedRxns,metProduction,res,turnedOnRxns,fluxes]=runINIT9(model,...
 %           rxnScores,presentMets,essentialRxns,prodWeight,allowExcretion,...
 %           remPosRev,params)
 

INIT/getExprForRxnScore.m

@@ -6,11 +6,11 @@
 %   define the reaction scores of rxns, but need to send in gene expression.
 %
 %   scores        Vector of scores to convert
-%   threshold     Gene threshold (opt, default 1)
+%   threshold     Gene threshold (optional, default 1)
 %
 %   expr          The resulting gene expression vector.
 %
-%   Usage: expr = getExprForRxnScore(scores, threshold)
+% Usage: expr = getExprForRxnScore(scores, threshold)
 
 if nargin < 2
     threshold = 1;

INIT/getINITModel.m

@@ -16,12 +16,12 @@
 %                       hpaData.tissues or arrayData.tissues
 %   celltype            cell type to score for. Should exist in either
 %                       hpaData.celltypes or arrayData.celltypes for this
-%                       tissue (opt, default is to use the best values
+%                       tissue (optional, default is to use the best values
 %                       among all the cell types for the tissue. Use [] if
 %                       you want to supply more arguments)
-%   hpaData             HPA data structure from parseHPA (opt if arrayData is
+%   hpaData             HPA data structure from parseHPA (optional if arrayData is
 %                       supplied, default [])
-%   arrayData           gene expression data structure (opt if hpaData is
+%   arrayData           gene expression data structure (optional if hpaData is
 %                       supplied, default [])
 %       genes           cell array with the unique gene names
 %       tissues         cell array with the tissue names. The list may not be
@@ -32,33 +32,33 @@
 %                       used when no measurement was performed
 %       threshold       a single value or a vector of gene expression 
 %                       thresholds, above which genes are considered to be
-%                       "expressed". (opt, by default, the mean expression
+%                       "expressed". (optional, by default, the mean expression
 %                       levels of each gene across all tissues in arrayData
 %                       will be used as the threshold values)
 %       singleCells     binary value selecting whether to use the
 %                       single-cell algorithm to identify expressed genes.
 %                       If used, specify cell subpopulations in CELLTYPES
-%                       (opt, default [])
+%                       (optional, default [])
 %       plotResults     true if single cell probability distributions
-%                       should be plotted (opt, default = False)
+%                       should be plotted (optional, default = False)
 %   metabolomicsData    cell array with metabolite names that the model
-%                       should produce (opt, default [])
+%                       should produce (optional, default [])
 %   taskFile            a task list in Excel format. See parseTaskList for
-%                       details (opt, default [])
+%                       details (optional, default [])
 %   useScoresForTasks   true if the calculated reaction scored should be used as
-%                       weights in the fitting to tasks (opt, default true)
+%                       weights in the fitting to tasks (optional, default true)
 %   printReport         true if a report should be printed to the screen
-%                       (opt, default true)
+%                       (optional, default true)
 %   taskStructure       task structure as from parseTaskList. Can be used
 %                       as an alternative way to define tasks when Excel
-%                       sheets are not suitable. Overrides taskFile (opt,
+%                       sheets are not suitable. Overrides taskFile (optional,
 %                       default [])
 %   params              parameter structure as used by getMILPParams. This is
 %                       for the INIT algorithm. For the the MILP problems
-%                       solved to fit tasks, see paramsFT (opt, default [])
+%                       solved to fit tasks, see paramsFT (optional, default [])
 %   paramsFT            parameter structure as used by getMILPParams. This is
 %                       for the fitTasks step. For the INIT algorithm, see
-%                       params (opt, default [])
+%                       params (optional, default [])
 %
 %
 %   Output:
@@ -102,7 +102,7 @@
 %   if any are present. Use importModel(file,false) to import a model with
 %   exchange metabolites remaining.
 %
-%   Usage: [model, metProduction, essentialRxnsForTasks, addedRxnsForTasks,...
+% Usage: [model, metProduction, essentialRxnsForTasks, addedRxnsForTasks,...
 %               deletedDeadEndRxns, deletedRxnsInINIT, taskReport]=...
 %               getINITModel(refModel, tissue, celltype, hpaData, arrayData,...
 %               metabolomicsData, taskFile, useScoresForTasks, printReport,...

INIT/getINITSteps.m

@@ -9,7 +9,7 @@
 %
 %   metsToIgnore  Structure describing mets that can be removed from the model
 %                 before running ftINIT, such as water etc.
-%                 (opt, default [])
+%                 (optional, default [])
 %       simpleMets
 %           mets  Names of metabolites to remove
 %           compsToKeep Compartments for which metabolites should be kept.
@@ -31,11 +31,11 @@
 %                 'full'         1-step run - similar to the old tINIT version but 
 %                                without simplifications. Accurate, but very slow.
 %                                This is mainly used for testing purposes.
-%                 (opt, default '1+1')
+%                 (optional, default '1+1')
 %
 %   steps         Cell array of steps, used as input to ftINIT
 %
-%   Usage: steps = getINITSteps(metsToIgnore, series)
+% Usage: steps = getINITSteps(metsToIgnore, series)
 if nargin < 1
     metsToIgnore = [];
 end

INIT/mergeLinear.m

@@ -16,7 +16,7 @@
 %                         0 means a reaction was not merged.
 %   reversedRxns          Vector of booleans, saying for each rxn if it is reversed in the combined rxns.
 %
-%   Usage: [reducedModel,origRxnIds,groupIds]=mergeLinear(model,noMergeRxns)
+% Usage: [reducedModel,origRxnIds,groupIds]=mergeLinear(model,noMergeRxns)
 
 
 reducedModel=model;

INIT/prepINITModel.m

@@ -8,13 +8,13 @@
 %                   Mouse-GEM, etc.
 % taskStruct        The essential tasks. Can be loaded with for example
 %                   taskStruct = parseTaskList('../data/metabolicTasks_Essential.txt');
-% spontRxnNames     The spontaneous rxns. (opt, default {})
+% spontRxnNames     The spontaneous rxns. (optional, default {})
 % convertGenes      If true the genes are converted to gene names (from 
-%                   ENSEMBL) (opt, default false)
+%                   ENSEMBL) (optional, default false)
 % customRxnsToIgnore These reactions can be ignored in the ignore mask 
-%                   (specifying b7=1) (opt, default = {})
+%                   (specifying b7=1) (optional, default = {})
 % extComp           Name of the external compartment, typically 's' or 'e'. This
-%                   is used for identifying exch and import rxns (opt, default = 'e')
+%                   is used for identifying exch and import rxns (optional, 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 
@@ -27,7 +27,7 @@
 %                   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)
+%                   Default: (optional, default = false)
 % 
 % Usage: prepData = prepINITModel(origRefModel, taskStruct, spontRxnNames, convertGenes, customRxnsToIgnore, extComp)
 

INIT/removeLowScoreGenes.m

@@ -43,11 +43,11 @@
 %
 %   isozymeScoring  Method used to combine the scores of multiple isozymes;
 %                   'min', 'max', 'median', or 'average'. 
-%                   (Opt, default 'max')
+%                   (optional, default 'max')
 %
 %   complexScoring  Method used to combine the scores of enzyme complex
 %                   subunits: 'min', 'max', 'median', or 'average'. 
-%                   (Opt, default 'min')
+%                   (optional, default 'min')
 %
 % Outputs:
 %

INIT/rescaleModelForINIT.m

@@ -11,7 +11,7 @@
 %
 % model         the model to be modified (input and output)
 % maxStoichVal  all reactions with stoichiometric coefficent higher than this 
-%               will be scaled down. (opt, default 250)
+%               will be scaled down. (optional, default 250)
 
 if (nargin < 2)
     maxStoichDiff = 25;