Skip to content

fix: gene field alignment in removeLowScoreGenes #670

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
edkerk merged 2 commits into from
Jul 7, 2026
Merged

fix: gene field alignment in removeLowScoreGenes #670

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
5b6e3c6
fix: gene field alignment in removeLowScoreGenes
edkerk Jul 7, 2026
aed0be3
chore: updateDocumentation
edkerk Jul 7, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
15 changes: 11 additions & 4 deletions INIT/removeLowScoreGenes.m
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -109,13 +109,20 @@

% regenerate "genes" and "rxnGeneMat" model fields
[genes,rxnGeneMat] = getGenesFromGrRules(newModel.grRules);
newModel.genes = genes;
newModel.rxnGeneMat = rxnGeneMat;

% update other gene-related fields
remInd = ~ismember(model.genes,newModel.genes);
% determine which of the original genes were removed
remInd = ~ismember(model.genes,genes);
remGenes = model.genes(remInd);

% Keep the retained genes in their original order rather than the sorted
% order returned by getGenesFromGrRules. Gene removal never introduces new
% genes, so the remaining genes are model.genes(~remInd). Preserving this
% order ensures the gene-associated fields trimmed below (geneShortNames,
% proteins, etc.), which are indexed by remInd, stay aligned with genes.
newModel.genes = model.genes(~remInd);
[~,reorderInd] = ismember(newModel.genes,genes);
newModel.rxnGeneMat = rxnGeneMat(:,reorderInd);

if isfield(newModel,'geneShortNames')
newModel.geneShortNames(remInd) = [];
end
Expand Down
100 changes: 51 additions & 49 deletions doc/INIT/INITStepDesc.html
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -70,55 +70,57 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0024 <span class="comment">% .mets Names of metabolites to remove</span>
0025 <span class="comment">% .compsToKeep Compartments for which metabolites should be kept.</span>
0026 MILPParams <span class="comment">%Cell array of MILPparams - dictates how many iterations that will be run in this step.</span>
0027 <span class="comment">%Typically, MIPGap and TimeLimit is specified</span>
0028 AbsMIPGaps <span class="comment">%If the objective is close to zero, a percentage of that is very small.</span>
0029 <span class="comment">%Therefore, also set an absolut value for this (typically 10 or 20).</span>
0030 <span class="comment">%For practical reasons, the first number is not used</span>
0031 <span class="keyword">end</span>
0032 methods
0033 <a name="_sub0" href="#_subfunctions" class="code">function obj = INITStepDesc(posRevOff_, AllowMetSecr_, howToUsePrevResults_, rxnsToIgnoreMask_, metsToIgnore_, MILPParams_, absMIPGaps_)</a>
0034 <span class="keyword">if</span> nargin &gt; 0
0035 obj.PosRevOff = posRevOff_;
0036 <span class="keyword">else</span>
0037 obj.PosRevOff = false;
0038 <span class="keyword">end</span>
0039 <span class="keyword">if</span> nargin &gt; 1
0040 obj.AllowMetSecr = AllowMetSecr_;
0041 <span class="keyword">else</span>
0042 obj.AllowMetSecr = false;
0043 <span class="keyword">end</span>
0044 <span class="keyword">if</span> nargin &gt; 2
0045 obj.HowToUsePrevResults = howToUsePrevResults_;
0046 <span class="keyword">else</span>
0047 obj.HowToUsePrevResults = <span class="string">'essential'</span>;
0048 <span class="keyword">end</span>
0049 <span class="keyword">if</span> nargin &gt; 3
0050 obj.RxnsToIgnoreMask = rxnsToIgnoreMask_;
0051 <span class="keyword">else</span>
0052 obj.RxnsToIgnoreMask = [1;0;0;0;0;0;0;0];
0053 <span class="keyword">end</span>
0054 <span class="keyword">if</span> nargin &gt; 4
0055 obj.MetsToIgnore = metsToIgnore_;
0056 <span class="keyword">else</span>
0057 obj.MetsToIgnore = [1;0;0;0;0;0;0;0];
0058 <span class="keyword">end</span>
0059 <span class="keyword">if</span> nargin &gt; 5
0060 obj.MILPParams = MILPParams_;
0061 <span class="keyword">else</span>
0062 params = struct();
0063 params.TimeLimit = 5000;
0064 params.MIPGap = 0.0004;
0065 obj.MILPParams = {params};
0066 <span class="keyword">end</span>
0067
0068 <span class="keyword">if</span> nargin &gt; 6
0069 obj.AbsMIPGaps = absMIPGaps_;
0070 <span class="keyword">else</span>
0071 obj.AbsMIPGaps = 10;
0072 <span class="keyword">end</span>
0073 <span class="keyword">end</span>
0074 <span class="keyword">end</span>
0075 <span class="keyword">end</span></pre></div>
0027 <span class="comment">%Typically, MIPGap and TimeLimit is specified. ftINIT additionally</span>
0028 <span class="comment">%defaults Threads to 1 (single-threaded Gurobi) for determinism;</span>
0029 <span class="comment">%set Threads here to override (0 = use all cores).</span>
0030 AbsMIPGaps <span class="comment">%If the objective is close to zero, a percentage of that is very small.</span>
0031 <span class="comment">%Therefore, also set an absolut value for this (typically 10 or 20).</span>
0032 <span class="comment">%For practical reasons, the first number is not used</span>
0033 <span class="keyword">end</span>
0034 methods
0035 <a name="_sub0" href="#_subfunctions" class="code">function obj = INITStepDesc(posRevOff_, AllowMetSecr_, howToUsePrevResults_, rxnsToIgnoreMask_, metsToIgnore_, MILPParams_, absMIPGaps_)</a>
0036 <span class="keyword">if</span> nargin &gt; 0
0037 obj.PosRevOff = posRevOff_;
0038 <span class="keyword">else</span>
0039 obj.PosRevOff = false;
0040 <span class="keyword">end</span>
0041 <span class="keyword">if</span> nargin &gt; 1
0042 obj.AllowMetSecr = AllowMetSecr_;
0043 <span class="keyword">else</span>
0044 obj.AllowMetSecr = false;
0045 <span class="keyword">end</span>
0046 <span class="keyword">if</span> nargin &gt; 2
0047 obj.HowToUsePrevResults = howToUsePrevResults_;
0048 <span class="keyword">else</span>
0049 obj.HowToUsePrevResults = <span class="string">'essential'</span>;
0050 <span class="keyword">end</span>
0051 <span class="keyword">if</span> nargin &gt; 3
0052 obj.RxnsToIgnoreMask = rxnsToIgnoreMask_;
0053 <span class="keyword">else</span>
0054 obj.RxnsToIgnoreMask = [1;0;0;0;0;0;0;0];
0055 <span class="keyword">end</span>
0056 <span class="keyword">if</span> nargin &gt; 4
0057 obj.MetsToIgnore = metsToIgnore_;
0058 <span class="keyword">else</span>
0059 obj.MetsToIgnore = [1;0;0;0;0;0;0;0];
0060 <span class="keyword">end</span>
0061 <span class="keyword">if</span> nargin &gt; 5
0062 obj.MILPParams = MILPParams_;
0063 <span class="keyword">else</span>
0064 params = struct();
0065 params.TimeLimit = 5000;
0066 params.MIPGap = 0.0004;
0067 obj.MILPParams = {params};
0068 <span class="keyword">end</span>
0069
0070 <span class="keyword">if</span> nargin &gt; 6
0071 obj.AbsMIPGaps = absMIPGaps_;
0072 <span class="keyword">else</span>
0073 obj.AbsMIPGaps = 10;
0074 <span class="keyword">end</span>
0075 <span class="keyword">end</span>
0076 <span class="keyword">end</span>
0077 <span class="keyword">end</span></pre></div>
<hr><address>Generated by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
</body>
</html>
Loading
Loading