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Merge branch 'develop' into feat/importModel
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@edkerk
edkerk authored Jun 30, 2023
2 parents 7ab8cae + 4db3072 commit 51f2a57
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Expand Up @@ -635,93 +635,94 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0578 <span class="comment">% end</span>
0579 <span class="comment">% end</span>
0580
0581 <span class="comment">% Make rxnGeneMat fields</span>
0582 [genes, rxnGeneMat] = getGenesFromGrRules(model.grRules, model.genes);
0583 <span class="keyword">if</span> isequal(sort(genes), sort(model.genes))
0584 model.rxnGeneMat = rxnGeneMat;
0585 model.genes = genes;
0586 <span class="keyword">else</span>
0587 error(<span class="string">'The gene list and grRules are inconsistent.'</span>);
0581 <span class="comment">% Make rxnGeneMat fields and map to the existing model.genes field</span>
0582 [genes, rxnGeneMat] = getGenesFromGrRules(model.grRules);
0583 model.rxnGeneMat = sparse(numel(model.rxns),numel(model.genes));
0584 [~,geneOrder] = ismember(genes,model.genes);
0585 <span class="keyword">if</span> any(geneOrder == 0)
0586 error([<span class="string">'The grRules includes the following gene(s), that are not in '</span><span class="keyword">...</span>
0587 <span class="string">'the list of model genes: '</span>, genes{~geneOrder}])
0588 <span class="keyword">end</span>
0589
0590 <span class="comment">% Finalize GECKO model</span>
0591 <span class="keyword">if</span> isGECKO
0592 <span class="comment">% Fill in empty fields and empty entries</span>
0593 <span class="keyword">for</span> i={<span class="string">'kcat'</span>,<span class="string">'source'</span>,<span class="string">'notes'</span>,<span class="string">'eccodes'</span>} <span class="comment">% Even keep empty</span>
0594 model.ec = <a href="#_sub1" class="code" title="subfunction model = emptyOrFill(model,field,emptyEntry,type,keepEmpty)">emptyOrFill</a>(model.ec,i{1},{<span class="string">''</span>},<span class="string">'rxns'</span>,true);
0595 <span class="keyword">end</span>
0596 <span class="keyword">for</span> i={<span class="string">'enzymes'</span>,<span class="string">'mw'</span>,<span class="string">'sequence'</span>}
0597 model.ec = <a href="#_sub1" class="code" title="subfunction model = emptyOrFill(model,field,emptyEntry,type,keepEmpty)">emptyOrFill</a>(model.ec,i{1},{<span class="string">''</span>},<span class="string">'genes'</span>,true);
0598 <span class="keyword">end</span>
0599 model.ec = <a href="#_sub1" class="code" title="subfunction model = emptyOrFill(model,field,emptyEntry,type,keepEmpty)">emptyOrFill</a>(model.ec,<span class="string">'concs'</span>,{<span class="string">'NaN'</span>},<span class="string">'genes'</span>,true);
0600 model.ec = <a href="#_sub1" class="code" title="subfunction model = emptyOrFill(model,field,emptyEntry,type,keepEmpty)">emptyOrFill</a>(model.ec,<span class="string">'kcat'</span>,{<span class="string">'0'</span>},<span class="string">'genes'</span>,true);
0601 <span class="comment">% Change string to double</span>
0602 <span class="keyword">for</span> i={<span class="string">'kcat'</span>,<span class="string">'mw'</span>,<span class="string">'concs'</span>}
0603 <span class="keyword">if</span> isfield(model.ec,i{1})
0604 model.ec.(i{1}) = str2double(model.ec.(i{1}));
0605 <span class="keyword">end</span>
0606 <span class="keyword">end</span>
0607 <span class="comment">% Fill rxnEnzMat</span>
0608 rxnIdx = cellfun(@isempty, enzStoich(:,1));
0609 enzStoich(rxnIdx,:) = <span class="string">''</span>;
0610 rxnIdx = cell2mat(enzStoich(:,1));
0611 [~,enzIdx] = ismember(enzStoich(:,2),model.ec.enzymes);
0612 coeffs = cell2mat(enzStoich(:,3));
0613 model.ec.rxnEnzMat = zeros(max(rxnIdx), max(enzIdx));
0614 linearIndices = sub2ind([max(rxnIdx), max(enzIdx)], rxnIdx, enzIdx);
0615 model.ec.rxnEnzMat(linearIndices) = coeffs;
0616 <span class="comment">%Parse ec-codes</span>
0617 <span class="keyword">if</span> ~isempty(ecGecko)
0618 locs = cell2mat(ecGecko(:,1));
0619 <span class="keyword">for</span> i=unique(locs)'
0620 ecGeckoCat=strjoin(ecGecko(locs==i,2),<span class="string">';'</span>);
0621 model.ec.eccodes{i,1}=ecGeckoCat;
0622 <span class="keyword">end</span>
0623 emptyEc=cellfun(@isempty,model.ec.eccodes);
0624 model.ec.eccodes(emptyEc)={<span class="string">''</span>};
0625 <span class="keyword">end</span>
0626 <span class="keyword">end</span>
0627
0628 <span class="keyword">if</span> verbose
0629 fprintf(<span class="string">' Done!\n'</span>);
0630 <span class="keyword">end</span>
0589 model.rxnGeneMat(:,geneOrder) = rxnGeneMat;
0590
0591 <span class="comment">% Finalize GECKO model</span>
0592 <span class="keyword">if</span> isGECKO
0593 <span class="comment">% Fill in empty fields and empty entries</span>
0594 <span class="keyword">for</span> i={<span class="string">'kcat'</span>,<span class="string">'source'</span>,<span class="string">'notes'</span>,<span class="string">'eccodes'</span>} <span class="comment">% Even keep empty</span>
0595 model.ec = <a href="#_sub1" class="code" title="subfunction model = emptyOrFill(model,field,emptyEntry,type,keepEmpty)">emptyOrFill</a>(model.ec,i{1},{<span class="string">''</span>},<span class="string">'rxns'</span>,true);
0596 <span class="keyword">end</span>
0597 <span class="keyword">for</span> i={<span class="string">'enzymes'</span>,<span class="string">'mw'</span>,<span class="string">'sequence'</span>}
0598 model.ec = <a href="#_sub1" class="code" title="subfunction model = emptyOrFill(model,field,emptyEntry,type,keepEmpty)">emptyOrFill</a>(model.ec,i{1},{<span class="string">''</span>},<span class="string">'genes'</span>,true);
0599 <span class="keyword">end</span>
0600 model.ec = <a href="#_sub1" class="code" title="subfunction model = emptyOrFill(model,field,emptyEntry,type,keepEmpty)">emptyOrFill</a>(model.ec,<span class="string">'concs'</span>,{<span class="string">'NaN'</span>},<span class="string">'genes'</span>,true);
0601 model.ec = <a href="#_sub1" class="code" title="subfunction model = emptyOrFill(model,field,emptyEntry,type,keepEmpty)">emptyOrFill</a>(model.ec,<span class="string">'kcat'</span>,{<span class="string">'0'</span>},<span class="string">'genes'</span>,true);
0602 <span class="comment">% Change string to double</span>
0603 <span class="keyword">for</span> i={<span class="string">'kcat'</span>,<span class="string">'mw'</span>,<span class="string">'concs'</span>}
0604 <span class="keyword">if</span> isfield(model.ec,i{1})
0605 model.ec.(i{1}) = str2double(model.ec.(i{1}));
0606 <span class="keyword">end</span>
0607 <span class="keyword">end</span>
0608 <span class="comment">% Fill rxnEnzMat</span>
0609 rxnIdx = cellfun(@isempty, enzStoich(:,1));
0610 enzStoich(rxnIdx,:) = <span class="string">''</span>;
0611 rxnIdx = cell2mat(enzStoich(:,1));
0612 [~,enzIdx] = ismember(enzStoich(:,2),model.ec.enzymes);
0613 coeffs = cell2mat(enzStoich(:,3));
0614 model.ec.rxnEnzMat = zeros(max(rxnIdx), max(enzIdx));
0615 linearIndices = sub2ind([max(rxnIdx), max(enzIdx)], rxnIdx, enzIdx);
0616 model.ec.rxnEnzMat(linearIndices) = coeffs;
0617 <span class="comment">%Parse ec-codes</span>
0618 <span class="keyword">if</span> ~isempty(ecGecko)
0619 locs = cell2mat(ecGecko(:,1));
0620 <span class="keyword">for</span> i=unique(locs)'
0621 ecGeckoCat=strjoin(ecGecko(locs==i,2),<span class="string">';'</span>);
0622 model.ec.eccodes{i,1}=ecGeckoCat;
0623 <span class="keyword">end</span>
0624 emptyEc=cellfun(@isempty,model.ec.eccodes);
0625 model.ec.eccodes(emptyEc)={<span class="string">''</span>};
0626 <span class="keyword">end</span>
0627 <span class="keyword">end</span>
0628
0629 <span class="keyword">if</span> verbose
0630 fprintf(<span class="string">' Done!\n'</span>);
0631 <span class="keyword">end</span>
0632
0633 <a name="_sub1" href="#_subfunctions" class="code">function model = emptyOrFill(model,field,emptyEntry,type,keepEmpty)</a>
0634 <span class="keyword">if</span> nargin&lt;5
0635 keepEmpty=false;
0636 <span class="keyword">end</span>
0637 <span class="keyword">if</span> isnumeric(emptyEntry)
0638 emptyCells=isempty(model.(field));
0639 <span class="keyword">else</span>
0640 emptyCells=cellfun(@isempty,model.(field));
0641 <span class="keyword">end</span>
0642 <span class="keyword">if</span> all(emptyCells) &amp;&amp; ~keepEmpty
0643 model = rmfield(model, field);
0644 <span class="keyword">elseif</span> numel(model.(field))&lt;numel(model.(type))
0645 model.(field)(end+1:numel(model.(type)),1)=emptyEntry;
0646 <span class="keyword">end</span>
0632 <span class="keyword">end</span>
0633
0634 <a name="_sub1" href="#_subfunctions" class="code">function model = emptyOrFill(model,field,emptyEntry,type,keepEmpty)</a>
0635 <span class="keyword">if</span> nargin&lt;5
0636 keepEmpty=false;
0637 <span class="keyword">end</span>
0638 <span class="keyword">if</span> isnumeric(emptyEntry)
0639 emptyCells=isempty(model.(field));
0640 <span class="keyword">else</span>
0641 emptyCells=cellfun(@isempty,model.(field));
0642 <span class="keyword">end</span>
0643 <span class="keyword">if</span> all(emptyCells) &amp;&amp; ~keepEmpty
0644 model = rmfield(model, field);
0645 <span class="keyword">elseif</span> numel(model.(field))&lt;numel(model.(type))
0646 model.(field)(end+1:numel(model.(type)),1)=emptyEntry;
0647 <span class="keyword">end</span>
0648
0649 <a name="_sub2" href="#_subfunctions" class="code">function model = readFieldValue(model, fieldName, value, pos)</a>
0650 <span class="keyword">if</span> numel(model.(fieldName))&lt;pos-1
0651 model.(fieldName)(end+1:pos,1) = {<span class="string">''</span>};
0652 <span class="keyword">end</span>
0653 model.(fieldName)(pos,1) = {value};
0654 <span class="keyword">end</span>
0655
0656 <a name="_sub3" href="#_subfunctions" class="code">function [miriams, miriamKey,entryNumber] = gatherAnnotation(pos,miriams,key,value,miriamKey,entryNumber)</a>
0657 <span class="keyword">if</span> isempty(key)
0658 key=miriamKey;
0659 <span class="keyword">else</span>
0660 miriamKey=key;
0661 <span class="keyword">end</span>
0662 <span class="keyword">if</span> ~isempty(value)
0663 miriams(entryNumber,1:3) = {pos, key, strip(value)};
0664 <span class="keyword">else</span>
0665 entryNumber = entryNumber - 1;
0666 <span class="keyword">end</span>
0667 <span class="keyword">end</span></pre></div>
0648 <span class="keyword">end</span>
0649
0650 <a name="_sub2" href="#_subfunctions" class="code">function model = readFieldValue(model, fieldName, value, pos)</a>
0651 <span class="keyword">if</span> numel(model.(fieldName))&lt;pos-1
0652 model.(fieldName)(end+1:pos,1) = {<span class="string">''</span>};
0653 <span class="keyword">end</span>
0654 model.(fieldName)(pos,1) = {value};
0655 <span class="keyword">end</span>
0656
0657 <a name="_sub3" href="#_subfunctions" class="code">function [miriams, miriamKey,entryNumber] = gatherAnnotation(pos,miriams,key,value,miriamKey,entryNumber)</a>
0658 <span class="keyword">if</span> isempty(key)
0659 key=miriamKey;
0660 <span class="keyword">else</span>
0661 miriamKey=key;
0662 <span class="keyword">end</span>
0663 <span class="keyword">if</span> ~isempty(value)
0664 miriams(entryNumber,1:3) = {pos, key, strip(value)};
0665 <span class="keyword">else</span>
0666 entryNumber = entryNumber - 1;
0667 <span class="keyword">end</span>
0668 <span class="keyword">end</span></pre></div>
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