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refactor: add & remove COBRA prefixes (#565)
* feat: dedicated funcs to add and rem ID prefixes * refactor: add and rem COBRA prefixes
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| <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" | ||
| "http://www.w3.org/TR/REC-html40/loose.dtd"> | ||
| <html> | ||
| <head> | ||
| <title>Description of addCOBRAstylePrefixes</title> | ||
| <meta name="keywords" content="addCOBRAstylePrefixes"> | ||
| <meta name="description" content="addCOBRAstylePrefixes"> | ||
| <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> | ||
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| <body> | ||
| <a name="_top"></a> | ||
| <div><a href="../index.html">Home</a> > <a href="index.html">struct_conversion</a> > addCOBRAstylePrefixes.m</div> | ||
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| <!--<table width="100%"><tr><td align="left"><a href="../index.html"><img alt="<" border="0" src="../left.png"> Master index</a></td> | ||
| <td align="right"><a href="index.html">Index for struct_conversion <img alt=">" border="0" src="../right.png"></a></td></tr></table>--> | ||
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| <h1>addCOBRAstylePrefixes | ||
| </h1> | ||
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| <h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2> | ||
| <div class="box"><strong>addCOBRAstylePrefixes</strong></div> | ||
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| <h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2> | ||
| <div class="box"><strong>function model=addCOBRAstylePrefixes(model,fields,printWarnings) </strong></div> | ||
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| <h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2> | ||
| <div class="fragment"><pre class="comment"> addCOBRAstylePrefixes | ||
| This function adds COBRA style identifier prefixes, which are: | ||
| "R_" for model.rxns, | ||
| "M_" for model.mets, | ||
| "C_" for model.comps; | ||
| "G_" for model.genes (and also represented in model.grRules). | ||
| If all entries in a field already have the prefix, then no additional | ||
| prefix will be added. | ||
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| Input: | ||
| model model whose identifiers should be modified | ||
| fields cell array with model field names to which the prefix | ||
| should be added, possible values: {'rxns', 'mets', | ||
| 'comps', 'genes'} (optional, by default prefixes are | ||
| added to all listed model fields will be checked). | ||
| printWarnings if warnings should be shown (optional, default true). | ||
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| Output: | ||
| model modified model | ||
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| Usage: model=addCOBRAstylePrefixes(model,fields,printWarnings)</pre></div> | ||
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| <!-- crossreference --> | ||
| <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2> | ||
| This function calls: | ||
| <ul style="list-style-image:url(../matlabicon.gif)"> | ||
| </ul> | ||
| This function is called by: | ||
| <ul style="list-style-image:url(../matlabicon.gif)"> | ||
| </ul> | ||
| <!-- crossreference --> | ||
|
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| <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2> | ||
| <div class="fragment"><pre>0001 <a name="_sub0" href="#_subfunctions" class="code">function model=addCOBRAstylePrefixes(model,fields,printWarnings)</a> | ||
| 0002 <span class="comment">% addCOBRAstylePrefixes</span> | ||
| 0003 <span class="comment">% This function adds COBRA style identifier prefixes, which are:</span> | ||
| 0004 <span class="comment">% "R_" for model.rxns,</span> | ||
| 0005 <span class="comment">% "M_" for model.mets,</span> | ||
| 0006 <span class="comment">% "C_" for model.comps;</span> | ||
| 0007 <span class="comment">% "G_" for model.genes (and also represented in model.grRules).</span> | ||
| 0008 <span class="comment">% If all entries in a field already have the prefix, then no additional</span> | ||
| 0009 <span class="comment">% prefix will be added.</span> | ||
| 0010 <span class="comment">%</span> | ||
| 0011 <span class="comment">% Input:</span> | ||
| 0012 <span class="comment">% model model whose identifiers should be modified</span> | ||
| 0013 <span class="comment">% fields cell array with model field names to which the prefix</span> | ||
| 0014 <span class="comment">% should be added, possible values: {'rxns', 'mets',</span> | ||
| 0015 <span class="comment">% 'comps', 'genes'} (optional, by default prefixes are</span> | ||
| 0016 <span class="comment">% added to all listed model fields will be checked).</span> | ||
| 0017 <span class="comment">% printWarnings if warnings should be shown (optional, default true).</span> | ||
| 0018 <span class="comment">%</span> | ||
| 0019 <span class="comment">% Output:</span> | ||
| 0020 <span class="comment">% model modified model</span> | ||
| 0021 <span class="comment">%</span> | ||
| 0022 <span class="comment">% Usage: model=addCOBRAstylePrefixes(model,fields,printWarnings)</span> | ||
| 0023 | ||
| 0024 <span class="keyword">if</span> nargin<2 || isempty(fields) | ||
| 0025 fields = {<span class="string">'rxns'</span>,<span class="string">'mets'</span>,<span class="string">'comps'</span>,<span class="string">'genes'</span>}; | ||
| 0026 <span class="keyword">end</span> | ||
| 0027 <span class="keyword">if</span> nargin<3 || isempty(printWarnings) | ||
| 0028 printWarnings = true; | ||
| 0029 <span class="keyword">end</span> | ||
| 0030 | ||
| 0031 modelFields = {<span class="string">'rxns'</span>,<span class="string">'R_'</span>; | ||
| 0032 <span class="string">'mets'</span>,<span class="string">'M_'</span>; | ||
| 0033 <span class="string">'comps'</span>,<span class="string">'C_'</span>; | ||
| 0034 <span class="string">'genes'</span>,<span class="string">'G_'</span>}; | ||
| 0035 | ||
| 0036 toChangeIdx = find(ismember(modelFields(:,1),fields)); | ||
| 0037 <span class="keyword">for</span> i=1:numel(toChangeIdx) | ||
| 0038 currName = modelFields{toChangeIdx(i),1}; | ||
| 0039 currPrefix = modelFields{toChangeIdx(i),2}; | ||
| 0040 <span class="keyword">if</span> isfield(model,currName) | ||
| 0041 currField = model.(currName); | ||
| 0042 <span class="keyword">else</span> | ||
| 0043 <span class="keyword">continue</span>; | ||
| 0044 <span class="keyword">end</span> | ||
| 0045 <span class="keyword">if</span> ~all(startsWith(currField,currPrefix)) | ||
| 0046 currField = strcat(currPrefix, currField); | ||
| 0047 <span class="keyword">if</span> strcmp(currName,<span class="string">'genes'</span>) | ||
| 0048 model.grRules = regexprep(model.grRules, <span class="string">'(\<[0-9_a-zA-Z])'</span>, <span class="string">'G_$1'</span>); | ||
| 0049 model.grRules = regexprep(model.grRules, <span class="string">' G_or '</span>, <span class="string">' or '</span>); | ||
| 0050 model.grRules = regexprep(model.grRules, <span class="string">' G_and '</span>, <span class="string">' and '</span>); | ||
| 0051 <span class="keyword">end</span> | ||
| 0052 model.(currName) = currField; | ||
| 0053 <span class="keyword">elseif</span> printWarnings | ||
| 0054 warning([<span class="string">'All identifiers in "model.'</span> currName <span class="string">'" already start '</span> <span class="keyword">...</span> | ||
| 0055 <span class="string">'with "'</span> currPrefix <span class="string">'", no additional prefix added.'</span>]) | ||
| 0056 <span class="keyword">end</span> | ||
| 0057 <span class="keyword">end</span> | ||
| 0058 <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> © 2005</address> | ||
| </body> | ||
| </html> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,133 @@ | ||
| <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" | ||
| "http://www.w3.org/TR/REC-html40/loose.dtd"> | ||
| <html> | ||
| <head> | ||
| <title>Description of removeCOBRAstylePrefixes</title> | ||
| <meta name="keywords" content="removeCOBRAstylePrefixes"> | ||
| <meta name="description" content="removeCOBRAstylePrefixes"> | ||
| <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> | ||
| <meta name="generator" content="m2html v1.5 © 2003-2005 Guillaume Flandin"> | ||
| <meta name="robots" content="index, follow"> | ||
| <link type="text/css" rel="stylesheet" href="../m2html.css"> | ||
| </head> | ||
| <body> | ||
| <a name="_top"></a> | ||
| <div><a href="../index.html">Home</a> > <a href="index.html">struct_conversion</a> > removeCOBRAstylePrefixes.m</div> | ||
|
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| <!--<table width="100%"><tr><td align="left"><a href="../index.html"><img alt="<" border="0" src="../left.png"> Master index</a></td> | ||
| <td align="right"><a href="index.html">Index for struct_conversion <img alt=">" border="0" src="../right.png"></a></td></tr></table>--> | ||
|
|
||
| <h1>removeCOBRAstylePrefixes | ||
| </h1> | ||
|
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| <h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2> | ||
| <div class="box"><strong>removeCOBRAstylePrefixes</strong></div> | ||
|
|
||
| <h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2> | ||
| <div class="box"><strong>function model=removeCOBRAstylePrefixes(model,fields,forceRemove) </strong></div> | ||
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| <h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2> | ||
| <div class="fragment"><pre class="comment"> removeCOBRAstylePrefixes | ||
| This function removes COBRA style identifier prefixes, which are: | ||
| "R_" for model.rxns, model.rxnNames and model.id, | ||
| "M_" for model.mets and model.metNames, | ||
| "C_" for model.comps; | ||
| "G_" for model.genes (and also represented in model.grRules). | ||
| By default, the prefixes are only removed if all entries in a | ||
| particular field has the prefix. | ||
|
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| Input: | ||
| model model whose identifiers should be modified | ||
| fields cell array with model field names from which the | ||
| identifiers should be removed, possible values: | ||
| 'rxns', 'mets', 'comps', 'genes', 'metNames', | ||
| 'rxnNames', 'id'. (optional, by default all listed | ||
| model fields will be checked). | ||
| forceRemove if prefixes should be removed even if not all entries | ||
| in a model field have the prefix (optional, default | ||
| false) | ||
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| Output: | ||
| model modified model | ||
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| Usage: model=removeCOBRAstylePrefixes(model,fields,forceRemove)</pre></div> | ||
|
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||
| <!-- crossreference --> | ||
| <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2> | ||
| This function calls: | ||
| <ul style="list-style-image:url(../matlabicon.gif)"> | ||
| </ul> | ||
| This function is called by: | ||
| <ul style="list-style-image:url(../matlabicon.gif)"> | ||
| </ul> | ||
| <!-- crossreference --> | ||
|
|
||
|
|
||
|
|
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| <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2> | ||
| <div class="fragment"><pre>0001 <a name="_sub0" href="#_subfunctions" class="code">function model=removeCOBRAstylePrefixes(model,fields,forceRemove)</a> | ||
| 0002 <span class="comment">% removeCOBRAstylePrefixes</span> | ||
| 0003 <span class="comment">% This function removes COBRA style identifier prefixes, which are:</span> | ||
| 0004 <span class="comment">% "R_" for model.rxns, model.rxnNames and model.id,</span> | ||
| 0005 <span class="comment">% "M_" for model.mets and model.metNames,</span> | ||
| 0006 <span class="comment">% "C_" for model.comps;</span> | ||
| 0007 <span class="comment">% "G_" for model.genes (and also represented in model.grRules).</span> | ||
| 0008 <span class="comment">% By default, the prefixes are only removed if all entries in a</span> | ||
| 0009 <span class="comment">% particular field has the prefix.</span> | ||
| 0010 <span class="comment">%</span> | ||
| 0011 <span class="comment">% Input:</span> | ||
| 0012 <span class="comment">% model model whose identifiers should be modified</span> | ||
| 0013 <span class="comment">% fields cell array with model field names from which the</span> | ||
| 0014 <span class="comment">% identifiers should be removed, possible values:</span> | ||
| 0015 <span class="comment">% 'rxns', 'mets', 'comps', 'genes', 'metNames',</span> | ||
| 0016 <span class="comment">% 'rxnNames', 'id'. (optional, by default all listed</span> | ||
| 0017 <span class="comment">% model fields will be checked).</span> | ||
| 0018 <span class="comment">% forceRemove if prefixes should be removed even if not all entries</span> | ||
| 0019 <span class="comment">% in a model field have the prefix (optional, default</span> | ||
| 0020 <span class="comment">% false)</span> | ||
| 0021 <span class="comment">%</span> | ||
| 0022 <span class="comment">% Output:</span> | ||
| 0023 <span class="comment">% model modified model</span> | ||
| 0024 <span class="comment">%</span> | ||
| 0025 <span class="comment">% Usage: model=removeCOBRAstylePrefixes(model,fields,forceRemove)</span> | ||
| 0026 | ||
| 0027 <span class="keyword">if</span> nargin<2 || isempty(fields) | ||
| 0028 fields = {<span class="string">'rxns'</span>,<span class="string">'mets'</span>,<span class="string">'comps'</span>,<span class="string">'genes'</span>,<span class="string">'metNames'</span>,<span class="string">'rxnNames'</span>,<span class="string">'id'</span>}; | ||
| 0029 <span class="keyword">end</span> | ||
| 0030 <span class="keyword">if</span> nargin<3 || isempty(forceRemove) | ||
| 0031 forceRemove = true; | ||
| 0032 <span class="keyword">end</span> | ||
| 0033 | ||
| 0034 modelFields = {<span class="string">'rxns'</span>, <span class="string">'R_'</span>; | ||
| 0035 <span class="string">'mets'</span>, <span class="string">'M_'</span>; | ||
| 0036 <span class="string">'comps'</span>, <span class="string">'C_'</span>; | ||
| 0037 <span class="string">'genes'</span>, <span class="string">'G_'</span>; | ||
| 0038 <span class="string">'metNames'</span>, <span class="string">'M_'</span>; | ||
| 0039 <span class="string">'rxnNames'</span>, <span class="string">'R_'</span>; | ||
| 0040 <span class="string">'id'</span>, <span class="string">'M_'</span>}; | ||
| 0041 | ||
| 0042 toChangeIdx = find(ismember(modelFields(:,1),fields)); | ||
| 0043 <span class="keyword">for</span> i=1:numel(toChangeIdx) | ||
| 0044 currName = modelFields{toChangeIdx(i),1}; | ||
| 0045 currPrefix = modelFields{toChangeIdx(i),2}; | ||
| 0046 currField = model.(currName); | ||
| 0047 | ||
| 0048 <span class="keyword">if</span> forceRemove | ||
| 0049 hasPrefix = true; | ||
| 0050 <span class="keyword">else</span> | ||
| 0051 hasPrefix = all(startsWith(currField,currPrefix)); | ||
| 0052 <span class="keyword">end</span> | ||
| 0053 <span class="keyword">if</span> hasPrefix | ||
| 0054 currField = regexprep(currField,[<span class="string">'^'</span> currPrefix],<span class="string">''</span>); | ||
| 0055 <span class="keyword">if</span> strcmp(currName,<span class="string">'genes'</span>) | ||
| 0056 model.grRules=regexprep(model.grRules,<span class="string">'^G_'</span>,<span class="string">''</span>); | ||
| 0057 model.grRules=regexprep(model.grRules,<span class="string">'\(G_'</span>,<span class="string">'('</span>); | ||
| 0058 model.grRules=regexprep(model.grRules,<span class="string">' G_'</span>,<span class="string">' '</span>); | ||
| 0059 <span class="keyword">end</span> | ||
| 0060 <span class="keyword">end</span> | ||
| 0061 model.(currName) = currField; | ||
| 0062 <span class="keyword">end</span> | ||
| 0063 <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> © 2005</address> | ||
| </body> | ||
| </html> |
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