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MP inconsistently removes "LPAREN" and "RPAREN" from GeneProduct names #138

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Schmoho opened this issue Dec 1, 2024 · 0 comments
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2.1 Issue in the 2.1 branch bug

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@Schmoho
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Schmoho commented Dec 1, 2024

Occurs on this model: https://www.ebi.ac.uk/biomodels/MODEL2310020001

This model contains a number of fbc:geneProduct elements with names like G_R_IEX_10fthf_LPAREN_e_RPAREN__Blood_Brain.

MP removes the strings "LPAREN" and "RPAREN" only on the id of the geneProduct, on on the reference of the corresponding reaction, which introduces errors.

I.e.

<reaction fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub" id="R_IEX_10fthf_LPAREN_e_RPAREN__Blood_Brain" name="10-Formyltetrahydrofolate exchange_Brain" reversible="false">
        <fbc:geneProductAssociation xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2">
          <fbc:geneProductRef fbc:geneProduct="G_R_IEX_10fthf_LPAREN_e_RPAREN__Blood_Brain"/>
        </fbc:geneProductAssociation>
        <listOfReactants> [...] </listOfReactants>
        <listOfProducts> [...] </listOfProducts>
      </reaction>

becomes

      <reaction compartment="e" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub" id="R_IEX_10fthf_LPAREN_e_RPAREN__Blood_Brain" name="10-Formyltetrahydrofolate exchange_Brain" reversible="false">
              <fbc:geneProductAssociation xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2">
          <fbc:geneProductRef fbc:geneProduct="G_R_IEX_10fthf_LPAREN_e_RPAREN__Blood_Brain" />
        </fbc:geneProductAssociation>
        <listOfReactants> [...] </listOfReactants>
        <listOfProducts> [...] </listOfProducts>
      </reaction>

and

<fbc:geneProduct fbc:id="G_R_IEX_10fthf_LPAREN_e_RPAREN__Blood_Brain" fbc:label="G_R_IEX_10fthf_LPAREN_e_RPAREN__Blood_Brain" fbc:name="G_R_IEX_10fthf_LPAREN_e_RPAREN__Blood_Brain"/>

becomes

<fbc:geneProduct fbc:id="G_R_IEX_10fthf_e_Blood_Brain" fbc:label="G_R_IEX_10fthf_LPAREN_e_RPAREN__Blood_Brain" fbc:name="G_R_IEX_10fthf_LPAREN_e_RPAREN__Blood_Brain" />
@Schmoho Schmoho added bug 2.1 Issue in the 2.1 branch labels Dec 1, 2024
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