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The policy drop removes each complex that has a subunit without an ortholog and removes the reaction when no complex remains. It removed the reaction as soon as one subunit had no ortholog.
…holog In the preferred-order step, a template gene that maps to a gene an earlier template already maps loses its mappings and follows complex_policy. For the rule (a and b) or x with a taken, flag gives (OLD_T2_a and nb) or nx. A reaction with no gene that keeps a mapping is not transferred.
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In the preferred-order step of
get_model_from_homology, a template gene that maps to a gene an earlier template already maps loses its mappings and counts as a subunit without an ortholog, andcomplex_policydecides what happens to it. For the rule(a and b) or xwithataken by an earlier template,flaggives(OLD_T2_a and nb) or nx,keepgivesnb or nxanddropgivesnx. A reaction that has genes, none of which keeps a mapping, is not transferred.The pull request builds on #199. The same rule is implemented in RAVEN#26.