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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.
In the preferred-order step, a gene that maps to a new gene an earlier model already maps loses its mappings and follows complexPolicy. For the rule (a and b) or x with a taken, flag gives (OLD_MODELID_a and nb) or nx. A reaction with no gene that keeps a mapping is removed, and a model without reactions is left out of the merge.
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Function test results542 tests 535 ✅ 2m 34s ⏱️ Results for commit d21e997. ♻️ This comment has been updated with latest results. |
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In the preferred-order step of
getModelFromHomology, a gene of a later model that maps to a new gene an earlier model already maps loses its mappings and counts as a subunit without an ortholog, andcomplexPolicydecides what happens to it. For the rule(a and b) or xwithataken by an earlier model,flaggives(OLD_MODELID_a and nb) or nx,keepgivesnb or nxanddropgivesnx. A reaction that has genes, none of which keeps a mapping, is not included, and a model without reactions is left out of the merge. The draft name lists every model.The pull request builds on #25. The same rule is implemented in raven-toolbox (the pull request follows).