post-processor: remove-orphans

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post-processor: remove-orphans #137

Open sammyjava opened 9 months ago

sammyjava commented 9 months ago

As part of the Crusade to Make Mines Perfect, run a post-processor to yank orphaned records created by sources that contain stuff that doesn't belong in the mine, see checklist below.

Be sure to run this BEFORE tallying routines like lis-create-genefamilytally. Actually, run it first of the LIS post-processors.

sammyjava commented 9 months ago

[x] Gene with empty protein collection
[x] Protein with empty genes collection OR null transcript reference
[x] Transcript with null protein reference OR null chromosome/supercontig reference
[x] CDS with null chromosome/supercontig reference
[x] OntologyTerm with null ontology reference
[x] OntologyAnnotation referencing an OntologyTerm with null ontology reference
[x] OntologyTerm.crossReferences that reference orphan OntologyTerms