Skip NCBIOrtholog xrefs in parse_ncbi_gff3.pl - #560
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Dbxref=NCBIOrtholog:... entries in NCBI RefSeq GFF3 files have no
corresponding external_db row in Ensembl core schemas, causing
GeneAdaptor::store to fail via DBEntryAdaptor::_check_external_db
("external_db [NCBIOrtholog] release [] does not exist").
Add NCBIOrtholog to %unknowndbs alongside the existing HPRD/Ensembl
entries so add_xrefs() skips it, consistent with how those other
unmapped Dbxref types are already handled.
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Dbxref=NCBIOrtholog:... entries in NCBI RefSeq GFF3 files have no corresponding external_db row in Ensembl core schemas, causing GeneAdaptor::store to fail via DBEntryAdaptor::_check_external_db ("external_db [NCBIOrtholog] release [] does not exist").
Add NCBIOrtholog to %unknowndbs alongside the existing HPRD/Ensembl entries so add_xrefs() skips it, consistent with how those other unmapped Dbxref types are already handled.
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PR details
Is this a fix/ update/ new feature?
Fix
Include a short description
parse_ncbi_gff3.plfails when storing genes/transcripts carrying aDbxref=NCBIOrtholog:...attribute from NCBI RefSeq GFF3 files, sinceNCBIOrthologhas no correspondingexternal_dbrow in Ensembl core schemas.GeneAdaptor::storecascades toDBEntryAdaptor::store, which calls_check_external_dband throwsexternal_db [NCBIOrtholog] release [] does not exist, failing the job.This PR adds
NCBIOrthologto the existing%unknowndbshash inadd_xrefs(), alongsideHPRDandEnsembl, so the xref is skipped rather than attached to the gene/transcript — consistent with how those other unmapped Dbxref types are already handled. Noexternal_dbtable changes required.Include links to JIRA tickets
https://embl.atlassian.net/browse/ENSGENEBUI-3937
Testing
Have you tested it?
Tested on turkey refseq_import, GCF_905368555.1
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@JackCurragh