RefSeqGPFFParser update #336
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Your build requires ensembl-io as a dependency |
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Due to performance issues related to the usage of ensembl-io, #338 has been submitted with the refactoring changes without the ensembl-io dependency. |
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Description
Update to the RefSeqGPFFParserr as part of the efforts of the xref sprint.
See ENSCORESW-2898.
Genbank parser from ensembl-io is now used to parse the source files instead of a custom parser.
This will require Ensembl/ensembl-io#69 to be merged.
There are a few differences introduced from the original parser. For instance, only refseq ids with the prefixes defined in $refseq_sources are considered. Previously for peptide files all other possible types were considered and treated as RefSeq_peptide.
Testing
No unit tests.
Tested with subset of rat, however related xrefs were absent.
Ongoing testing with full dataset.