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jorainer / ensembldb

This is the ensembldb development repository.
https://jorainer.github.io/ensembldb
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How to specify the version of Ensembl Genomes not the main Ensembl database #108

Closed altairwei closed 3 years ago

altairwei commented 3 years ago

Ensembl Genomes database includes genome data for bacteria, fungi, invertebrate metazoa, plants, and protists. It's release version is different from main Ensembl database.

In order to make plant annotation packages, I have to use fetchTablesFromEnsembl(101, host = "mysql-eg-publicsql.ebi.ac.uk", port = 4157, species = "triticum aestivum") instead of fetchTablesFromEnsembl(48, host = "mysql-eg-publicsql.ebi.ac.uk", port = 4157, species = "triticum aestivum"). Otherwise I'll get this error:

https://github.com/jorainer/ensembldb/blob/388f139ec3b1e1908f477bb24b5b4326842e49ea/inst/perl/get_gene_transcript_exon_tables.pl#L106

However, 48 is the real version for EnsemblPlants. So I don't know what version of annotation package I'm creating.

jorainer commented 3 years ago

Hi @altairwei , the databases from ensemblgenomes 48 work with the ensembl perl API version 101 (see also in the release notes). Thus you have to make sure you have the latest Perl API version installed (i.e. 101) to generate EnsDb databases for Ensemblgenomes version 48. Your first call was thus correct.

altairwei commented 3 years ago

Thank you very much for your reply!