openvax / pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Apache License 2.0
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Save arbitrary genomes as entities in the DB #100

Open tavinathanson opened 9 years ago

tavinathanson commented 9 years ago

For example:

pyensembl add-genome --name "mouse_81" --gtf-path <URL> --transcript-fasta-path <URL> pyensembl install "mouse_81"

rather than:

pyensembl install --gtf-path <URL> --transcript-fasta-path <URL>

From @iskander:

we want to even extend it to:

pyensembl add-genome-sequence "mouse" --transcript-fasta-path <URL> pyensembl add-genome --name "mouse_81" --gtf-path <URL> --genome-sequence "mouse"

This would allow for easy integration into topiary, via:

topiary --genome "mouse_81"

This PR should, I think, also autopopulate the current Ensembl release mappings in the DB.