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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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Add support for downloading plant species with pyEnsembl #305

Closed pamonlan closed 3 months ago

pamonlan commented 3 months ago

This commit introduces the ability to download plant species data using pyEnsembl. We've added the 'is_plant' parameter to the Species class, and registered two new species: Arabidopsis Thaliana and Oryza Sativa (Rice).

We've also added the ENSEMBL_PLANTS_FTP_SERVER URL, and the PLANTS_GTF_SUBDIR_TEMPLATE and PLANTS_FASTA_SUBDIR_TEMPLATE for creating the download links. The code checks if the species is a plant to determine which templates to use.

coveralls commented 3 months ago

Coverage Status

coverage: 96.024% (-0.1%) from 96.172% when pulling 8c32bc17b8ee65a3fc4b6e362a481108cf36c5d1 on pamonlan:main into 2208f87a7c7ade9d04b502304a415599f0e15d94 on openvax:main.