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Add support for downloading plant species with pyEnsembl #305

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merged 1 commit into from
Mar 28, 2024

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pamonlan
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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.

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.
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Coverage Status

coverage: 96.024% (-0.1%) from 96.172%
when pulling 8c32bc1 on pamonlan:main
into 2208f87 on openvax:main.

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LGTM!

@iskandr iskandr merged commit ad206e3 into openvax:main Mar 28, 2024
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3 participants