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sequence/proteome/:species GET endpoint for whole proteome download

Marek Szuba requested to merge github/fork/vsitnik/vb_proteome_download into master

Created by: vsitnik


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New endpoint allows downloading all protein sequences for the specified species. Only species having 'true' meta.proteome_download_allowed in the core databases will be affected. For others this feature will be forbidden.

Use case

Will be use by uniprot to download protein fastas from wget --header='Content-type:text/x-fasta' ' atroparvus?' -O - | gzip - > Aatr.prot.fasta.gz


The endpoint allows to download all 'canonical' protein sequences for Anopheles atroparvus in 2 minutes 25 seconds instead of approximately 3 hours when using current approach.

Possible Drawbacks

Still slow. Won't be appropriate for a large genomes, probably. Thus, setting meta.proteome_download_allowed should be done with cautious. seq_regions should have proper 'coding_cnt' and 'toplevel' attributes set.


t/sequences.t updated to test the new endpoint behaviour. No regression was seen for the affected features.

VectorBase prod db anopheles_atroparvus_core_1810_93_3 was used fot the performance testing.


It's a new endpoint, which allows whole proteome fasta downloads.

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