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sequence/proteome/:species GET endpoint added

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

Created by: vsitnik

sequence/proteome/:species GET endpoint added, allowing bulk/whole proteome download.

core.meta.proteome_download_allowed used as guard for vb_proteome_download.


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    • do not modify code without testing for regression
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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 I.e. allows to download all 'canonical' protein sequences for Anopheles atroparvus in 2 minutes 36 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.


Have you added/modified unit tests to test the changes?

If so, do the tests pass/fail?

Have you run the entire test suite and no regression was detected?


sequence/proteome/:species allows whole proteome downloads, only for subset of species.

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