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KosinskiLab / AlphaPulldown

https://doi.org/10.1093/bioinformatics/btac749
GNU General Public License v3.0
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database setup - HHblits reference #310

Closed WardDeb closed 5 months ago

WardDeb commented 5 months ago

Hi,

I'm trying to set up the alphapulldown, and have followed the instructions to create the database. Upon trying the test files, I received an error regarding the uniref30 / HHBlits database: ValueError: Could not find HHBlits database REDACTED/uniref30/UniRef30_2023_02

The default "uniref30/UniRef30_2023_02" string is hardcoded in create_individual_features.py. The download link under the alphafold repository points to a version from 2021.

Should the link be updated to one from 2023 ? Or should the default be changed to the 2021 version ?

Thanks

WardDeb

dingquanyu commented 5 months ago

Hi,

Sorry we cannot change their instructions on AlphaFold's github repo so our colleagues have downloaded set up 2023 version of the database themselves. By default 2023 version of the uniref should be used but I don't know why AlphaFold hasn't updated their instruction.

Yours Dingquan

WardDeb commented 5 months ago

Great, thanks for the confirmation !