Take another look at pubmlst updating script

[ryanjameskennedy]

Bactopia-py looks like the way to go here.

Register at PubMLST here.

The singularity image is here.

https://github.com/kjolley/BIGSdb_downloader

[Emkago]

Could this be of any help?
https://github.com/himal2007/mlstdb

[Emkago]

Re-opening the issue since it is about updating a way how files need to be downloaded since authorisation is needed to acces the files newer then 2024-12-31.

[Emkago]

Info from PubMLST

Change of data access policy:

Please note that registration is now necessary to access allele, profile, and isolate data added after 31 December 2024 for all PubMLST databases. See further details.Programmatic access
Please note that if you are scripting downloads of alleles then you should use the application programming interface (API) to do this.

See the API documentation for more details - in particular, the method call for downloading a FASTA file for a specified locus.