search

bvalot / pyMLST

whole genome MLST analysis
Other
33 stars 5 forks source link

claMLST - cannot install Klebsiella pneumoniae #30

Closed marchoeppner closed 4 months ago

marchoeppner commented 4 months ago

Hi,

and thanks for the feedback on the other issues.

I noticed that it is currently not possible to use "claMLST import" to build a database for Klebsiella pneumoniae. Given that this is a somewhat "important" species, I was wondering why that is. I understand that the profile is hosted over on the Pasteur website, but pubmlst does link to it via their REST API, surely? It does leave me with the need to come up with a work-around via "claMLST create" with the downloaded alleles and profile csv just for this single bacterium. Would be nice if that wasn't necessary.

Cheers, Marc

bvalot commented 4 months ago

Hi Marc,

Yes, the Klebsiella pneumoniae species data was not present on the REST API of pubmlst. However, I make a recent update of the tools to 2.1.6 and add the possibility to upload data from Pasteur too.

Becarefull, because in Pasteur REST API, only genus name is indicate. For your purpose, you can use the following command line:

claMLST import -r pasteur /path/to/db  Klebsiella

If you want a more stable option, download all alleles and profiles and use create option.