tseemann / mlst

:id: Scan contig files against PubMLST typing schemes
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How to deal with changes of MLST scheme names in PubMLST? #114

Open bioprojects opened 2 years ago

bioprojects commented 2 years ago

I'm trying to update the local DB of PubMLST (~/miniconda2/envs/mlst/db/pubmlst) and modified ~/miniconda2/envs/mlst/scripts/mlst-download_pub_mlst according to https://github.com/tseemann/mlst/issues/98#issuecomment-746943661

However, in the downloaded files using the modified script, the following changes of MLST scheme names appeared: kpneumoniae -> klebsiella senterica -> senterica_2 ypseudotuberculosis -> ypseudotuberculosis_3 In other words, kpneumoniae, senterica, ypseudotuberculosis don't exist in the downloaded files. Therefore, just replacing ~/miniconda2/envs/mlst/db/pubmlst with the downloaded pubmlst directory caused a runtime error.

Could you let me know the latest information about how to update the local DB of PubMLST?

Thank you very much in advance.

Koji Yahara Group Leader Antimicrobial Resistance Research Center National Institute of Infectious Diseases Aoba-cho 4-2-1, Higashimurayama-shi, Tokyo 189-0002 Japan