search

tseemann / mlst

:id: Scan contig files against PubMLST typing schemes
GNU General Public License v2.0
201 stars 47 forks source link

Serratia MLST Schemes #136

Open erinyoung opened 8 months ago

erinyoung commented 8 months ago

I learned through the ubioinfo slack channel that there is a MLST scheme for Serratia, but it doesn't appear to be included in the files that mlst-download_pub_mlst downloads.

Is there a reason this organism hasn't been added? Is there a way I can request that this organism gets added?

schorlton-bugseq commented 2 months ago

Hi @erinyoung, you may have figured this out by now but if not, this issue is not specific to this tool. The download script pulls the XML from PubMLST (https://github.com/tseemann/mlst/blob/v2.23.0/scripts/mlst-download_pub_mlst#L11), and the PubMLST XML file is missing the Serratia scheme. The XML or download script can be modified to add the missing scheme. Hope that helps!

erinyoung commented 2 months ago

Is there a recommended way to edit the xml file or download script?

schorlton-bugseq commented 2 months ago

Not sure "recommended" but you'll notice the XML follows a pretty standard format so the serratia scheme with its loci can be slotted in and then the download script hacked to read from local XML or the Serratia files can be manually downloaded and placed in the folder with the rest of the schemes. Probably best/easiest to report this to PubMLST though? If they fix it (I would hope it would be a trivial fix on their end?), then no modifications would be needed here.