schorlton-bugseq

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),...

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...

Sure! This is a mock example to show, I understand it is somewhat ridiculous. ``` >query AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ``` ``` >target GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG ``` ```bash mmseqs easy-search --format-mode 1 --search-type 2 query.fna...

Update: I'm thinking it might be something about the x axis coordinates wrapped in quotes in the JSON, which is a limitation of JSON, as it works properly with YAML.

Awesome. Thank you :smile: