Update PLSDB version to include archaeal plasmids #62
Description
Hi :)
Currently, plassembler uses the PLSDB version 2023_11_03_v2, but the most recent one is 2024_05_31_v2, which brings some changes with it.
I would love to have the updated version included in plassembler, because they
- added 12,465 new records vs 2023_11_03.
- Incorporated the Archaea kingdom (which would be the main benefit for me).
I fear that having the PLSDB check be mandatory (see #61 ) but with an outdated DB that does not include all Kingdoms, might also degrade the performance of Hybracter assemblies for Archaea.
There is unfortunately a caveat, because the PLSDB changed the structure of their files a lot for the newest release. The mash sketch file is still available as download, but the "plsdb.tsv" metadata file seems to now be split into multiple files? I don't know how much of this metadata is really required by plassembler, so I don't know which files would need to be combined. There is also some confusion in the plsdb repo about the split files.
Best,
Richard