Update PLSDB version to include archaeal plasmids
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 35/100
Research direction
Start by inspecting how plassembler currently consumes the PLSDB 2023_11_03_v2 mash sketch and plsdb.tsv metadata. Compare those inputs with the 2024_05_31_v2 release and determine which split metadata files are required. Done means the newer release is supported, including archaeal records, without breaking the existing PLSDB check.
Written by the indexing model from the issue text.
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I fear that having the PLSDB check be mandatory (see #61 ) but with an outdated DB that does not include all Kingdoms, might also degrade the performance of Hybracter assemblies for Archaea.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
- Dominant language
- Python
- Stars
- 91
- Forks
- 11
- PR merge metrics
- No merged PRs in 30d
Getting set up
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- Read the contributing guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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