Release Commec v2.0.0 · ibbis-bio/common-mechanism

Summary

Smaller databases and faster search: commec now entirely uses custom databases, which can be downloaded from databases.commec.io using commec setup. No direct download of full NCBI databases.
Region-specific flagging: by supplying a --regions argument to commec screen, you can now adjust which national or multilateral control lists are used for flagging (for example, flagging only hits from Brazilian export controls or the UK screening guidance). HTML and JSON outputs also specify which control lists apply to each best match hit. Available lists can be viewed with commec list.
Removed DIAMOND and commec split: protein best match search now always uses BLASTX, and runs faster when multiple queries are searched in parallel.
Smaller changes: Config YAML is validated more strictly, HTML report has been completely rebuilt, optimization of BLAST parameters

Overhaul of the output HTML report.
New JSON output formats.
Overhaul of commec setup for ease of use, and better automation options.
Added config.yaml setting to allow commec screen to check for and auto-update to the latest databases.
Adds the retrieval and use of a new set of custom commec databases, vastly improving screen performance.
Adds 19 control lists across ~10 jurisdictions, including European Union, and The Australia Group.
Adds the ingestion of jurisdiction/regional control lists, which alter commec screen flag and pass behaviour depending on regional context.
Adds --region cli argument, to apply jurisdictional context to commec screen e.g: -r/--region UK,US,EU
Blast parameter mt-mode can be configured via config.yaml, useful under some hardware situations.
Removed no-hit warning, as it is no longer applicable with the use of commec best match databases.
Removed Diamond support, commec now runs fully with BLAST(x/n), HMMSCAN, and CMSCAN.
Removed commec split cli functionality.
IAdds commec list as a cli option, for quickly interacting with Control Lists.
Updated example data.
Performance improvements to commec screen between screening tool calls.

Improvements and stricter parsing of input config and cli parameters to reduce silent configuration unintended use.
Fixes an issue with comment characters in blast descriptions sabotaging blast results in some circumstances.
Fixes an issue with incorrect filtering logic for some low concern steps.
Fixes an issue with non-coding region calculations affecting other queries
Improved handling of Fasta query names and descriptions.