[WIP] Force the creation of a pangenome database by skipping empty lineages #26
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ctb
reviewed
Aug 9, 2025
| for k in get_close_matches(ident, taxdb): | ||
| print(f"* '{k}'") | ||
| sys.exit(-1) | ||
| if not getattr(args, "skip_missing_lineages", False): |
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Here you could if not args.skip_missing_lineages - no need to use getattr, since with argparse it will always create the attribute on the args object.
Suggest printing something out for continuing vs failing (i.e. "continuing past error because --skip-missing-lineages is set" or "error exiting!"). Helps people debug!
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fixes #25
This pull request introduces a
skip-missing-lineagesargument to the CLI for the user to force the creation of the pangenome rank database.However, the first step a user should try is checking that the taxonomy file is current and updating the taxonomy files that are used to create the pangenomic databases.