gtdblib.cli package
Submodules
gtdblib.cli.tree module
- gtdblib.cli.tree.bootstrap_merge(tree: ~pathlib.Path = <typer.models.ArgumentInfo object>, output: ~pathlib.Path = <typer.models.ArgumentInfo object>, replicates: ~typing.List[~pathlib.Path] = <typer.models.ArgumentInfo object>, cpus: int = <typer.models.OptionInfo object>)
Calculate non-parametric bootstrap values using multiple trees.
- gtdblib.cli.tree.convert_to_canonical(tree: ~pathlib.Path = <typer.models.ArgumentInfo object>, output: ~pathlib.Path = <typer.models.ArgumentInfo object>)
Convert accessions in the tree to canonical form (e.g. GCA_123456789.1 -> G123456789).
- gtdblib.cli.tree.polytomy(tree: ~pathlib.Path = <typer.models.ArgumentInfo object>, output: ~pathlib.Path = <typer.models.ArgumentInfo object>, support: float = <typer.models.ArgumentInfo object>)
Collapse nodes with low bootstrap support.