alifestd_from_newick_polars

alifestd_from_newick_polars(newick: str, *, allow_forest: bool | None = None, branch_length_dtype: type = <class 'float'>, create_ancestor_list: bool = False, dtype_id: ~polars.datatypes.classes.DataType | None = Int64, replace_unquoted: ~typing.Mapping[str, str] = mappingproxy({})) → DataFrame

Convert a Newick format string to a phylogeny dataframe.

Parses a Newick tree string and returns a polars DataFrame in alife standard format with columns: id, ancestor_id, taxon_label, origin_time_delta, and branch_length. Optionally includes ancestor_list.

Parameters

newickstr

A phylogeny in Newick format.

allow_forestbool or None, default None

Policy for a Newick string holding multiple ;-terminated trees (a forest). None parses the forest but warns; True parses it silently; False raises ValueError unless there is a single tree.

branch_length_dtypetype, default float

Dtype for branch length values. Use int to get nullable integer columns (pl.Int64). Missing branch lengths will be null for integer dtypes or NaN for float dtypes.

create_ancestor_listbool, default False

If True, include an ancestor_list column in the result.

dtype_idpl.DataType or None, default pl.Int64

Polars dtype for the id and ancestor_id columns. If None, the smallest signed integer dtype that can hold all node ids is chosen automatically based on the node count of the Newick string.

replace_unquotedMapping[str, str], optional

Character substitutions to apply to unquoted taxon labels only, leaving quoted labels verbatim. Keys must be single characters. Pass {"_": " "} to follow the strict Newick convention in which an unquoted underscore denotes a space.

Returns

pl.DataFrame

Phylogeny dataframe in alife standard format.

Notes

By default, unquoted underscores in taxon labels are preserved literally; they are not converted to spaces. This diverges from the strict Newick convention (in which an unquoted _ denotes a space), but matches the round-trip behavior of alifestd_as_newick_asexual. Pass replace_unquoted={"_": " "} to follow the strict convention.

See Also

alifestd_from_newick :

Pandas-based implementation.

alifestd_as_newick_asexual :

Inverse conversion, from alife standard to Newick format.