descend_template_phylogeny_biopython

descend_template_phylogeny_biopython(tree: ~Bio.Phylo.BaseTree.Tree, seed_column: ~hstrat.genome_instrumentation.HereditaryStratigraphicColumn, extant_nodes: ~typing.Iterable[~Bio.Phylo.BaseTree.Clade] | None = None, progress_wrap: ~typing.Callable = <function <lambda>>) → List[HereditaryStratigraphicColumn]

Generate a population of hereditary stratigraphic columns that could have resulted from the template phylogeny.

Parameters

treebiopython Tree

Phylogeny record as a biopython Tree.

seed_columnHereditaryStratigraphicColumn

Hereditary stratigraphic column to seed at root node of phylogeny.

Returned hereditary stratigraphic column population will be generated as if repeatedly calling CloneDescendant() on seed_column. As such, specifies configuration (i.e., differentia bit width and stratum retention policy) for returned columns. May already have strata deposited, which will be incorporated into generated extant population.

extant_nodesoptional list of biopython Clade

Which organisms should hereditary stratigraphic columns be created for?

Designates content and order of returned list of hereditary stratigraphic column.

If None, hereditary stratigraphic columns will be created for all phylogenetic leaves (organisms without offspring) in order of appearance in tree.leaf_node_iter().

progress_wrapCallable, default identity function

Wrapper applied around generation iterator and row generator for final phylogeny compilation process.

Pass tqdm or equivalent to display progress bars.

Returns

list of HereditaryStratigraphicColumn

Population of hereditary stratigraphic columns for extant lineage members (i.e., phylogeny leaf nodes).

Columns ordered in order of appearance of corresponding extant organism id.