descend_template_phylogeny_biopython

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

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

Parameters

treebiopython Tree

Phylogeny record as a biopython Tree.

seed_instrumentHereditaryStratigraphicInstrument

Hereditary stratigraphic instrument to seed at root node of phylogeny.

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

extant_nodesoptional list of biopython Clade

Which organisms should hereditary stratigraphic instruments be created for?

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

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

progress_wrapCallable, optional

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

Pass tqdm or equivalent to display progress bars.

Returns

list of HereditaryStratigraphicInstrument

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

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