torchtree.evolution.io#

Classes#

`read_tree`(tree[, dated, heterochornous])
`read_tree_and_alignment`(tree, alignment[, dated, ...])
`to_nexus`(node, fp)
`convert_samples_to_nexus`(tree, sample, output)
`random_tree_from_heights`(→ Node)
`parse_translate`(fp)
`parse_trees`(fp[, count])
`parse_taxa`(fp)
`split_newick`(→ list[str])	Split tree in newick format around (),;
`extract_taxa`(→ list[str])	Extract taxon list from a nexus file.

torchtree.evolution.io.read_tree(tree, dated=True, heterochornous=True)[source]#

torchtree.evolution.io.read_tree_and_alignment(tree, alignment, dated=True, heterochornous=True)[source]#

torchtree.evolution.io.convert_samples_to_nexus(tree, sample, output)[source]#

class torchtree.evolution.io.Node(name, height=0.0)[source]#

torchtree.evolution.io.random_tree_from_heights(sampling: torch.Tensor, heights: torch.Tensor) → Node[source]#

torchtree.evolution.io.split_newick(newick: str) → list[str][source]#

Split tree in newick format around (),;

Example

>>> newick = '((a:1[&a={1,2}],b:1):1,c:1);'
>>> split_newick('((a:1,b:1):1,c:1);')
['(', '(', 'a:1', ',', 'b:1', ')', ':1', ',', 'c:1', ')', ';']

torchtree.evolution.io.extract_taxa(file_name: str) → list[str][source]#

Extract taxon list from a nexus file.

This function will try get the taxon names from the taxa and trees blocks.