biopython

v1.71.0

biopython v1.71.0 Bio.Phylo.NewickIO.Parser

Parse a Newick tree given a file handle.

Based on the parser in Bio.Nexus.Trees.

Link to this section Summary

Functions

__init__()

Initialize file handle for the Newick Tree

_parse_tree()

Parses the text representation into an Tree object

from_string()

Instantiate the Newick Tree class from the given string

new_clade()

Returns a new Newick.Clade, optionally with a temporary reference to its parent clade

parse()

Parse the text stream this object was initialized with

process_clade()

Final processing of a parsed clade. Removes the node’s parent and returns it

Link to this section Functions

Link to this function __init__()

Initialize file handle for the Newick Tree.

Link to this function _parse_tree()

Parses the text representation into an Tree object.

Link to this function from_string()

Instantiate the Newick Tree class from the given string.

Link to this function new_clade()

Returns a new Newick.Clade, optionally with a temporary reference to its parent clade.

Link to this function parse()

Parse the text stream this object was initialized with.

Link to this function process_clade()

Final processing of a parsed clade. Removes the node’s parent and returns it.