biopython

v1.71.0

biopython v1.71.0 Bio.Phylo.PhyloXMLIO.Parser

Methods for parsing all phyloXML nodes from an XML stream.

To minimize memory use, the tree of ElementTree parsing events is cleared after completing each phylogeny, clade, and top-level ‘other’ element. Elements below the clade level are kept in memory until parsing of the current clade is finished — this shouldn’t be a problem because clade is the only recursive element, and non-clade nodes below this level are of bounded size.

Link to this section Summary

Functions

__init__()

Initialize the class

_parse_clade()

Parse a Clade node and its children, recursively

_parse_phylogeny()

Parse a single phylogeny within the phyloXML tree

parse()

Parse the phyloXML file incrementally and return each phylogeny

read()

Parse the phyloXML file and create a single Phyloxml object

Link to this section Functions

Link to this function __init__()

Initialize the class.

Link to this function _parse_clade()

Parse a Clade node and its children, recursively.

Link to this function _parse_phylogeny()

Parse a single phylogeny within the phyloXML tree.

Recursively builds a phylogenetic tree with help from parse_clade, then clears the XML event history for the phylogeny element and returns control to the top-level parsing function.

Link to this function parse()

Parse the phyloXML file incrementally and return each phylogeny.

Link to this function read()

Parse the phyloXML file and create a single Phyloxml object.