Bio.Phylo.PhyloXMLIO module

PhyloXML reader/parser, writer, and associated functions.

Instantiates tree elements from a parsed PhyloXML file, and constructs an XML file from a Bio.Phylo.PhyloXML object.

About capitalization:

• phyloXML means the file format specification

• PhyloXML means the Biopython module Bio.Phylo.PhyloXML and its classes

• Phyloxml means the top-level class used by PhyloXMLIO.read (but not Bio.Phylo.read!), containing a list of Phylogenies (objects derived from BaseTree.Tree)

exception Bio.Phylo.PhyloXMLIO.PhyloXMLError

Bases: Exception

Exception raised when PhyloXML object construction cannot continue.

XML syntax errors will be found and raised by the underlying ElementTree module; this exception is for valid XML that breaks the phyloXML specification.

Bio.Phylo.PhyloXMLIO.read(file)

Parse a phyloXML file or stream and build a tree of Biopython objects.

The children of the root node are phylogenies and possibly other arbitrary (non-phyloXML) objects.

Returns:

a single Bio.Phylo.PhyloXML.Phyloxml object.

Bio.Phylo.PhyloXMLIO.parse(file)

Iterate over the phylogenetic trees in a phyloXML file.

This ignores any additional data stored at the top level, but may be more memory-efficient than the read function.

Returns:

a generator of Bio.Phylo.PhyloXML.Phylogeny objects.

Bio.Phylo.PhyloXMLIO.write(obj, file, encoding=DEFAULT_ENCODING, indent=True)

Write a phyloXML file.

Parameters:

obj

an instance of Phyloxml, Phylogeny or BaseTree.Tree, or an iterable of either of the latter two. The object will be converted to a Phyloxml object before serialization.

file

either an open handle or a file name.

class Bio.Phylo.PhyloXMLIO.Parser(file)

Bases: object

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.

__init__(file)

Initialize the class.

read()

Parse the phyloXML file and create a single Phyloxml object.

parse()

Parse the phyloXML file incrementally and return each phylogeny.

other(elem, namespace, localtag)

Create an Other object, a non-phyloXML element.

accession(elem)

Create accession object.

annotation(elem)

Create annotation object.

binary_characters(elem)

Create binary characters object.

clade_relation(elem)

Create clade relationship object.

color(elem)

Create branch color object.

confidence(elem)

Create confidence object.

date(elem)

Create date object.

distribution(elem)

Create geographic distribution object.

domain(elem)

Create protein domain object.

domain_architecture(elem)

Create domain architecture object.

events(elem)

Create events object.

id(elem)

Create identifier object.

mol_seq(elem)

Create molecular sequence object.

point(elem)

Create point object, coordinates of a point.

polygon(elem)

Create polygon object, list of points.

property(elem)

Create properties from external resources.

reference(elem)

Create literature reference object.

sequence_relation(elem)

Create sequence relationship object, relationship between two sequences.

uri(elem)

Create uri object, expected to be a url.

class Bio.Phylo.PhyloXMLIO.Writer(phyloxml)

Bases: object

Methods for serializing a PhyloXML object to XML.

__init__(phyloxml)

Build an ElementTree from a PhyloXML object.

write(file, encoding=DEFAULT_ENCODING, indent=True)

Write PhyloXML to a file.

phyloxml(obj)

Convert phyloxml to Etree element.

other(obj)

Convert other to Etree element.

phylogeny(obj)

Serialize a phylogeny and its subnodes, in order.

clade(obj)

Serialize a clade and its subnodes, in order.

accession(obj)

Serialize a accession and its subnodes, in order.

annotation(obj)

Serialize a annotation and its subnodes, in order.

binary_characters(obj)

Serialize a binary_characters node and its subnodes.

clade_relation(obj)

Serialize a clade_relation and its subnodes, in order.

color(obj)

Serialize a color and its subnodes, in order.

confidence(obj)

Serialize a confidence and its subnodes, in order.

date(obj)

Serialize a date and its subnodes, in order.

distribution(obj)

Serialize a distribution and its subnodes, in order.

domain(obj)

Serialize a domain node.

domain_architecture(obj)

Serialize a domain_architecture and its subnodes, in order.

events(obj)

Serialize a events and its subnodes, in order.

id(obj)

Serialize a id and its subnodes, in order.

mol_seq(obj)

Serialize a mol_seq and its subnodes, in order.

node_id(obj)

Serialize a node_id and its subnodes, in order.

point(obj)

Serialize a point and its subnodes, in order.

polygon(obj)

Serialize a polygon and its subnodes, in order.

property(obj)

Serialize a property and its subnodes, in order.

reference(obj)

Serialize a reference and its subnodes, in order.

sequence(obj)

Serialize a sequence and its subnodes, in order.

sequence_relation(obj)

Serialize a sequence_relation and its subnodes, in order.

taxonomy(obj)

Serialize a taxonomy and its subnodes, in order.

uri(obj)

Serialize a uri and its subnodes, in order.

alt(obj)

Serialize a simple alt node.

branch_length(obj)

Serialize a simple branch_length node.

lat(obj)

Serialize a simple lat node.

long(obj)

Serialize a simple long node.

maximum(obj)

Serialize a simple maximum node.

minimum(obj)

Serialize a simple minimum node.

value(obj)

Serialize a simple value node.

width(obj)

Serialize a simple width node.

blue(obj)

Serialize a simple blue node.

duplications(obj)

Serialize a simple duplications node.

green(obj)

Serialize a simple green node.

losses(obj)

Serialize a simple losses node.

red(obj)

Serialize a simple red node.

speciations(obj)

Serialize a simple speciations node.

bc(obj)

Serialize a simple bc node.

code(obj)

Serialize a simple code node.

common_name(obj)

Serialize a simple common_name node.

desc(obj)

Serialize a simple desc node.

description(obj)

Serialize a simple description node.

location(obj)

Serialize a simple location node.

name(obj)

Serialize a simple name node.

rank(obj)

Serialize a simple rank node.

scientific_name(obj)

Serialize a simple scientific_name node.

symbol(obj)

Serialize a simple symbol node.

synonym(obj)

Serialize a simple synonym node.

type(obj)

Serialize a simple type node.