Package Bio :: Package Phylo :: Module PhyloXMLIO :: Class Parser

Class Parser

object --+
         |
        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.

Instance Methods

[hide private]

__init__(self, file)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

source code

read(self)
Parse the phyloXML file and create a single Phyloxml object.

source code

parse(self)
Parse the phyloXML file incrementally and return each phylogeny.

source code

_parse_phylogeny(self, parent)
Parse a single phylogeny within the phyloXML tree.

source code

_parse_clade(self, parent)
Parse a Clade node and its children, recursively.

source code

_parse_sequence(self, parent)

source code

_parse_taxonomy(self, parent)

source code

other(self, elem, namespace, localtag)

source code

accession(self, elem)

source code

annotation(self, elem)

source code

binary_characters(self, elem)

source code

clade_relation(self, elem)

source code

color(self, elem)

source code

confidence(self, elem)

source code

date(self, elem)

source code

distribution(self, elem)

source code

domain(self, elem)

source code

domain_architecture(self, elem)

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events(self, elem)

source code

id(self, elem)

source code

mol_seq(self, elem)

source code

point(self, elem)

source code

polygon(self, elem)

source code

property(self, elem)

source code

reference(self, elem)

source code

sequence_relation(self, elem)

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uri(self, elem)

source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables

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_clade_complex_types = ['color', 'events', 'binary_characters'...

_clade_list_types = {'confidence': 'confidences', 'distributio...

_clade_tracked_tags = set(['binary_characters', 'branch_length...

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, file)
(Constructor)

source code

x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__: (inherited documentation)

_parse_phylogeny(self, parent)

source code

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.

Class Variable Details

[hide private]

_clade_complex_types

Value:

['color', 'events', 'binary_characters', 'date']

_clade_list_types

Value:

{'confidence': 'confidences',
 'distribution': 'distributions',
 'property': 'properties',
 'reference': 'references'}

_clade_tracked_tags

Value:

set(['binary_characters',
     'branch_length',
     'color',
     'confidence',
     'date',
     'distribution',
     'events',
     'name',
...

Class Parser

__init__(self, file) (Constructor)

_parse_phylogeny(self, parent)

_clade_complex_types

_clade_list_types

_clade_tracked_tags

init(self, file)
(Constructor)