Package Bio :: Package Phylo :: Module PhyloXMLIO

Module PhyloXMLIO

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`)

Classes

[hide private]

PhyloXMLError
Exception raised when PhyloXML object construction cannot continue.

Parser
Methods for parsing all phyloXML nodes from an XML stream.

Writer
Methods for serializing a PhyloXML object to XML.

Functions

[hide private]

register_namespace(prefix, uri)

source code

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

source code

parse(file)
Iterate over the phylogenetic trees in a phyloXML file.

source code

write(obj, file, encoding='utf-8', indent=True)
Write a phyloXML file. source code

_local(tag)
Extract the local tag from a namespaced tag name.

source code

_split_namespace(tag)
Split a tag into namespace and local tag strings.

source code

_ns(tag, namespace='http://www.phyloxml.org')
Format an XML tag with the given namespace. source code

_get_child_as(parent, tag, construct)
Find a child node by tag, and pass it through a constructor.

source code

_get_child_text(parent, tag, construct=<type 'unicode'>)
Find a child node by tag; pass its text through a constructor.

source code

_get_children_as(parent, tag, construct)
Find child nodes by tag; pass each through a constructor.

source code

_get_children_text(parent, tag, construct=<type 'unicode'>)
Find child nodes by tag; pass each node's text through a constructor.

source code

_indent(elem, level=0)
Add line breaks and indentation to ElementTree in-place.

source code

_str2bool(text)

source code

_dict_str2bool(dct, keys)

source code

_int(text)

source code

_float(text)

source code

_collapse_wspace(text)
Replace all spans of whitespace with a single space character.

source code

_replace_wspace(text)
Replace tab, LF and CR characters with spaces, but don't collapse.

source code

_serialize(value)
Convert a Python primitive to a phyloXML-compatible Unicode string.

source code

_clean_attrib(obj, attrs)
Create a dictionary from an object's specified, non-None attributes.

source code

_handle_complex(tag, attribs, subnodes, has_text=False)

source code

_handle_simple(tag)

source code

Variables

[hide private]

NAMESPACES = {'phy': 'http://www.phyloxml.org', 'xs': 'http://...

prefix = 'phy'

uri = 'http://www.phyloxml.org'

Function Details

[hide private]

read(file)

source code

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.

parse(file)

source code

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.

write(obj, file, encoding=`'utf-8'`, indent=True)

source code

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.

_get_child_as(parent, tag, construct)

source code

Find a child node by tag, and pass it through a constructor.

Returns None if no matching child is found.

_get_child_text(parent, tag, construct=<type 'unicode'>)

source code

Find a child node by tag; pass its text through a constructor.

Returns None if no matching child is found.

_get_children_as(parent, tag, construct)

source code

Find child nodes by tag; pass each through a constructor.

Returns an empty list if no matching child is found.

_get_children_text(parent, tag, construct=<type 'unicode'>)

source code

Find child nodes by tag; pass each node's text through a constructor.

Returns an empty list if no matching child is found.

_indent(elem, level=0)

source code

Add line breaks and indentation to ElementTree in-place.

Sources:

- http://effbot.org/zone/element-lib.htm#prettyprint
- http://infix.se/2007/02/06/gentlemen-indent-your-xml

_collapse_wspace(text)

source code

Replace all spans of whitespace with a single space character.

Also remove leading and trailing whitespace. See "Collapse Whitespace
Policy" in the phyloXML spec glossary:
http://phyloxml.org/documentation/version_100/phyloxml.xsd.html#Glossary

_replace_wspace(text)

source code

Replace tab, LF and CR characters with spaces, but don't collapse.

See "Replace Whitespace Policy" in the phyloXML spec glossary:
http://phyloxml.org/documentation/version_100/phyloxml.xsd.html#Glossary

Variables Details

[hide private]

NAMESPACES

Value:

{'phy': 'http://www.phyloxml.org',
 'xs': 'http://www.w3.org/2001/XMLSchema'}

Module PhyloXMLIO

read(file)

parse(file)

write(obj, file, encoding='utf-8', indent=True)

_get_child_as(parent, tag, construct)

_get_child_text(parent, tag, construct=<type 'unicode'>)

_get_children_as(parent, tag, construct)

_get_children_text(parent, tag, construct=<type 'unicode'>)

_indent(elem, level=0)

_collapse_wspace(text)

_replace_wspace(text)

NAMESPACES

write(obj, file, encoding=`'utf-8'`, indent=True)