Package Bio :: Package Phylo :: Module _io

Module _io

I/O function wrappers for phylogenetic tree formats.

This API follows the same semantics as Biopython's `SeqIO` and `AlignIO`.

Functions

[hide private]

parse(file, format, **kwargs)
Iteratively parse a file and return each of the trees it contains.

source code

read(file, format, **kwargs)
Parse a file in the given format and return a single tree.

source code

write(trees, file, format, **kwargs)
Write a sequence of trees to file in the given format.

source code

convert(in_file, in_format, out_file, out_format, **kwargs)
Convert between two tree file formats.

source code

Variables

[hide private]

supported_formats = {'newick': <module 'Bio.Phylo.NewickIO' fr...

Function Details

[hide private]

parse(file, format, **kwargs)

source code

Iteratively parse a file and return each of the trees it contains.

If a file only contains one tree, this still returns an iterable object that
contains one element.

Example
-------

>>> trees = parse('../../Tests/PhyloXML/apaf.xml', 'phyloxml')
>>> for tree in trees:
...     print tree.rooted
True

read(file, format, **kwargs)

source code

Parse a file in the given format and return a single tree.

Raises a `ValueError` if there are zero or multiple trees -- if this occurs,
use `parse` instead to get the complete sequence of trees.

Variables Details

[hide private]

supported_formats

Value:

{'newick': <module 'Bio.Phylo.NewickIO' from '/home/pjcock/lib/python2
.5/site-packages/Bio/Phylo/NewickIO.pyc'>,
 'nexus': <module 'Bio.Phylo.NexusIO' from '/home/pjcock/lib/python2.5
/site-packages/Bio/Phylo/NexusIO.pyc'>,
 'phyloxml': <module 'Bio.Phylo.PhyloXMLIO' from '/home/pjcock/lib/pyt
hon2.5/site-packages/Bio/Phylo/PhyloXMLIO.pyc'>}