Module _io

source code

I/O function wrappers for phylogenetic tree formats.

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

Functions

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

source code

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

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

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

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Variables

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

__package__ = 'Bio.Phylo'

Function Details

[hide private]

parse(file, format)

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)

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/mandrake/rpm/BUILD
/biopython-1.56/Bio/Phylo/NewickIO.py'>,
 'nexus': <module 'Bio.Phylo.NexusIO' from '/home/mandrake/rpm/BUILD/b
iopython-1.56/Bio/Phylo/NexusIO.py'>,
 'phyloxml': <module 'Bio.Phylo.PhyloXMLIO' from '/home/mandrake/rpm/B
UILD/biopython-1.56/Bio/Phylo/PhyloXMLIO.py'>}