Package Bio :: Package Phylo :: Module NexusIO

Module NexusIO

I/O function wrappers for `Bio.Nexus` trees.

Functions

[hide private]

parse(handle)
Parse the trees in a Nexus file.

source code

write(obj, handle, **kwargs)
Write a new Nexus file containing the given trees.

source code

Variables

[hide private]

NEX_TEMPLATE = '#NEXUS\nBegin Taxa;\n Dimensions NTax=%(count)...

TREE_TEMPLATE = 'Tree tree%(index)d=[&U]%(tree)s;'

Function Details

[hide private]

parse(handle)

source code

Parse the trees in a Nexus file.

Uses the old Nexus.Trees parser to extract the trees, converts them back to
plain Newick trees, and feeds those strings through the new Newick parser.
This way we don't have to modify the Nexus module yet. (Perhaps we'll
eventually change Nexus to use the new NewickIO parser directly.)

write(obj, handle, **kwargs)

source code

Write a new Nexus file containing the given trees.

Uses a simple Nexus template and the NewickIO writer to serialize just the
trees and minimal supporting info needed for a valid Nexus file.

Variables Details

[hide private]

NEX_TEMPLATE

Value:

'''#NEXUS
Begin Taxa;
 Dimensions NTax=%(count)d;
 TaxLabels %(labels)s;
End;
Begin Trees;
 %(trees)s
End;
...