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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
Implementation of NEWICK-schema tree iterator.
"""
import sys
from dendropy.dataio import ioservice
from dendropy.dataio import newickreader
from dendropy.dataio import nexusprocessing
class NewickTreeDataYielder(ioservice.TreeDataYielder):
def __init__(self,
files=None,
taxon_namespace=None,
tree_type=None,
**kwargs):
"""
Parameters
----------
files : iterable of sources
Iterable of sources, which can either be strings specifying file
paths or file-like objects open for reading. If a source element is
a stringm then it is assumed to be a path to a file. Otherwise, the
source is assumed to be a file-like object.
taxon_namespace : |TaxonNamespace| instance
The operational taxonomic unit concept namespace to use to manage
taxon definitions.
\*\*kwargs : keyword arguments
These will be passed directly to the base `newickreader.NexusReader`
class. See `newickreader.NexusReader` for details.
"""
ioservice.TreeDataYielder.__init__(self,
files=files,
taxon_namespace=taxon_namespace,
tree_type=tree_type)
self.newick_reader = newickreader.NewickReader(**kwargs)
###########################################################################
## Implementation of DataYielder interface
def _yield_items_from_stream(self, stream):
nexus_tokenizer = nexusprocessing.NexusTokenizer(stream,
preserve_unquoted_underscores=self.newick_reader.preserve_unquoted_underscores)
taxon_symbol_mapper = nexusprocessing.NexusTaxonSymbolMapper(
taxon_namespace=self.attached_taxon_namespace,
enable_lookup_by_taxon_number=False,
case_sensitive=self.newick_reader.case_sensitive_taxon_labels)
while True:
tree = self.newick_reader._parse_tree_statement(
nexus_tokenizer=nexus_tokenizer,
tree_factory=self.tree_factory,
taxon_symbol_map_fn=taxon_symbol_mapper.require_taxon_for_symbol)
if tree is None:
break
yield tree
|
