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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 NEXUS-schema tree iterator.
"""
import sys
if not (sys.version_info.major >= 3 and sys.version_info.minor >= 4):
from dendropy.utility.filesys import pre_py34_open as open
from dendropy.utility import textprocessing
from dendropy.dataio import ioservice
from dendropy.dataio import nexusreader
from dendropy.dataio import nexusprocessing
class NexusTreeDataYielder(
ioservice.TreeDataYielder,
nexusreader.NexusReader):
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 string (``isinstance(i,str) == True``), 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 `nexusreader.NexusReader`
class. See `nexusreader.NexusReader` for details.
"""
ioservice.TreeDataYielder.__init__(self,
files=files,
taxon_namespace=taxon_namespace,
tree_type=tree_type)
self.assume_newick_if_not_nexus = kwargs.pop("assume_newick_if_not_nexus", False)
kwargs["attached_taxon_namespace"] = self.attached_taxon_namespace
nexusreader.NexusReader.__init__(self, **kwargs)
self.exclude_chars = True
self.exclude_trees = False
###########################################################################
## Implementation of DataYielder interface
def _yield_items_from_stream(self, stream):
if self._nexus_tokenizer is None:
self.create_tokenizer(stream,
preserve_unquoted_underscores=self.preserve_underscores)
else:
self._nexus_tokenizer.set_stream(stream)
token = self._nexus_tokenizer.next_token()
if token.upper() != "#NEXUS":
if self.assume_newick_if_not_nexus:
taxon_symbol_mapper = self._get_taxon_symbol_mapper(
taxon_namespace=self.attached_taxon_namespace,
enable_lookup_by_taxon_number=False,
)
while True:
tree = self._build_tree_from_newick_tree_string(
tree_factory=self.tree_factory,
taxon_symbol_mapper=taxon_symbol_mapper)
if tree is None:
break
yield tree
else:
raise self._nexus_error("Expecting '#NEXUS', but found '{}'".format(token),
nexusreader.NexusReader.NotNexusFileError)
while not self._nexus_tokenizer.is_eof():
token = self._nexus_tokenizer.next_token_ucase()
while token != None and token != 'BEGIN' and not self._nexus_tokenizer.is_eof():
token = self._nexus_tokenizer.next_token_ucase()
self._nexus_tokenizer.process_and_clear_comments_for_item(
self._global_annotations_target,
self.extract_comment_metadata)
token = self._nexus_tokenizer.next_token_ucase()
if token == 'TAXA':
self._parse_taxa_block()
elif token == 'TREES':
for tree in self._yield_from_trees_block():
yield tree
elif token == 'BEGIN':
raise self._nexus_error("'BEGIN' found without completion of previous block",
nexusreader.NexusReader.IncompleteBlockError)
else:
# unknown block
token = self._consume_to_end_of_block(token)
###########################################################################
## Supporting Functions
def _yield_from_trees_block(self):
"""
Expectations:
- current token: "TREES" [part of "BEGIN TREES"]
"""
token = self._nexus_tokenizer.cast_current_token_to_ucase()
if token != "TREES":
raise self._nexus_error("Expecting 'TREES' token, but instead found '{}'".format(token))
if self.exclude_trees:
self._consume_to_end_of_block(self._nexus_tokenizer.current_token)
return
self._nexus_tokenizer.skip_to_semicolon() # move past "BEGIN TREES" command
link_title = None
taxon_namespace = None
taxon_symbol_mapper = None
trees_block = None
block_title = None
while ((not self._nexus_tokenizer.is_eof())
and token is not None
and token != 'END'
and token != 'ENDBLOCK'):
token = self._nexus_tokenizer.next_token_ucase()
if token == 'LINK':
link_title = self._parse_link_statement().get("taxa")
elif token == 'TITLE':
block_title = self._parse_title_statement()
token = "" # clear; repopulate at start of loop
elif token == 'TRANSLATE':
if taxon_namespace is None:
taxon_namespace = self._get_taxon_namespace(link_title)
taxon_symbol_mapper = self._parse_translate_statement(taxon_namespace)
token = "" # clear; repopulate at start of loop
elif token == 'TREE':
if taxon_namespace is None:
taxon_namespace = self._get_taxon_namespace(link_title)
if taxon_symbol_mapper is None:
taxon_symbol_mapper = self._get_taxon_symbol_mapper(taxon_namespace=taxon_namespace)
pre_tree_comments = self._nexus_tokenizer.pull_captured_comments()
tree_factory = self.tree_factory
while True:
## After the following, the current token
## will be the token immediately following
## the terminating semi-colon of a tree
## statement. Typically, this will be
## 'TREE' if there is another tree, or
## 'END'/'ENDBLOCK'.
tree = self._parse_tree_statement(
tree_factory=tree_factory,
taxon_symbol_mapper=taxon_symbol_mapper)
yield tree
if self._nexus_tokenizer.is_eof() or not self._nexus_tokenizer.current_token:
break
if self._nexus_tokenizer.cast_current_token_to_ucase() != "TREE":
token = self._nexus_tokenizer.current_token
break
elif token == 'BEGIN':
raise self._nexus_error("'BEGIN' found without completion of previous block",
nexusreader.NexusReader.IncompleteBlockError)
self._nexus_tokenizer.skip_to_semicolon() # move past END command
raise StopIteration
class NexusNewickTreeDataYielder(NexusTreeDataYielder):
def __init__(self,
files=None,
taxon_namespace=None,
tree_type=None,
**kwargs):
kwargs["assume_newick_if_not_nexus"] = kwargs.get("assume_newick_if_not_nexus", True)
NexusTreeDataYielder.__init__(self,
files=files,
taxon_namespace=taxon_namespace,
tree_type=tree_type,
**kwargs)
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