#! /usr/bin/env python # -*- coding: utf-8 -*- ############################################################################## ## 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 return 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)