1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
|
#! /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 NEXML-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.dataio import ioservice
from dendropy.dataio import nexmlreader
from dendropy.dataio import xmlprocessing
class NexmlTreeDataYielder(
ioservice.TreeDataYielder,
nexmlreader.NexmlReader):
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, 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 `nexmlreader.NexusReader`
class. See `nexmlreader.NexusReader` for details.
"""
ioservice.TreeDataYielder.__init__(self,
files=files,
taxon_namespace=taxon_namespace,
tree_type=tree_type)
nexmlreader.NexmlReader.__init__(self,
**kwargs)
self.attached_taxon_namespace = self.taxon_namespace
###########################################################################
## Implementation of DataYielder interface
def _yield_items_from_stream(self, stream):
xml_doc = xmlprocessing.XmlDocument(file_obj=stream,
subelement_factory=self._subelement_factory)
self._namespace_registry = xml_doc.namespace_registry
xml_root = xml_doc.root
self._parse_taxon_namespaces(xml_root)
tree_parser = nexmlreader._NexmlTreeParser(
id_taxon_map=self._id_taxon_map,
annotations_processor_fn=self._parse_annotations,
)
for trees_idx, trees_element in enumerate(xml_root.iter_trees()):
trees_id = trees_element.get('id', "Trees" + str(trees_idx))
trees_label = trees_element.get('label', None)
otus_id = trees_element.get('otus', None)
if otus_id is None:
raise Exception("Taxa block not specified for trees block '{}'".format(otus_id))
taxon_namespace = self._id_taxon_namespace_map.get(otus_id, None)
if not taxon_namespace:
raise Exception("Tree block '{}': Taxa block '{}' not found".format(trees_id, otus_id))
for tree_element in trees_element.findall_tree():
tree_obj = self.tree_factory()
tree_parser.build_tree(tree_obj, tree_element, otus_id)
yield tree_obj
|
