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
89
90
|
from __future__ import absolute_import
# #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE). http://etetoolkit.org
#
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ETE is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
# License for more details.
#
# You should have received a copy of the GNU General Public License
# along with ETE. If not, see <http://www.gnu.org/licenses/>.
#
#
# ABOUT THE ETE PACKAGE
# =====================
#
# ETE is distributed under the GPL copyleft license (2008-2015).
#
# If you make use of ETE in published work, please cite:
#
# Jaime Huerta-Cepas, Joaquin Dopazo and Toni Gabaldon.
# ETE: a python Environment for Tree Exploration. Jaime BMC
# Bioinformatics 2010,:24doi:10.1186/1471-2105-11-24
#
# Note that extra references to the specific methods implemented in
# the toolkit may be available in the documentation.
#
# More info at http://etetoolkit.org. Contact: huerta@embl.de
#
#
# #END_LICENSE#############################################################
from sys import stdout
from . import _nexml
from ._nexml import *
from ._nexml_tree import NexmlTree
#_nexml.AbstractTree.subclass = NexmlTree
_nexml.FloatTree.subclass = NexmlTree
_nexml.IntTree.subclass = NexmlTree
class Nexml(_nexml.Nexml):
""" Creates a new nexml project. """
def __repr__(self):
return "NeXML project <%s>" %hex(hash(self))
def __init__(self, *args, **kargs):
_nexml.Nexml.__init__(self, *args, **kargs)
def build_from_file(self, fname, index_otus=True):
""" Populate Nexml project with data in a nexml file. """
doc = _nexml.parsexml_(fname)
rootNode = doc.getroot()
rootTag, rootClass = _nexml.get_root_tag(rootNode)
if rootClass is None:
rootTag = 'Nexml'
rootClass = self.__class__
#rootObj = rootClass.factory()
self.build(rootNode)
# This keeps a pointer from all trees to the parent nexml
# project. This way I can access other parts, such as otus,
# etc...
if index_otus:
id2taxa = {}
for taxa in self.get_otus():
id2taxon = {}
for taxon in taxa.otu:
id2taxon[taxon.id] = taxon
id2taxa[taxa.id] = [taxa, id2taxon]
for trees in self.get_trees():
for t in trees.get_tree():
t.set_nexml_project(self)
if trees.otus in id2taxa:
t.nexml_otus = id2taxa[trees.otus][0]
def export(self, outfile=stdout, level=0):
namespace='xmlns:nex="http://www.nexml.org/2009"'
return super(Nexml, self).export(outfile=outfile, level=level, namespacedef_=namespace)
__all__ = _nexml.__all__ + ["Nexml", "NexmlTree"]
|
