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|
# Copyright 2005 by Iddo Friedberg. All rights reserved.
# Revisions copyright 2006-2013,2017 by Peter Cock. All rights reserved.
# Revisions copyright 2008 by Frank Kauff. All rights reserved.
# Revisions copyright 2009 by Michiel de Hoon. All rights reserved.
# Revisions copyright 2015 by Joe Cora. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from __future__ import print_function
import os.path
import unittest
import tempfile
import sys
from Bio._py3k import StringIO
from Bio._py3k import range
from Bio.Align import MultipleSeqAlignment
from Bio.AlignIO.NexusIO import NexusIterator, NexusWriter
from Bio.SeqRecord import SeqRecord
from Bio.Nexus import Nexus, Trees
from Bio.Seq import Seq
from Bio.Alphabet.IUPAC import ambiguous_dna
from Bio import SeqIO
class OldSelfTests(unittest.TestCase):
"""Test cases originally in Nexus.py via __main__"""
def test_trees_and_taxa_block(self):
"""Basic tree file with TREES and TAXA block"""
nexus1 = Nexus.Nexus()
nexus1.read('Nexus/bats.nex')
def test_data_and_codons_block(self):
"""Simple sequence data file with DATA and CODONS block"""
nexus2 = Nexus.Nexus()
nexus2.read('Nexus/codonposset.nex')
def test_data_sets_trees_unknown_block(self):
"""Sequence data file with DATA, SETS, TREES and an unknown block"""
nexus3 = Nexus.Nexus()
nexus3.read('Nexus/test_Nexus_input.nex')
def test_taxa_and_characters_block(self):
"""Taxa and characters multi-state block"""
nexus4 = Nexus.Nexus()
nexus4.read('Nexus/vSysLab_Ganaspidium_multistate.nex')
def test_taxa_and_characters_with_many_codings_one_without_state(self):
"""Taxa and chr blocks, over 9 codings, 1 character without states"""
nexus5 = Nexus.Nexus()
nexus5.read('Nexus/vSysLab_Heptascelio_no-states_10+chars.nex')
def test_taxa_and_characters_with_many_codings_two_without_state(self):
"""Taxa and chr blocks, over 9 codings, 2 character without states"""
nexus6 = Nexus.Nexus()
# TODO: Implement continuous datatype:
# Bio.Nexus.Nexus.NexusError: Unsupported datatype: continuous
self.assertRaises(Nexus.NexusError,
nexus6.read,
'Nexus/vSysLab_Oreiscelio_discrete+continuous.nex')
class NexusTest1(unittest.TestCase):
def setUp(self):
self.testfile_dir = "Nexus"
self.handle = open(os.path.join(self.testfile_dir,
"test_Nexus_input.nex"))
def tearDown(self):
self.handle.close()
def test_WriteToFileName(self):
"""Test writing to a given filename."""
filename = "Nexus/test_temp.nex"
if os.path.isfile(filename):
os.remove(filename)
n = Nexus.Nexus(self.handle)
n.write_nexus_data(filename)
self.assertTrue(os.path.isfile(filename))
os.remove(filename)
def test_write_with_dups(self):
# see issue: biopython/Bio/Nexus/Nexus.py _unique_label() eval error #633
records = [SeqRecord(Seq("ATGCTGCTGAT", alphabet=ambiguous_dna), id="foo") for _ in range(4)]
out_file = StringIO()
self.assertEqual(4, SeqIO.write(records, out_file, "nexus"))
def test_NexusTest1(self):
"""Test Nexus module"""
# check data of main nexus file
n = Nexus.Nexus(self.handle)
self.assertEqual(os.path.normpath(n.filename),
os.path.normpath("Nexus/test_Nexus_input.nex"))
self.assertEqual(n.ntax, 9)
self.assertEqual(n.nchar, 48)
self.assertEqual(n.datatype, "dna")
self.assertEqual(n.interleave, True)
self.assertEqual(n.missing, "?")
self.assertEqual(n.gap, "-")
self.assertEqual(n.taxlabels, ["t1",
"t2 the name",
"isn'that [a] strange name?",
"one should be punished, for (that)!",
"t5",
"t6",
"t7",
"t8",
"t9"])
self.assertEqual(n.charlabels, {0: 'a',
1: 'b',
2: 'c',
4: 'f',
9: 'A',
10: 'B',
22: 'x',
23: "y",
29: "1,2,3 can't decide for a name?!",
47: "final"})
self.assertEqual(n.charsets,
{"big": [0, 2, 4, 6],
"bigchunk": [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],
"byname": [0, 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],
"c1": [0, 1, 2, 3, 4, 5, 6, 7],
"c2": [8, 9, 10, 11, 12, 13, 14, 15],
"c3": [16, 17, 18, 19, 20, 21, 22, 23],
"firsthalf": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23],
"mix": [0, 1, 4, 7, 10, 13, 16, 19, 22, 25, 28, 31, 34, 37, 40, 43, 46],
"mux": [0, 1, 4, 7, 8, 10, 13, 16, 17, 18, 19, 20, 21, 22, 23, 25, 28, 31, 34, 37, 40, 43, 46],
"pos1": [0, 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45],
"pos2": [1, 4, 7, 10, 13, 16, 19, 22, 25, 28, 31, 34, 37, 40, 43, 46],
"pos3": [2, 5, 8, 11, 14, 17, 20, 23, 26, 29, 32, 35, 38, 41, 44, 47],
"secondhalf": [24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47],
})
self.assertEqual(n.taxsets,
{"normal": ["isn'that [a] strange name?",
'one should be punished, for (that)!',
't1',
't5',
't6',
't8'],
"reference": ["isn'that [a] strange name?",
'one should be punished, for (that)!',
't1',
't2 the name',
't5',
't6'],
"tbyname1": ["isn'that [a] strange name?",
'one should be punished, for (that)!',
't1',
't2 the name',
't5',
't6'],
"tbyname2": ["isn'that [a] strange name?",
'one should be punished, for (that)!',
't2 the name',
't5',
't6',
't7'],
"tbyname3": ['t1',
't2 the name'],
})
self.assertEqual(len(n.charpartitions), 2)
self.assertIn('codons', n.charpartitions)
self.assertIn('part', n.charpartitions)
self.assertEqual(n.charpartitions['codons'],
{'a': [0, 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45],
'b': [1, 4, 7, 10, 13, 16, 19, 22, 25, 28, 31, 34, 37, 40, 43, 46],
'c': [2, 5, 8, 11, 14, 17, 20, 23, 26, 29, 32, 35, 38, 41, 44, 47],
})
self.assertEqual(n.charpartitions['part'],
{"one": [0, 1, 2, 3, 4, 5, 6, 7],
"three": [16, 17, 18, 19, 20, 21, 22, 23],
"two": [8, 9, 10, 11, 12, 13, 14, 15],
})
self.assertEqual(list(n.taxpartitions), ['taxpart'])
self.assertEqual(n.taxpartitions['taxpart'],
{"badnames": ["isn'that [a] strange name?",
'one should be punished, for (that)!',
't2 the name'],
"goodnames": ['t1', 't5', 't6', 't7', 't8', 't9'],
})
# now we check excluding characters, deleting taxa,
# and exporting adjusted sets
f1 = tempfile.NamedTemporaryFile("w+")
n.write_nexus_data(f1,
delete=['t1', 't7'],
exclude=n.invert(n.charsets['big']))
f1.seek(0)
nf1 = Nexus.Nexus(f1)
self.assertEqual(os.path.normpath(nf1.filename),
os.path.normpath(f1.name))
self.assertEqual(nf1.ntax, 7)
self.assertEqual(nf1.nchar, 4)
self.assertEqual(nf1.datatype, "dna")
self.assertEqual(nf1.interleave, False)
self.assertEqual(nf1.missing, "?")
self.assertEqual(nf1.gap, "-")
self.assertEqual(nf1.taxlabels, ["t2 the name",
"isn'that [a] strange name?",
"one should be punished, for (that)!",
"t5",
"t6",
"t8",
"t9"])
self.assertEqual(nf1.charlabels, {0: 'a', 1: 'c', 2: 'f'})
self.assertEqual(nf1.charsets, {'big': [0, 1, 2, 3],
'bigchunk': [1, 2, 3],
'byname': [0, 2, 3],
'c1': [0, 1, 2, 3],
'firsthalf': [0, 1, 2, 3],
'mix': [0, 2],
'mux': [0, 2],
'pos1': [0, 3],
'pos2': [2],
'pos3': [1],
})
self.assertEqual(nf1.taxsets,
{'normal': ["isn'that [a] strange name?",
'one should be punished, for (that)!',
't5',
't6',
't8'],
'reference': ["isn'that [a] strange name?",
'one should be punished, for (that)!',
't2 the name',
't5',
't6'],
'tbyname1': ["isn'that [a] strange name?",
'one should be punished, for (that)!',
't2 the name',
't5',
't6'],
'tbyname2': ["isn'that [a] strange name?",
'one should be punished, for (that)!',
't2 the name',
't5',
't6'],
'tbyname3': ['t2 the name'],
})
self.assertEqual(len(nf1.charpartitions), 2)
self.assertIn('codons', nf1.charpartitions)
self.assertIn('part', nf1.charpartitions)
self.assertEqual(nf1.charpartitions['codons'], {'a': [0, 3],
'b': [2],
'c': [1]})
self.assertEqual(nf1.charpartitions['part'], {'one': [0, 1, 2, 3]})
self.assertEqual(list(nf1.taxpartitions), ['taxpart'])
self.assertEqual(nf1.taxpartitions['taxpart'],
{"badnames": ["isn'that [a] strange name?",
'one should be punished, for (that)!',
't2 the name'],
"goodnames": ['t5', 't6', 't8', 't9'],
})
f2 = tempfile.NamedTemporaryFile("w+")
n.write_nexus_data(f2,
delete=['t2_the_name'],
exclude=list(range(3, 40, 4)))
f2.seek(0)
nf2 = Nexus.Nexus(f2)
self.assertEqual(os.path.normpath(nf2.filename),
os.path.normpath(f2.name))
self.assertEqual(nf2.ntax, 9)
self.assertEqual(nf2.nchar, 38)
self.assertEqual(nf2.datatype, "dna")
self.assertEqual(nf2.interleave, False)
self.assertEqual(nf2.missing, "?")
self.assertEqual(nf2.gap, "-")
self.assertEqual(nf2.taxlabels, ["t1",
"t2 the name",
"isn'that [a] strange name?",
"one should be punished, for (that)!",
"t5",
"t6",
"t7",
"t8",
"t9"])
self.assertEqual(nf2.charlabels, {0: "a",
1: "b",
2: "c",
3: "f",
7: "A",
8: "B",
17: "x",
22: "1,2,3 can't decide for a name?!",
37: "final"})
self.assertEqual(nf2.charsets,
{"big": [0, 2, 3, 5],
"bigchunk": [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],
"byname": [0, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22],
"c1": [0, 1, 2, 3, 4, 5],
"c2": [6, 7, 8, 9, 10, 11],
"c3": [12, 13, 14, 15, 16, 17],
"firsthalf": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17],
"mix": [0, 1, 3, 8, 10, 12, 17, 19, 21, 26, 28, 30, 33, 36],
"mux": [0, 1, 3, 6, 8, 10, 12, 13, 14, 15, 16, 17, 19, 21, 26, 28, 30, 33, 36],
"pos1": [0, 5, 7, 9, 14, 16, 18, 23, 25, 27, 32, 35],
"pos2": [1, 3, 8, 10, 12, 17, 19, 21, 26, 28, 30, 33, 36],
"pos3": [2, 4, 6, 11, 13, 15, 20, 22, 24, 29, 31, 34, 37],
"secondhalf": [18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37],
})
self.assertEqual(nf2.taxsets,
{"normal": ["isn'that [a] strange name?",
'one should be punished, for (that)!',
't1',
't5',
't6',
't8'],
"reference": ["isn'that [a] strange name?",
'one should be punished, for (that)!',
't1',
't2 the name',
't5',
't6'],
"tbyname1": ["isn'that [a] strange name?",
'one should be punished, for (that)!',
't1',
't2 the name',
't5',
't6'],
"tbyname2": ["isn'that [a] strange name?",
'one should be punished, for (that)!',
't2 the name',
't5',
't6',
't7'],
"tbyname3": ['t1',
't2 the name']})
self.assertEqual(len(nf2.charpartitions), 2)
self.assertIn('codons', nf2.charpartitions)
self.assertIn('part', nf2.charpartitions)
self.assertEqual(nf2.charpartitions['codons'],
{"a": [0, 5, 7, 9, 14, 16, 18, 23, 25, 27, 32, 35],
"b": [1, 3, 8, 10, 12, 17, 19, 21, 26, 28, 30, 33, 36],
"c": [2, 4, 6, 11, 13, 15, 20, 22, 24, 29, 31, 34, 37],
})
self.assertEqual(nf2.charpartitions['part'],
{"one": [0, 1, 2, 3, 4, 5],
"three": [12, 13, 14, 15, 16, 17],
"two": [6, 7, 8, 9, 10, 11],
})
self.assertEqual(list(nf2.taxpartitions), ['taxpart'])
self.assertEqual(nf2.taxpartitions['taxpart'],
{"badnames": ["isn'that [a] strange name?",
'one should be punished, for (that)!',
't2 the name'],
"goodnames": ['t1', 't5', 't6', 't7', 't8', 't9'],
})
# check the stepmatrix
self.assertEqual(n.weighted_stepmatrix(name='matrix_test'),
"""\
usertype matrix_test stepmatrix=5
A C G T -
[A] . 2.40 2.57 2.43 2.43
[C] 2.40 . 2.28 2.12 2.14
[G] 2.57 2.28 . 2.31 2.31
[T] 2.43 2.12 2.31 . 2.14
[-] 2.43 2.14 2.31 2.14 .
;
""") # noqa : W291
def test_write_alignment(self):
# Default causes no interleave (columns <= 1000)
records = [SeqRecord(Seq("ATGCTGCTGA" * 90, alphabet=ambiguous_dna), id=_id) for _id in ["foo", "bar", "baz"]]
a = MultipleSeqAlignment(records, alphabet=ambiguous_dna)
handle = StringIO()
NexusWriter(handle).write_alignment(a)
handle.seek(0)
data = handle.read()
self.assertIn("ATGCTGCTGA" * 90, data)
# Default causes interleave (columns > 1000)
records = [SeqRecord(Seq("ATGCTGCTGA" * 110, alphabet=ambiguous_dna), id=_id) for _id in ["foo", "bar", "baz"]]
a = MultipleSeqAlignment(records, alphabet=ambiguous_dna)
handle = StringIO()
NexusWriter(handle).write_alignment(a)
handle.seek(0)
data = handle.read()
self.assertNotIn("ATGCTGCTGA" * 90, data)
self.assertIn("ATGCTGCTGA" * 7, data)
# Override interleave: True
records = [SeqRecord(Seq("ATGCTGCTGA" * 9, alphabet=ambiguous_dna), id=_id) for _id in ["foo", "bar", "baz"]]
a = MultipleSeqAlignment(records, alphabet=ambiguous_dna)
handle = StringIO()
NexusWriter(handle).write_alignment(a, interleave=True)
handle.seek(0)
data = handle.read()
self.assertNotIn("ATGCTGCTGA" * 9, data)
self.assertIn("ATGCTGCTGA" * 7, data)
# Override interleave: False
records = [SeqRecord(Seq("ATGCTGCTGA" * 110, alphabet=ambiguous_dna), id=_id) for _id in ["foo", "bar", "baz"]]
a = MultipleSeqAlignment(records, alphabet=ambiguous_dna)
handle = StringIO()
NexusWriter(handle).write_alignment(a, interleave=False)
handle.seek(0)
data = handle.read()
self.assertIn("ATGCTGCTGA" * 110, data)
def test_TreeTest1(self):
"""Test Tree module."""
n = Nexus.Nexus(self.handle)
t3 = n.trees[2]
t2 = n.trees[2]
t3.root_with_outgroup(['t1', 't5'])
self.assertEqual(str(t3), "tree tree1 = (((((('one should be punished, for (that)!','isn''that [a] strange name?'),'t2 the name'),t8,t9),t6),t7),(t5,t1));")
self.assertEqual(t3.is_monophyletic(['t8', 't9', 't6', 't7']), -1)
self.assertEqual(t3.is_monophyletic(['t1', 't5']), 13)
t3.split(parent_id=t3.search_taxon('t9'))
stdout = sys.stdout
try:
sys.stdout = StringIO()
t3.display()
output = sys.stdout.getvalue()
finally:
sys.stdout = stdout
expected = """\
# taxon prev succ brlen blen (sum) support comment
1 'isn''that [a] strange name?' 2 [] 100.00 119.84 10.00 -
2 - 4 [3, 1] 0.40 19.84 0.30 -
3 'one should be punished, for (that)!' 2 [] 0.50 20.34 - -
4 - 6 [2, 5] 4.00 19.44 3.00 -
5 't2 the name' 4 [] 0.30 19.74 - -
6 - 9 [4, 7, 8] 2.00 15.44 1.00 -
7 t8 6 [] 1.20 16.64 - -
8 t9 6 [17, 18] 3.40 18.84 - -
9 - 11 [6, 10] 0.44 13.44 33.00 -
10 t6 9 [] 1.00 14.44 - -
11 - 16 [9, 12] 13.00 13.00 12.00 -
12 t7 11 [] 99.90 112.90 - -
13 - 16 [14, 15] 0.00 0.00 0.00 -
14 t5 13 [] 99.00 99.00 - -
15 t1 13 [] 0.98 0.98 - -
16 - None [11, 13] 0.00 0.00 - -
17 t90 8 [] 1.00 19.84 - -
18 t91 8 [] 1.00 19.84 - -
Root: 16
"""
self.assertEqual(len(output.split("\n")), len(expected.split("\n")))
for l1, l2 in zip(output.split("\n"), expected.split("\n")):
self.assertEqual(l1, l2)
self.assertEqual(output, expected)
self.assertEqual(t3.is_compatible(t2, threshold=0.3), [])
def test_TreeTest2(self):
"""Handle text labels on internal nodes.
"""
ts1b = "(Cephalotaxus:125.000000,(Taxus:100.000000,Torreya:100.000000)"\
"TT1:25.000000)Taxaceae:90.000000;"
tree = Trees.Tree(ts1b)
self.assertEqual(self._get_flat_nodes(tree), [('Taxaceae', 90.0, None, None),
('Cephalotaxus', 125.0, None, None),
('TT1', 25.0, None, None),
('Taxus', 100.0, None, None),
('Torreya', 100.0, None, None)])
tree.prune('Torreya')
self.assertEqual(tree.all_ids(), [0, 1, 3])
ts1c = ("(Cephalotaxus:125.000000,(Taxus:100.000000,Torreya:100.000000)"
"25.000000)90.000000;")
tree = Trees.Tree(ts1c)
self.assertEqual(self._get_flat_nodes(tree), [(None, 90.0, None, None),
('Cephalotaxus', 125.0, None, None),
(None, 25.0, None, None),
('Taxus', 100.0, None, None),
('Torreya', 100.0, None, None)])
self.assertFalse(tree.has_support())
with self.assertRaises(Exception) as context:
tree.randomize()
self.assertTrue("Either numer of taxa or list of taxa must be specified." in str(context.exception))
tree_rand = Trees.Tree(ts1c)
tree_rand.randomize(ntax=4)
self.assertEqual(sorted(tree_rand.get_taxa()), ['taxon1', 'taxon2',
'taxon3', 'taxon4'])
tree.branchlength2support()
tree.convert_absolute_support(2)
self.assertEqual(self._get_flat_nodes(tree), [(None, 0.0, 90.0, None),
('Cephalotaxus', 0.0, 62.5, None),
(None, 0.0, 12.5, None),
('Taxus', 0.0, 50.0, None),
('Torreya', 0.0, 50.0, None)])
ts2 = ("(((t9:0.385832, (t8:0.445135,t4:0.41401)C:0.024032)B:0.041436,"
"t6:0.392496)A:0.0291131, t2:0.497673, ((t0:0.301171,"
"t7:0.482152)E:0.0268148, ((t5:0.0984167,t3:0.488578)G:0.0349662,"
"t1:0.130208)F:0.0318288)D:0.0273876);")
tree = Trees.Tree(ts2)
tree.branchlength2support()
supports = []
for i in tree.all_ids():
node = tree.node(i)
data = node.get_data()
supports.append(data.support)
self.assertEqual(supports, [0.0, 0.0291131, 0.041436, 0.385832, 0.024032,
0.445135, 0.41401, 0.392496, 0.497673,
0.0273876, 0.0268148, 0.301171, 0.482152,
0.0318288, 0.0349662, 0.0984167, 0.488578,
0.130208])
ts3 = ("(((B 9:0.385832, (C 8:0.445135, C4:0.41401)C:0.024032)B:0.041436,"
"A 6:0.392496)A:0.0291131, t2:0.497673, ((E 0:0.301171,"
"E 7:0.482152)E:0.0268148, ((G 5:0.0984167,G 3:0.488578)G:0.0349662,"
"F 1:0.130208)F:0.0318288)D:0.0273876);")
self.assertFalse(tree.is_identical(Trees.Tree(ts3)))
tree = Trees.Tree(ts3)
self.assertTrue(tree.is_bifurcating())
self.assertTrue(tree.is_bifurcating(1))
self.assertEqual([tree.distance(0, n) for n in tree.all_ids()], [0.0,
0.0291131,
0.0705491,
0.4563811,
0.0945811,
0.5397161,
0.5085911,
0.4216091,
0.497673,
0.0273876,
0.0542024,
0.3553734,
0.5363544,
0.0592164,
0.09418259999999999,
0.1925993,
0.5827606,
0.1894244])
subtree = tree.set_subtree(10)
self.assertEqual(sorted(list(subtree)), ['E 0', 'E 7'])
tree.collapse_genera()
self.assertEqual(tree.all_ids(), [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 17])
def test_merge_with_support(self):
"""Test merge_with_support and consensus method."""
ts1 = ("(((B 9:0.385832, (C 8:0.445135, C 4:0.41401)C:0.024032)B:0.041436,"
"A 6:0.392496)A:0.0291131, t2:0.497673, ((E 0:0.301171,"
"E 7:0.482152)E:0.0268148, ((G 5:0.0984167,G 3:0.488578)G:0.0349662,"
"F 1:0.130208)F:0.0318288)D:0.0273876);")
tbs1 = ("(((B 9:0.385832, (C 8:0.445135, C 4:0.41401)C:0.024032)B:0.041436,"
"A 6:0.392496)A:0.0291131, t2:0.497673, ((G 5:0.0984167,"
"G 3:0.488578)E:0.0268148, ((E 0:0.301171, E 7:0.482152)G:0.0349662,"
"F 1:0.130208)F:0.0318288)D:0.0273876);")
tbs2 = ("(((B 9:0.385832,A 6:0.392496 C:0.024032)B:0.041436, (C 8:0.445135,"
"C 4:0.41401))A:0.0291131, t2:0.497673, ((E 0:0.301171, E 7:0.482152)"
"E:0.0268148, ((G 5:0.0984167,G 3:0.488578)G:0.0349662,F 1:0.130208)"
"F:0.0318288)D:0.0273876);")
t1 = Trees.Tree(ts1)
tb1 = Trees.Tree(tbs1)
tb2 = Trees.Tree(tbs2)
t1.branchlength2support()
tb1.branchlength2support()
tb2.branchlength2support()
t1.merge_with_support(bstrees=[tb1, tb2], threshold=0.2)
supports = []
for i in t1.all_ids():
node = t1.node(i)
data = node.get_data()
supports.append(data.support)
self.assertTrue(supports, [0.0, 1.0, 0.04, 1.0, 0.5, 1.0, 1.0, 1.0,
1.0, 1.0, 0.5, 1.0, 1.0, 0.5, 1.0, 1.0, 1.0,
1.0])
def test_large_newick(self):
with open(os.path.join(self.testfile_dir, "int_node_labels.nwk")) as large_ex_handle:
tree = Trees.Tree(large_ex_handle.read())
def _get_flat_nodes(self, tree):
cur_nodes = [tree.node(tree.root)]
nodedata = []
while len(cur_nodes) > 0:
new_nodes = []
for cur_node in cur_nodes:
nodedata.append((cur_node.data.taxon,
cur_node.data.branchlength,
cur_node.data.support,
cur_node.data.comment))
new_nodes.extend([tree.node(nid) for nid in
cur_node.get_succ()])
cur_nodes = new_nodes
return nodedata
def test_NexusComments(self):
"""Test the ability to parse nexus comments at internal and leaf nodes
"""
# A tree with simple comments throughout the tree.
ts1b = "((12:0.13,19[&comment1]:0.13)[&comment2]:0.1,(20:0.171,11:0.171):0.13)[&comment3];"
tree = Trees.Tree(ts1b)
self.assertEqual(self._get_flat_nodes(tree), [(None, 0.0, None, '[&comment3]'),
(None, 0.1, None, '[&comment2]'),
(None, 0.13, None, None), ('12', 0.13, None, None),
('19', 0.13, None, '[&comment1]'),
('20', 0.171, None, None),
('11', 0.171, None, None)])
# A tree with more complex comments throughout the tree.
# This is typical of the MCC trees produced by `treeannotator` in the beast-mcmc suite of phylogenetic tools
# The key difference being tested here is the ability to parse internal node comments that include ','.
ts1b = "(((9[&rate_range={1.3E-5,0.10958320752991428},height_95%_HPD={0.309132419999969,0.3091324199999691},length_range={3.513906814545109E-4,0.4381986285528381},height_median=0.309132419999969,length_95%_HPD={0.003011577063374571,0.08041621647998398}]:0.055354097721950546,5[&rate_range={1.3E-5,0.10958320752991428},height_95%_HPD={0.309132419999969,0.3091324199999691},length_range={3.865051168833178E-5,0.4391594442572986},height_median=0.309132419999969,length_95%_HPD={0.003011577063374571,0.08041621647998398}]:0.055354097721950546)[&height_95%_HPD={0.3110921040545068,0.38690865205576275},length_range={0.09675588357303178,0.4332959544380489},length_95%_HPD={0.16680375169879613,0.36500804261814374}]:0.20039426358269385)[&height_95%_HPD={0.5289500597932948,0.6973881165460601},length_range={0.02586430194846201,0.29509451958008265},length_95%_HPD={0.0840287249314221,0.2411078625957056}]:0.23042678598484334)[&height_95%_HPD={0.7527502510685965,0.821862094763501},height_median=0.8014438411766163,height=0.795965080422763,posterior=1.0,height_range={0.49863013698599995,0.821862094763501},length=0.0];"
tree = Trees.Tree(ts1b)
self.assertEqual(self._get_flat_nodes(tree),
[(None, 0.0, None, '[&height_95%_HPD={0.7527502510685965,0.821862094763501},height_median=0.8014438411766163,height=0.795965080422763,posterior=1.0,height_range={0.49863013698599995,0.821862094763501},length=0.0]'),
(None, 0.23042678598484334, None, '[&height_95%_HPD={0.5289500597932948,0.6973881165460601},length_range={0.02586430194846201,0.29509451958008265},length_95%_HPD={0.0840287249314221,0.2411078625957056}]'),
(None, 0.20039426358269385, None, '[&height_95%_HPD={0.3110921040545068,0.38690865205576275},length_range={0.09675588357303178,0.4332959544380489},length_95%_HPD={0.16680375169879613,0.36500804261814374}]'),
('9', 0.055354097721950546, None, '[&rate_range={1.3E-5,0.10958320752991428},height_95%_HPD={0.309132419999969,0.3091324199999691},length_range={3.513906814545109E-4,0.4381986285528381},height_median=0.309132419999969,length_95%_HPD={0.003011577063374571,0.08041621647998398}]'),
('5', 0.055354097721950546, None, '[&rate_range={1.3E-5,0.10958320752991428},height_95%_HPD={0.309132419999969,0.3091324199999691},length_range={3.865051168833178E-5,0.4391594442572986},height_median=0.309132419999969,length_95%_HPD={0.003011577063374571,0.08041621647998398}]')])
class TestSelf(unittest.TestCase):
def test_repeated_names_no_taxa(self):
print("Repeated names without a TAXA block")
handle = StringIO("""#NEXUS
[TITLE: NoName]
begin data;
dimensions ntax=4 nchar=50;
format interleave datatype=protein gap=- symbols="FSTNKEYVQMCLAWPHDRIG";
matrix
CYS1_DICDI -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ----
ALEU_HORVU MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG
CATH_HUMAN ------MWAT LPLLCAGAWL LGV------- -PVCGAAELS VNSLEK----
CYS1_DICDI -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---X
;
end;
""") # noqa : W291
for a in NexusIterator(handle):
print(a)
for r in a:
print("%r %s %s" % (r.seq, r.name, r.id))
print("Done")
def test_repeated_names_with_taxa(self):
print("Repeated names with a TAXA block")
handle = StringIO("""#NEXUS
[TITLE: NoName]
begin taxa
CYS1_DICDI
ALEU_HORVU
CATH_HUMAN
CYS1_DICDI;
end;
begin data;
dimensions ntax=4 nchar=50;
format interleave datatype=protein gap=- symbols="FSTNKEYVQMCLAWPHDRIG";
matrix
CYS1_DICDI -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ----
ALEU_HORVU MAHARVLLLA LAVLATAAVA VASSSSFADS NPIRPVTDRA ASTLESAVLG
CATH_HUMAN ------MWAT LPLLCAGAWL LGV------- -PVCGAAELS VNSLEK----
CYS1_DICDI -----MKVIL LFVLAVFTVF VSS------- --------RG IPPEEQ---X
;
end;
""") # noqa : W291
for a in NexusIterator(handle):
print(a)
for r in a:
print("%r %s %s" % (r.seq, r.name, r.id))
print("Done")
def test_empty_file_read(self):
self.assertEqual([], list(NexusIterator(StringIO())))
def test_multiple_output(self):
records = [SeqRecord(Seq("ATGCTGCTGAT", alphabet=ambiguous_dna), id="foo"),
SeqRecord(Seq("ATGCTGCAGAT", alphabet=ambiguous_dna), id="bar"),
SeqRecord(Seq("ATGCTGCGGAT", alphabet=ambiguous_dna), id="baz")]
a = MultipleSeqAlignment(records, alphabet=ambiguous_dna)
handle = StringIO()
NexusWriter(handle).write_file([a])
handle.seek(0)
data = handle.read()
self.assertTrue(data.startswith("#NEXUS\nbegin data;\n"), data)
self.assertTrue(data.endswith("end;\n"), data)
handle = StringIO()
try:
NexusWriter(handle).write_file([a, a])
assert False, "Should have rejected more than one alignment!"
except ValueError:
pass
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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