# 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)