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# ----------------------------------------------------------------------------
# Copyright (c) 2016-2023, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
import os
import pkg_resources
import shutil
import unittest
import skbio
import tempfile
from qiime2.plugin.testing import TestPluginBase
from qiime2.util import redirected_stdio
from q2_types.feature_data import AlignedDNAFASTAFormat
from q2_phylogeny import raxml, raxml_rapid_bootstrap
from q2_phylogeny._raxml import (run_command, _build_rapid_bootstrap_command,
_set_raxml_version)
class RaxmlTests(TestPluginBase):
package = 'q2_phylogeny.tests'
@classmethod
def setUpClass(cls):
super(TestPluginBase, cls).setUpClass()
tmpdir = tempfile.mkdtemp()
src = pkg_resources.resource_filename(cls.package, 'data')
dst = os.path.join(tmpdir, 'data')
shutil.copytree(src, dst)
cls.data_dir = dst
@classmethod
def tearDownClass(cls):
super(TestPluginBase, cls).setUpClass()
shutil.rmtree(cls.data_dir)
def get_data_path(self, filename):
# Override TestPluginBase.get_data_path so that it returns paths to
# temporary copies of test data.
return os.path.join(self.data_dir, filename)
def test_raxml(self):
# Test that output tree is made.
# Reads tree output and compares tip labels to expected labels.
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
with redirected_stdio(stderr=os.devnull):
obs = raxml(input_sequences)
obs_tree = skbio.TreeNode.read(str(obs))
# load the resulting tree and test that it has the right number of
# tips and the right tip ids
tips = list(obs_tree.tips())
tip_names = [t.name for t in tips]
self.assertEqual(set(tip_names),
set(['GCA001510755', 'GCA001045515', 'GCA000454205',
'GCA000473545', 'GCA000196255', 'GCA000686145',
'GCA001950115', 'GCA001971985', 'GCA900007555']))
def test_raxml_underscore_ids(self):
# Test that output tree is made with underscores in tip IDs.
# Some programs and python wrappers may strip underscores.
# Reads tree output and compares tip labels to expected labels.
input_fp = self.get_data_path('aligned-dna-sequences-4.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
with redirected_stdio(stderr=os.devnull):
obs = raxml(input_sequences)
obs_tree = skbio.TreeNode.read(str(obs), convert_underscores=False)
# load the resulting tree and test that it has the right number of
# tips and the right tip ids
tips = list(obs_tree.tips())
tip_names = [t.name for t in tips]
self.assertEqual(set(tip_names),
set(['GCA_001510755_1', 'GCA_001045515_1',
'GCA_000454205_1', 'GCA_000473545_1',
'GCA_000196255_1', 'GCA_002142615_1',
'GCA_000686145_1', 'GCA_001950115_1',
'GCA_001971985_1', 'GCA_900007555_1']))
def test_set_raxml_version(self):
obs_stand_1 = _set_raxml_version(raxml_version='Standard',
n_threads=1)
self.assertTrue('raxmlHPC' in str(obs_stand_1[0]))
self.assertTrue(len(obs_stand_1) == 1)
obs_sse3_1 = _set_raxml_version(raxml_version='SSE3', n_threads=1)
self.assertTrue('raxmlHPC-SSE3' in str(obs_sse3_1[0]))
self.assertTrue(len(obs_sse3_1) == 1)
obs_avx2_1 = _set_raxml_version(raxml_version='AVX2', n_threads=1)
self.assertTrue('raxmlHPC-AVX2' in str(obs_avx2_1[0]))
self.assertTrue(len(obs_avx2_1) == 1)
obs_stand_4 = _set_raxml_version(raxml_version='Standard',
n_threads=4)
self.assertTrue('raxmlHPC-PTHREADS' in str(obs_stand_4[0]))
self.assertTrue('4' in str(obs_stand_4[1]))
self.assertTrue(len(obs_stand_4) == 2)
obs_sse3_4 = _set_raxml_version(raxml_version='SSE3', n_threads=4)
self.assertTrue('raxmlHPC-PTHREADS-SSE3' in str(obs_sse3_4[0]))
self.assertTrue('4' in str(obs_sse3_4[1]))
self.assertTrue(len(obs_sse3_4) == 2)
obs_avx2_4 = _set_raxml_version(raxml_version='AVX2', n_threads=4)
self.assertTrue('raxmlHPC-PTHREADS-AVX2' in str(obs_avx2_4[0]))
self.assertTrue('4' in str(obs_avx2_4[1]))
self.assertTrue(len(obs_avx2_4) == 2)
def test_raxml_version(self):
# Test that an output tree is made when invoking threads.
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
with redirected_stdio(stderr=os.devnull):
obs = raxml(input_sequences, raxml_version='SSE3')
obs_tree = skbio.TreeNode.read(str(obs), convert_underscores=False)
# load the resulting tree and test that it has the right number of
# tips and the right tip ids
tips = list(obs_tree.tips())
tip_names = [t.name for t in tips]
self.assertEqual(set(tip_names),
set(['GCA001510755', 'GCA001045515', 'GCA000454205',
'GCA000473545', 'GCA000196255', 'GCA000686145',
'GCA001950115', 'GCA001971985', 'GCA900007555']))
def test_raxml_n_threads(self):
# Test that an output tree is made when invoking threads.
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
with redirected_stdio(stderr=os.devnull):
obs = raxml(input_sequences, n_threads=2)
obs_tree = skbio.TreeNode.read(str(obs), convert_underscores=False)
# load the resulting tree and test that it has the right number of
# tips and the right tip ids
tips = list(obs_tree.tips())
tip_names = [t.name for t in tips]
self.assertEqual(set(tip_names),
set(['GCA001510755', 'GCA001045515', 'GCA000454205',
'GCA000473545', 'GCA000196255', 'GCA000686145',
'GCA001950115', 'GCA001971985', 'GCA900007555']))
def test_raxml_with_seed(self):
# Test tip-to-tip dists are identical to manually run RAxML output.
# This test is comparing an ordered series of tip-to-tip distances
# to a tree output from a manual run of the default command:
# raxmlHPC -m GTRGAMMA -p 1723 -s aligned-dna-sequences-3.fasta -n q2
# NOTE: I cleanly rounded the tip-to-tip dists (i.e. `%.4f`) as RAxML
# may return slightly different rounding errors on different
# systems.
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
with redirected_stdio(stderr=os.devnull):
obs = raxml(input_sequences, seed=1723)
obs_tree = skbio.TreeNode.read(str(obs), convert_underscores=False)
obs_tl = list(obs_tree.tip_tip_distances().to_series())
obs_series = set(['%.4f' % e for e in obs_tl])
exp_tree = skbio.TreeNode.read(self.get_data_path('test.tre'))
exp_tl = list(exp_tree.tip_tip_distances().to_series())
exp_series = set(['%.4f' % e for e in exp_tl])
self.assertEqual(obs_series, exp_series)
def test_raxml_model_choice(self):
# Tip to tip dists should NOT be identical under different models.
# Default is GTRGAMMA, we'll compare ouput to GRTGAMMAI & GTRCAT.
# This test is comparing an ordered series of tip-to-tip distances.
# Take note, that for this comparison to work, all must have the same
# seed value set.
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
# default GTRGAMMA
with redirected_stdio(stderr=os.devnull):
gtrg = raxml(input_sequences, seed=1723)
gtrg_tree = skbio.TreeNode.read(
str(gtrg), convert_underscores=False)
gtrg_td = set(gtrg_tree.tip_tip_distances().to_series())
# set GTRGAMMAI
with redirected_stdio(stderr=os.devnull):
gtrgi = raxml(input_sequences, seed=1723,
substitution_model='GTRGAMMAI')
gtrgi_tree = skbio.TreeNode.read(
str(gtrgi), convert_underscores=False)
gtrgi_td = set(gtrgi_tree.tip_tip_distances().to_series())
# set GTRCAT
with redirected_stdio(stderr=os.devnull):
gtrcat = raxml(input_sequences, seed=1723,
substitution_model='GTRCAT')
gtrcat_tree = skbio.TreeNode.read(
str(gtrcat), convert_underscores=False)
gtrcat_td = set(gtrcat_tree.tip_tip_distances().to_series())
# test pairs are not equivalent
self.assertNotEqual(gtrg_td, gtrgi_td)
self.assertNotEqual(gtrg_td, gtrcat_td)
self.assertNotEqual(gtrgi_td, gtrcat_td)
def test_raxml_num_searches(self):
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
with redirected_stdio(stderr=os.devnull):
obs = raxml(input_sequences, seed=1723, n_searches=5)
obs_tree = skbio.TreeNode.read(str(obs), convert_underscores=False)
obs_tl = list(obs_tree.tip_tip_distances().to_series())
obs_series = set(['%.4f' % e for e in obs_tl])
exp_tree = skbio.TreeNode.read(self.get_data_path('test3.tre'))
exp_tl = list(exp_tree.tip_tip_distances().to_series())
exp_series = set(['%.4f' % e for e in exp_tl])
self.assertEqual(obs_series, exp_series)
def test_rapid_bootstrap_command(self):
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
with tempfile.TemporaryDirectory() as temp_dir:
with redirected_stdio(stderr=os.devnull):
obs = _build_rapid_bootstrap_command(input_sequences, 1723,
8752, 15, 'GTRGAMMA',
temp_dir, 'bs')
self.assertTrue(str(input_sequences) in str(obs[11]))
self.assertTrue('1723' in obs[5])
self.assertTrue('8752' in obs[7])
self.assertTrue('15' in obs[9])
self.assertTrue('GTRGAMMA' in obs[3])
self.assertTrue(str(temp_dir) in obs[13])
self.assertTrue('bs' in obs[15])
def test_raxml_rapid_bootstrap(self):
# Test that output tree is made.
# Reads tree output and compares tip labels to expected labels.
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
with redirected_stdio(stderr=os.devnull):
obs = raxml_rapid_bootstrap(input_sequences)
obs_tree = skbio.TreeNode.read(str(obs))
# load the resulting tree and test that it has the right number of
# tips and the right tip ids
tips = list(obs_tree.tips())
tip_names = [t.name for t in tips]
self.assertEqual(set(tip_names),
set(['GCA001510755', 'GCA001045515', 'GCA000454205',
'GCA000473545', 'GCA000196255', 'GCA000686145',
'GCA001950115', 'GCA001971985', 'GCA900007555']))
def test_raxml_rapid_bootstrap_n_threads(self):
# Test that an output tree is made when invoking threads.
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
with redirected_stdio(stderr=os.devnull):
obs = raxml_rapid_bootstrap(input_sequences, n_threads=2)
obs_tree = skbio.TreeNode.read(str(obs), convert_underscores=False)
# load the resulting tree and test that it has the right number of
# tips and the right tip ids
tips = list(obs_tree.tips())
tip_names = [t.name for t in tips]
self.assertEqual(set(tip_names),
set(['GCA001510755', 'GCA001045515', 'GCA000454205',
'GCA000473545', 'GCA000196255', 'GCA000686145',
'GCA001950115', 'GCA001971985', 'GCA900007555']))
def test_raxml_rapid_bootstrap_with_seed(self):
# Test tip-to-tip dists are identical to manually run RAxML output.
# This test is comparing an ordered series of tip-to-tip distances
# to a tree output from a manual run of the default command:
# raxmlHPC -f a -m GTRGAMMA -p 1723 -x 3871 -N 10
# -s aligned-dna-sequences-3.fasta -n q2
# NOTE: I cleanly rounded the tip-to-tip dists (i.e. `%.4f`) as RAxML
# may return slightly different rounding errors on different
# systems (and at times, between conda environments).
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
# test that branchlengths are identical
with redirected_stdio(stderr=os.devnull):
obs = raxml_rapid_bootstrap(input_sequences, seed=1723,
rapid_bootstrap_seed=3871,
bootstrap_replicates=10)
obs_tree = skbio.TreeNode.read(str(obs), convert_underscores=False)
# sometimes we lose the last set of numbers on long floats
obs_tl = list(obs_tree.tip_tip_distances().to_series())
obs_series = set(['%.4f' % e for e in obs_tl])
exp_tree = skbio.TreeNode.read(self.get_data_path('test2.tre'),
convert_underscores=True)
exp_tl = list(exp_tree.tip_tip_distances().to_series())
exp_series = set(['%.4f' % e for e in exp_tl])
self.assertEqual(obs_series, exp_series)
# test that bootstrap supports are identical
obs_bs = [node.name for node in obs_tree.non_tips()].sort()
exp_bs = [node.name for node in exp_tree.non_tips()].sort()
self.assertEqual(obs_bs, exp_bs)
def test_run_not_verbose(self):
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
aligned_fp = str(input_sequences)
with tempfile.TemporaryDirectory() as temp_dir:
cmd = ['raxmlHPC',
'-m', 'GTRGAMMA',
'-p', '1723',
'-s', aligned_fp,
'-w', temp_dir,
'-n', 'q2']
with redirected_stdio(stderr=os.devnull):
run_command(cmd, verbose=False)
obs_tree_fp = os.path.join(temp_dir, 'RAxML_bestTree.q2')
obs_tree = skbio.TreeNode.read(str(obs_tree_fp),
convert_underscores=False)
# load the resulting tree and test that it has the right number of
# tips and the right tip ids
tips = list(obs_tree.tips())
tip_names = [t.name for t in tips]
self.assertEqual(set(tip_names),
set(['GCA001510755', 'GCA001045515',
'GCA000454205', 'GCA000473545',
'GCA000196255', 'GCA000686145',
'GCA001950115', 'GCA001971985',
'GCA900007555']))
def test_run_rapid_bs_not_verbose(self):
input_fp = self.get_data_path('aligned-dna-sequences-3.fasta')
input_sequences = AlignedDNAFASTAFormat(input_fp, mode='r')
aligned_fp = str(input_sequences)
with tempfile.TemporaryDirectory() as temp_dir:
cmd = ['raxmlHPC',
'-m', 'GTRGAMMA',
'-p', '1723',
'-s', aligned_fp,
'-w', temp_dir,
'-n', 'q2',
'-f', 'a',
'-x', '9834',
'-N', '10']
with redirected_stdio(stderr=os.devnull):
run_command(cmd, verbose=False)
obs_tree_fp = os.path.join(temp_dir, 'RAxML_bipartitions.q2')
obs_tree = skbio.TreeNode.read(str(obs_tree_fp),
convert_underscores=False)
# load the resulting tree and test that it has the right number of
# tips and the right tip ids
tips = list(obs_tree.tips())
tip_names = [t.name for t in tips]
self.assertEqual(set(tip_names),
set(['GCA001510755', 'GCA001045515',
'GCA000454205', 'GCA000473545',
'GCA000196255', 'GCA000686145',
'GCA001950115', 'GCA001971985',
'GCA900007555']))
if __name__ == "__main__":
unittest.main()
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