def test_MrAIC(self):
"""Tests that creating genetrees with the --mraic
command set calculates the correct evolutionary models.
"""
test_data = open('alignments/3.oneliners', 'rU')
mr_job = ProcessPhyloData([
'-r', 'local', '--setup-cmd', 'mkdir -p tmp', '--gene-trees',
'--mraic', '--archive=../gzips/osx.phylo.tar.gz#bin', "-"
])
mr_job.sandbox(stdin=test_data)
results = []
with mr_job.make_runner() as runner:
runner.run()
for line in runner.stream_output():
# Use the job's specified protocol to read the output
key, value = mr_job.parse_output_line(line)
results.append(value)
# get models from output
models = [
item.split(" ")[1].strip("'").split('=')[-1] for item in results
]
# check results.
# result looks like: ['GTR', 'HKY', 'HKY'])
self.assertIn('GTR', models)
self.assertIn('HKY', models)
self.assertEqual(len(results), 3)
def test_Bootstrapping(self):
"""Tests that bootstraps produces the correct number or replicates"""
test_data = open('alignments/3.oneliners', 'rU')
mr_job = ProcessPhyloData([
'-r', 'local', '--setup-cmd', 'mkdir -p tmp', '--full-analysis',
'--bootreps=5', '--archive=../gzips/osx.phylo.tar.gz#bin', "-"
])
mr_job.sandbox(stdin=test_data)
results = []
with mr_job.make_runner() as runner:
runner.run()
for line in runner.stream_output():
# Use the job's specified protocol to read the output
key, value = mr_job.parse_output_line(line)
results.append(value)
self.assertEqual(len(results), 15)
def test_GeneTrees(self):
"""Tests that creating genetrees with Cloudforest
makes the appropriate number of trees.
"""
test_data = open('alignments/3.oneliners', 'rU')
mr_job = ProcessPhyloData([
'-r', 'local', '--setup-cmd', 'mkdir -p tmp', '--gene-trees',
'--archive=../gzips/osx.phylo.tar.gz#bin', "-"
])
mr_job.sandbox(stdin=test_data)
results = []
with mr_job.make_runner() as runner:
runner.run()
for line in runner.stream_output():
# Use the job's specified protocol to read the output
key, value = mr_job.parse_output_line(line)
results.append(value)
self.assertEqual(len(results), 3)
def test_get_genetrees(self):
"""[MrJob] Generate genetrees"""
test_data = open('alignments/3.oneliners', 'rU')
mr_job = ProcessPhyloData([
'-r', 'local',
'--setup-cmd',
'mkdir -p tmp',
'--gene-trees',
'--archive=../gzips/osx.phylo.tar.gz#bin',
"-"]
)
mr_job.sandbox(stdin=test_data)
results = []
with mr_job.make_runner() as runner:
runner.run()
for line in runner.stream_output():
# Use the job's specified protocol to read the output
key, value = mr_job.parse_output_line(line)
results.append(value)
#TODO:better checking of tree structure here - do distance checking
self.assertEqual(len(results), 3)
def test_MrAIC(self):
"""[MrJob] Select model and generate genetrees"""
test_data = open('alignments/3.oneliners', 'rU')
mr_job = ProcessPhyloData([
'-r', 'local',
'--setup-cmd',
'mkdir -p tmp',
'--gene-trees',
'--mraic',
'--archive=../gzips/osx.phylo.tar.gz#bin',
'-']
)
mr_job.sandbox(stdin=test_data)
results = []
with mr_job.make_runner() as runner:
runner.run()
for line in runner.stream_output():
# Use the job's specified protocol to read the output
key, value = mr_job.parse_output_line(line)
results.append(value)
# check models
expected_models = ['HKY', 'GTR', 'HKY']
observed_models = self.get_models_from_mrjob_out(results)
assert observed_models == expected_models