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test_tools_kraken.py
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test_tools_kraken.py
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# Unit tests for kraken
from builtins import super
import os.path
import tempfile
import unittest
import mock
import subprocess
import unittest
import util.file
import util.misc
import tools.kraken
from test import TestCaseWithTmp
class TestToolKrakenMocked(TestCaseWithTmp):
def setUp(self):
super().setUp()
patcher = mock.patch('util.misc.run', autospec=True)
self.addCleanup(patcher.stop)
self.mock_run = patcher.start()
patcher = mock.patch('subprocess.check_call', autospec=True)
self.addCleanup(patcher.stop)
self.mock_check_call = patcher.start()
patcher = mock.patch('tools.CondaPackage', autospec=True)
self.addCleanup(patcher.stop)
self.mock_conda = patcher.start()
self.mock_conda.return_value.verify_install.return_value = "mock"
self.mock_conda.return_value.is_attempted.return_value = True
self.mock_conda.return_value.is_installed.return_value = True
self.mock_conda.return_value.require_executability = False
self.mock_conda.return_value.executable_path.return_value = "/dev/null"
self.kraken = tools.kraken.Kraken()
self.inBam = os.path.join(util.file.get_test_input_path(), 'almost-empty.bam')
self.db = tempfile.mkdtemp('db')
def test_kraken_classify(self):
out_reads = util.file.mkstempfname('.reads.txt')
self.kraken.classify(self.inBam, self.db, out_reads)
args = self.mock_check_call.call_args[0][0]
self.assertEqual('kraken', os.path.basename(args[0]))
self.assertTrue(util.misc.list_contains(['--db', self.db], args), args)
self.assertTrue(util.misc.list_contains(['--output', out_reads], args), args)
self.assertTrue(util.misc.list_contains(['--threads', str(util.misc.available_cpu_count())], args), args)
self.assertIn('--paired', args)
def test_kraken_filter(self):
in_reads = util.file.mkstempfname('.kraken_reads.unfilt.txt')
out_reads = util.file.mkstempfname('.kraken_reads.filt.txt')
for thresh in (0.05, 0.3, 0.81):
self.kraken.filter(in_reads, self.db, out_reads, thresh)
args = self.mock_run.call_args[0][0]
self.assertEqual('kraken-filter', os.path.basename(args[0]))
self.assertIn(in_reads, args)
self.assertTrue(util.misc.list_contains(['--db', self.db], args), args)
self.assertTrue(util.misc.list_contains(['--threshold', str(thresh)], args), args)
def test_kraken_report(self):
in_reads = util.file.mkstempfname('.kraken_reads.txt')
out_report = util.file.mkstempfname('.kraken_report.txt')
self.kraken.report(in_reads, self.db, out_report)
args = self.mock_run.call_args[0][0]
self.assertEqual('kraken-report', os.path.basename(args[0]))
self.assertIn(in_reads, args)
self.assertTrue(util.misc.list_contains(['--db', self.db], args), args)
def test_classify_num_threads(self):
out_reads = util.file.mkstempfname('.reads.txt')
self.kraken.classify(self.inBam, self.db, out_reads)
args = self.mock_check_call.call_args[0][0]
self.assertEqual('kraken', os.path.basename(args[0]))
self.assertIn('--threads', args)
actual = args[args.index('--threads')+1]
self.assertEqual(actual, str(util.misc.available_cpu_count()), args)
for requested in (1,2,3,8,11,20):
expected = min(util.misc.available_cpu_count(), requested)
self.kraken.classify(self.inBam, self.db, out_reads, numThreads=requested)
args = self.mock_check_call.call_args[0][0]
self.assertEqual('kraken', os.path.basename(args[0]))
self.assertIn('--threads', args)
actual = args[args.index('--threads')+1]
self.assertEqual(actual, str(expected), "failure for requested %s, expected %s, actual %s" % (requested, expected, actual))
@unittest.skipIf(tools.is_osx(), "kraken osx binary does not yet exist on bioconda")
class TestToolKrakenExecute(TestCaseWithTmp):
def setUp(self):
super().setUp()
input_dir = os.path.join(util.file.get_test_input_path(), 'TestMetagenomicsViralMix')
self.kraken_db_viral_mix = tempfile.mkdtemp('-kraken_db_viral_mix')
cmd = ['tar', '-C', self.kraken_db_viral_mix, '-xzf', os.path.join(input_dir, 'kraken_db.tar.gz')]
subprocess.check_call(cmd)
self.kraken = tools.kraken.Kraken()
def test_kraken_execution(self):
input_bam = os.path.join(util.file.get_test_input_path(), 'TestMetagenomicsViralMix', 'test-reads.bam')
outdir = tempfile.mkdtemp('-kraken_execute')
out = os.path.join(outdir, 'viral_mix.kraken')
out_filtered = os.path.join(outdir, 'viral_mix.filtered-kraken')
out_report = os.path.join(outdir, 'viral_mix.kraken-report')
expected_filtered = os.path.join(util.file.get_test_input_path(self), 'expected-kraken-mix.reads.txt')
expected_report = os.path.join(util.file.get_test_input_path(self), 'expected-kraken-mix.report.txt')
self.kraken.classify(input_bam, self.kraken_db_viral_mix, out)
self.kraken.filter(out, self.kraken_db_viral_mix, out_filtered, 0.05)
self.kraken.report(out_filtered, self.kraken_db_viral_mix, out_report)
self.assertEqualContents(out_filtered, expected_filtered)
self.assertEqualContents(out_report, expected_report)
def test_kraken_on_empty(self):
input_bam = os.path.join(util.file.get_test_input_path(), 'empty.bam')
out = util.file.mkstempfname('.empty.kraken.raw.txt')
out_filtered = util.file.mkstempfname('.empty.filtered-kraken.txt')
out_report = util.file.mkstempfname('.empty.kraken-report.txt')
expected_report = os.path.join(util.file.get_test_input_path(self), 'empty-report.txt')
self.kraken.classify(input_bam, self.kraken_db_viral_mix, out)
self.kraken.filter(out, self.kraken_db_viral_mix, out_filtered, 0.05)
self.kraken.report(out_filtered, self.kraken_db_viral_mix, out_report)
self.assertEqual(os.path.getsize(out), 0)
self.assertEqual(os.path.getsize(out_filtered), 0)
with open(out_report, 'rt') as inf:
out_report_contents = inf.readlines()
self.assertEqual(len(out_report_contents), 1)
out_report_contents = out_report_contents[0].rstrip('\n').split('\t')
self.assertEqual(out_report_contents, ['100.00', '0', '0', 'U', '0', 'unclassified'])
def test_kraken_filter_empty_input(self):
input_reads = util.file.mkstempfname('.reads.txt')
output_reads = util.file.mkstempfname('.filtered.reads.txt')
os.unlink(output_reads)
self.kraken.filter(input_reads, self.kraken_db_viral_mix, output_reads, 0.05)
self.assertEqual(os.path.getsize(output_reads), 0)
def test_kraken_report_empty_input(self):
input_reads = util.file.mkstempfname('.reads.txt')
output_report = util.file.mkstempfname('.report.txt')
expected_report = os.path.join(util.file.get_test_input_path(self), 'empty-report.txt')
self.kraken.report(input_reads, self.kraken_db_viral_mix, output_report)
with open(output_report, 'rt') as inf:
out_report_contents = inf.readlines()
self.assertEqual(len(out_report_contents), 1)
out_report_contents = out_report_contents[0].rstrip('\n').split('\t')
self.assertEqual(out_report_contents, ['100.00', '0', '0', 'U', '0', 'unclassified'])