def test_out_reads(self):
out_reads = util.file.mkstempfname('.kraken_reads.gz')
metagenomics.kraken(self.inBam, self.db, outReads=out_reads)
self.mock_samtofastq().execute.assert_called_once_with(
self.inBam,
mock.ANY,
mock.ANY,
picardOptions=mock.ANY,
JVMmemory=mock.ANY)
picard_opts = self.mock_samtofastq(
).execute.call_args[1]['picardOptions']
six.assertCountEqual(self, picard_opts, [
'CLIPPING_ACTION=X',
'CLIPPING_ATTRIBUTE=%s' %
tools.picard.SamToFastqTool.illumina_clipping_attribute
])
self.mock_kraken().classify.assert_called_once_with(self.db,
mock.ANY,
mock.ANY,
options={
'--paired':
None,
'--threads': 1,
})
# Exists due to test. Need a better tmpfile patcher.
self.assertTrue(os.path.isfile(out_reads))
def test_num_threads(self):
out_reads = util.file.mkstempfname('.kraken_reads.gz')
metagenomics.kraken(self.inBam, self.db, outReads=out_reads, numThreads=11)
self.mock_kraken().classify.assert_called_once_with(
self.db, mock.ANY, mock.ANY, options={
'--paired': None,
'--threads': min(util.misc.available_cpu_count(), 11),
})
def test_out_reads_and_report(self):
out_reads = util.file.mkstempfname('.kraken_reads.gz')
out_report = util.file.mkstempfname('.kraken_report.txt')
metagenomics.kraken(self.inBam, self.db, outReads=out_reads, outReport=out_report)
self.mock_kraken().classify.assert_called_once_with(
self.db, mock.ANY, mock.ANY, options={
'--paired': None,
'--threads': 1,
})
self.mock_kraken().execute.assert_called_with(
'kraken-report', self.db, out_report, args=[mock.ANY])
def test_filter_threshold(self):
out_reads = util.file.mkstempfname('.kraken_reads.gz')
metagenomics.kraken(self.inBam, self.db, outReads=out_reads, filterThreshold=0.05)
self.mock_kraken().execute.assert_called_with(
'kraken-filter', self.db, mock.ANY, args=[mock.ANY], options={
'--threshold': 0.05
})
self.mock_kraken().classify.assert_called_once_with(
self.db, mock.ANY, mock.ANY, options={
'--paired': None,
'--threads': 1,
})
def test_num_threads(self):
out_reads = util.file.mkstempfname('.kraken_reads.gz')
metagenomics.kraken(self.inBam,
self.db,
outReads=out_reads,
numThreads=11)
self.mock_kraken().classify.assert_called_once_with(
self.db,
mock.ANY,
mock.ANY,
options={
'--paired': None,
'--threads': min(util.misc.available_cpu_count(), 11),
})
def test_out_report(self):
out_report = util.file.mkstempfname('.kraken_report.txt')
metagenomics.kraken(self.inBam, self.db, outReport=out_report)
self.mock_kraken().classify.assert_called_once_with(self.db,
mock.ANY,
mock.ANY,
options={
'--paired':
None,
'--threads': 1,
})
self.mock_kraken().execute.assert_called_with('kraken-report',
self.db,
out_report,
args=[mock.ANY])
def test_filter_threshold(self):
out_reads = util.file.mkstempfname('.kraken_reads.gz')
metagenomics.kraken(self.inBam,
self.db,
outReads=out_reads,
filterThreshold=0.05)
self.mock_kraken().execute.assert_called_with(
'kraken-filter',
self.db,
mock.ANY,
args=[mock.ANY],
options={'--threshold': 0.05})
self.mock_kraken().classify.assert_called_once_with(self.db,
mock.ANY,
mock.ANY,
options={
'--paired':
None,
'--threads': 1,
})
def test_out_reads(self):
out_reads = util.file.mkstempfname('.kraken_reads.gz')
metagenomics.kraken(self.inBam, self.db, outReads=out_reads)
self.mock_samtofastq().execute.assert_called_once_with(
self.inBam, mock.ANY, mock.ANY, picardOptions=mock.ANY,
JVMmemory=mock.ANY)
picard_opts = self.mock_samtofastq().execute.call_args[1]['picardOptions']
six.assertCountEqual(
self, picard_opts,
['CLIPPING_ACTION=X', 'CLIPPING_ATTRIBUTE=%s'
% tools.picard.SamToFastqTool.illumina_clipping_attribute])
self.mock_kraken().classify.assert_called_once_with(
self.db, mock.ANY, mock.ANY, options={
'--paired': None,
'--threads': 1,
})
# Exists due to test. Need a better tmpfile patcher.
self.assertTrue(os.path.isfile(out_reads))
def test_assert(self):
with self.assertRaises(AssertionError):
metagenomics.kraken(self.inBam, self.db)
def test_assert(self):
with self.assertRaises(AssertionError):
metagenomics.kraken(self.inBam, self.db)