def test_num_threads(self, mock_dfs):
out_report = util.file.mkstempfname('report.txt')
metagenomics.diamond(self.inBam,
self.db,
self.tax_db,
out_report,
numThreads=11)
cmd = self.mock_popen.call_args[0][0]
self.assertIn('--threads 11', cmd)
def test_num_threads(self, mock_dfs):
out_report = util.file.mkstempfname('report.txt')
metagenomics.diamond(self.inBam,
self.db,
self.tax_db,
out_report,
threads=11)
expected_threads = min(11, _CPUS)
expected_threads = '--threads {}'.format(expected_threads)
cmd = self.mock_popen.call_args[0][0]
self.assertIn(expected_threads, cmd)
def test_num_threads(self, mock_blast_lca, mock_dfs):
out_report = util.file.mkstempfname('report.txt')
metagenomics.diamond(self.inBam,
self.db,
self.tax_db,
out_report,
numThreads=11)
self.mock_diamond().blastx.assert_called_once_with(
self.db, mock.ANY, mock.ANY, options={'--threads': 11})
self.assertEqual(
self.mock_diamond().view.call_args[1]['options']['--threads'], 11)
def test_output_reads(self, mock_dfs):
out_report = util.file.mkstempfname('report.txt')
out_reads = util.file.mkstempfname('lca.gz')
metagenomics.diamond(self.inBam,
self.db,
self.tax_db,
out_report,
outReads=out_reads)
cmd = self.mock_popen.call_args[0][0]
self.assertIn(out_reads, cmd)
assert isinstance(metagenomics.kraken_dfs_report.call_args[0][0],
metagenomics.TaxonomyDb)
def test_output_lca(self, mock_blast_lca, mock_dfs):
out_report = util.file.mkstempfname('report.txt')
metagenomics.diamond(self.inBam, self.db, self.tax_db, out_report)
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_diamond().install.assert_called_once_with()
self.mock_diamond().blastx.assert_called_once_with(
self.db, mock.ANY, mock.ANY, options={'--threads': 1})
assert self.mock_diamond().view.called
assert isinstance(metagenomics.blast_lca.call_args[0][0], metagenomics.TaxonomyDb)
assert isinstance(metagenomics.kraken_dfs_report.call_args[0][0], metagenomics.TaxonomyDb)
def test_output_lca(self, mock_blast_lca, mock_dfs):
out_report = util.file.mkstempfname('report.txt')
metagenomics.diamond(self.inBam, self.db, self.tax_db, out_report)
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_diamond().install.assert_called_once_with()
self.mock_diamond().blastx.assert_called_once_with(
self.db, mock.ANY, mock.ANY, options={'--threads': 1})
assert self.mock_diamond().view.called
assert isinstance(metagenomics.blast_lca.call_args[0][0],
metagenomics.TaxonomyDb)
assert isinstance(metagenomics.kraken_dfs_report.call_args[0][0],
metagenomics.TaxonomyDb)
def test_num_threads(self, mock_blast_lca, mock_dfs):
out_report = util.file.mkstempfname('report.txt')
metagenomics.diamond(self.inBam, self.db, self.tax_db, out_report, numThreads=11)
self.mock_diamond().blastx.assert_called_once_with(
self.db, mock.ANY, mock.ANY, options={'--threads': 11})
self.assertEqual(self.mock_diamond().view.call_args[1]['options']['--threads'], 11)
