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)