def test_blat_nt_database_mapper_alt_min_id(self): """blat_nt_database_mapper functions as expected """ blat_nt_database_mapper(query_fp=self.inseqs2_fp, refseqs_fp=self.refseqs2_fp, output_dir=self.test_out, evalue=1e-10, min_id=1.0, HALT_EXEC=False) observation_map_fp = join(self.test_out, 'observation_map.txt') self.assertTrue(exists(observation_map_fp)) observation_table_fp = join(self.test_out, 'observation_table.biom') table = parse_biom_table(open(observation_table_fp, 'U')) self.assertItemsEqual(table.SampleIds, ['s2', 's1']) self.assertItemsEqual(table.ObservationIds, ['r2', 'r3', 'r4', 'r5']) self.assertEqual(table.sum(), 5)
def test_blat_nt_database_mapper_alt_min_id(self): """blat_nt_database_mapper functions as expected """ blat_nt_database_mapper(query_fp=self.inseqs2_fp, refseqs_fp=self.refseqs2_fp, output_dir=self.test_out, evalue=1e-10, min_id=1.0, HALT_EXEC=False) observation_map_fp = join(self.test_out,'observation_map.txt') self.assertTrue(exists(observation_map_fp)) observation_table_fp = join(self.test_out,'observation_table.biom') table = parse_biom_table(open(observation_table_fp,'U')) self.assertEqualItems(table.SampleIds,['s2','s1']) self.assertEqualItems(table.ObservationIds,['r2','r3','r4','r5']) self.assertEqual(table.sum(),5)
def test_blat_nt_database_mapper(self): """blat_nt_database_mapper functions as expected """ blat_nt_database_mapper(query_fp=self.inseqs2_fp, refseqs_fp=self.refseqs2_fp, output_dir=self.test_out, evalue=1e-10, min_id=0.75, HALT_EXEC=False) observation_map_fp = join(self.test_out, 'observation_map.txt') self.assertTrue(exists(observation_map_fp)) observation_table_fp = join(self.test_out, 'observation_table.biom') table = load_table(observation_table_fp) self.assertItemsEqual(table.ids(), ['s2', 's1']) self.assertItemsEqual(table.ids(axis='observation'), ['r1', 'r2', 'r3', 'r4', 'r5']) self.assertEqual(table.sum(), 6)
def test_blat_nt_database_mapper_alt_min_id(self): """blat_nt_database_mapper functions as expected """ blat_nt_database_mapper( query_fp=self.inseqs2_fp, refseqs_fp=self.refseqs2_fp, output_dir=self.test_out, evalue=1e-10, min_id=1.0, HALT_EXEC=False, ) observation_map_fp = join(self.test_out, "observation_map.txt") self.assertTrue(exists(observation_map_fp)) observation_table_fp = join(self.test_out, "observation_table.biom") table = parse_biom_table(open(observation_table_fp, "U")) self.assertEqualItems(table.SampleIds, ["s2", "s1"]) self.assertEqualItems(table.ObservationIds, ["r2", "r3", "r4", "r5"]) self.assertEqual(table.sum(), 5)
def test_blat_nt_database_mapper(self): """blat_nt_database_mapper functions as expected """ blat_nt_database_mapper(query_fp=self.inseqs2_fp, refseqs_fp=self.refseqs2_fp, output_dir=self.test_out, evalue=1e-10, min_id=0.75, HALT_EXEC=False) observation_map_fp = join(self.test_out, 'observation_map.txt') self.assertTrue(exists(observation_map_fp)) observation_table_fp = join(self.test_out, 'observation_table.biom') table = load_table(observation_table_fp) self.assertItemsEqual(table.ids(), ['s2', 's1']) self.assertItemsEqual( table.ids(axis='observation'), ['r1', 'r2', 'r3', 'r4', 'r5']) self.assertEqual(table.sum(), 6)