def test_bwa_short_database_mapper(self): """bwa_short_database_mapper functions as expected """ bwa_short_database_mapper(query_fp=self.inseqs2_fp, refseqs_fp=self.refseqs2_fp, output_dir=self.test_out, max_diff=None, 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,['r1','r2','r3','r4','r5']) self.assertEqual(table.sum(),6)
def test_bwa_short_database_mapper(self): """bwa_short_database_mapper functions as expected """ bwa_short_database_mapper(query_fp=self.inseqs2_fp, refseqs_fp=self.refseqs2_fp, output_dir=self.test_out, max_diff=None, 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, ['r1', 'r2', 'r3', 'r4', 'r5']) self.assertEqual(table.sum(), 6)
def test_bwa_short_database_mapper(self): """bwa_short_database_mapper functions as expected """ bwa_short_database_mapper( query_fp=self.inseqs2_fp, refseqs_fp=self.refseqs2_fp, output_dir=self.test_out, max_diff=None, 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, ["r1", "r2", "r3", "r4", "r5"]) self.assertEqual(table.sum(), 6)
def test_bwa_short_database_mapper(self): """bwa_short_database_mapper functions as expected """ bwa_short_database_mapper(query_fp=self.inseqs2_fp, refseqs_fp=self.refseqs2_fp, output_dir=self.test_out, max_diff=None, 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_bwa_short_database_mapper_alt_params(self): """bwa_short_database_mapper functions as expected """ bwa_short_database_mapper(query_fp=self.inseqs2_fp, refseqs_fp=self.refseqs2_fp, output_dir=self.test_out, max_diff=1, 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.sample_ids, ['s2', 's1']) self.assertItemsEqual(table.observation_ids, ['r2', 'r3', 'r4', 'r5']) self.assertEqual(table.sum(), 5) # float can also be passed for max_diff bwa_short_database_mapper(query_fp=self.inseqs2_fp, refseqs_fp=self.refseqs2_fp, output_dir=self.test_out, max_diff=0.01, 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')
def test_bwa_short_database_mapper_alt_params(self): """bwa_short_database_mapper functions as expected """ bwa_short_database_mapper(query_fp=self.inseqs2_fp, refseqs_fp=self.refseqs2_fp, output_dir=self.test_out, max_diff=1, 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'), ['r2', 'r3', 'r4', 'r5']) self.assertEqual(table.sum(), 5) # float can also be passed for max_diff bwa_short_database_mapper(query_fp=self.inseqs2_fp, refseqs_fp=self.refseqs2_fp, output_dir=self.test_out, max_diff=0.01, 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')