def test_blat_database_mapper(self):
"""blat_database_mapper functions as expected """
blat_database_mapper(query_fp=self.inseqs1_fp,
refseqs_fp=self.refseqs1_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 = parse_biom_table(open(observation_table_fp,'U'))
self.assertEqualItems(table.SampleIds,['s2','s1'])
self.assertEqualItems(table.ObservationIds,['eco:b0122-pr','eco:b0015-pr'])
self.assertEqual(table.sum(),5)
def test_blat_database_mapper_alt_params(self):
"""blat_database_mapper functions as expected w alt e-value"""
blat_database_mapper(query_fp=self.inseqs1_fp,
refseqs_fp=self.refseqs1_fp,
output_dir=self.test_out,
evalue=1e-2,
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 = parse_biom_table(open(observation_table_fp, 'U'))
self.assertEqualItems(table.SampleIds, ['s2', 's1'])
self.assertEqualItems(table.ObservationIds,
['eco:b0122-pr', 'eco:b0015-pr', 'eco:b0001-pr'])
self.assertEqual(table.sum(), 6)
def test_blat_database_mapper_alt_params(self):
"""blat_database_mapper functions as expected w alt e-value"""
blat_database_mapper(query_fp=self.inseqs1_fp,
refseqs_fp=self.refseqs1_fp,
output_dir=self.test_out,
evalue=1e-2,
min_id=0.75,
genetic_code=2,
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'),
['eco:b0122-pr', 'eco:b0015-pr', 'eco:b0001-pr'])
self.assertEqual(table.sum(), 6)
def test_blat_database_mapper_alt_params(self):
"""blat_database_mapper functions as expected w alt e-value"""
blat_database_mapper(query_fp=self.inseqs1_fp,
refseqs_fp=self.refseqs1_fp,
output_dir=self.test_out,
evalue=1e-2,
min_id=0.75,
genetic_code=2,
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'),
['eco:b0122-pr', 'eco:b0015-pr', 'eco:b0001-pr'])
self.assertEqual(table.sum(), 6)
def test_blat_database_mapper_alt_params(self):
"""blat_database_mapper functions as expected w alt e-value"""
blat_database_mapper(
query_fp=self.inseqs1_fp,
refseqs_fp=self.refseqs1_fp,
output_dir=self.test_out,
evalue=1e-2,
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 = parse_biom_table(open(observation_table_fp, "U"))
self.assertEqualItems(table.SampleIds, ["s2", "s1"])
self.assertEqualItems(table.ObservationIds, ["eco:b0122-pr", "eco:b0015-pr", "eco:b0001-pr"])
self.assertEqual(table.sum(), 6)
