def test_usearch_database_mapper(self):
"""usearch_database_mapper functions as expected """
usearch_database_mapper(query_fp=self.inseqs1_fp,
refseqs_fp=self.refseqs1_fp,
output_dir=self.test_out,
evalue=1e-10,
min_id=0.75,
queryalnfract=0.35,
targetalnfract=0.0,
maxaccepts=1,
maxrejects=8,
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_usearch_database_mapper(self):
"""usearch_database_mapper functions as expected """
usearch_database_mapper(query_fp=self.inseqs1_fp,
refseqs_fp=self.refseqs1_fp,
output_dir=self.test_out,
evalue=1e-10,
min_id=0.75,
queryalnfract=0.35,
targetalnfract=0.0,
maxaccepts=1,
maxrejects=8,
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,
['eco:b0122-pr', 'eco:b0015-pr'])
self.assertEqual(table.sum(), 5)