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)
Пример #2
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 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)
Пример #5
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 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')
Пример #6
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 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')