def test_buildIdxLUT(self):
     idx_lut = indexing.buildIdxLUT(RECODED_GENOME_FP,
                                    REFERENCE_GENOME_FP,
                                    RECODED_GB_STR,
                                    REFERENCE_GB_STR,
                                    cache_dir=TEST_CACHE_DIR)
     # check_idx_lut = np.save(os.path.join(TEST_OUTPUT_DIR,
     #                                      'test_buildidxlut'), idx_lut)
     check_idx_lut = np.load(
         os.path.join(TEST_OUTPUT_DIR, 'test_buildidxlut.npy'))
     self.assertTrue((idx_lut == check_idx_lut).all())
Beispiel #2
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 def test_buildIdxLUT(self):
     idx_lut = indexing.buildIdxLUT(
         RECODED_GENOME_FP,
         REFERENCE_GENOME_FP,
         RECODED_GB_STR,
         REFERENCE_GB_STR,
         cache_dir=TEST_CACHE_DIR)
     # check_idx_lut = np.save(os.path.join(TEST_OUTPUT_DIR,
     #                                      'test_buildidxlut'), idx_lut)
     check_idx_lut = np.load(os.path.join(TEST_OUTPUT_DIR,
                                          'test_buildidxlut.npy'))
     self.assertTrue((idx_lut == check_idx_lut).all())
 def test_buildEdgeLUT(self):
     idx_lut = indexing.buildIdxLUT(RECODED_GENOME_FP,
                                    REFERENCE_GENOME_FP,
                                    RECODED_GB_STR,
                                    REFERENCE_GB_STR,
                                    cache_dir=TEST_CACHE_DIR)
     edge_lut = indexing.buildEdgeLUT(idx_lut, TEST_CACHE_DIR)
     # with open(os.path.join(TEST_OUTPUT_DIR,
     #                       'test_buildedgelut.out'), 'wb') as fd:
     #     edge_lut.tofile(fd)
     with open(os.path.join(TEST_OUTPUT_DIR, 'test_buildedgelut.out'),
               'rb') as fd:
         check_edge_lut = bt.bitarray()
         check_edge_lut.fromfile(fd)
     self.assertEqual(edge_lut, check_edge_lut[:len(edge_lut)],
                      'Edge LUTs not equal')
Beispiel #4
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 def test_buildEdgeLUT(self):
     idx_lut = indexing.buildIdxLUT(
         RECODED_GENOME_FP,
         REFERENCE_GENOME_FP,
         RECODED_GB_STR,
         REFERENCE_GB_STR,
         cache_dir=TEST_CACHE_DIR)
     edge_lut = indexing.buildEdgeLUT(
         idx_lut,
         TEST_CACHE_DIR)
     # with open(os.path.join(TEST_OUTPUT_DIR,
     #                       'test_buildedgelut.out'), 'wb') as fd:
     #     edge_lut.tofile(fd)
     with open(os.path.join(TEST_OUTPUT_DIR,
                           'test_buildedgelut.out'), 'rb') as fd:
         check_edge_lut = bt.bitarray()
         check_edge_lut.fromfile(fd)
     self.assertEqual(edge_lut, check_edge_lut[:len(edge_lut)],
                      'Edge LUTs not equal')