Python assign_taxonomy Examples

Example #1

File: test_rtax.py Project: biocore/burrito-fillings

 def test_single_end_classification(self):
     self._paths_to_clean_up += cleanAll(self.read_1_seqs_fp)
     result = assign_taxonomy(self.input_seqs_fp, self.reference_seqs_fp, self.id_to_taxonomy_fp, self.read_1_seqs_fp, None ,header_id_regex="\\S+\\s+(\\S+?)\/")
     self.assertEqual(result, rtax_expected_result_single)

Example #2

File: test_rtax.py Project: biocore/burrito-fillings

 def test_paired_end_classification_with_fallback(self):
     self._paths_to_clean_up += cleanAll(self.read_1_seqs_fp)
     self._paths_to_clean_up += cleanAll(self.read_2_seqs_fp)
     result = assign_taxonomy(self.input_seqs_fp, self.reference_seqs_fp, self.id_to_taxonomy_fp, self.read_1_seqs_fp, self.read_2_seqs_fp,single_ok=True,header_id_regex="\\S+\\s+(\\S+?)\/")
     self.assertEqual(result, rtax_expected_result_paired_with_fallback)