diff --git a/tests/test_get_read_orientation.py b/tests/test_get_read_orientation.py index fba4bd25..10894334 100644 --- a/tests/test_get_read_orientation.py +++ b/tests/test_get_read_orientation.py @@ -4,8 +4,6 @@ from htsinfer.exceptions import ( FileProblem, - SamFileProblem, - StarProblem, ) from htsinfer.get_read_orientation import GetOrientation from htsinfer.models import ( @@ -18,11 +16,8 @@ StatesTypeRelationship, ) from tests.utils import ( - FILE_2000_RECORDS, - FILE_DUMMY, FILE_EMPTY_ALIGNED_SAM, FILE_BAD_ALIGNED_SAM, - FILE_INVALID_TRANSCRIPTS, FILE_MATE_1, FILE_MATE_2, FILE_ORIENTATION_ISF_1, @@ -38,14 +33,9 @@ FILE_UNMAPPED_PAIRED_1, FILE_UNMAPPED_PAIRED_2, FILE_UNMAPPED_SINGLE, - FILE_IDS_NOT_MATCH_1, FILE_IDS_NOT_MATCH_2, CONFIG, MAPPING, - RaiseError, - SubprocessError, - SOURCE_HUMAN, - SOURCE_FRUIT_FLY, ) diff --git a/tests/test_mapping.py b/tests/test_mapping.py index 733900c3..6492ed32 100644 --- a/tests/test_mapping.py +++ b/tests/test_mapping.py @@ -8,36 +8,20 @@ ) from htsinfer.mapping import Mapping from htsinfer.models import ( - ResultsOrientation, ResultsSource, ResultsType, Source, - StatesOrientation, - StatesOrientationRelationship, StatesTypeRelationship, ) from tests.utils import ( FILE_2000_RECORDS, FILE_DUMMY, - FILE_EMPTY_ALIGNED_SAM, - FILE_BAD_ALIGNED_SAM, FILE_INVALID_TRANSCRIPTS, - FILE_INVALID_SEQ_1, FILE_MATE_1, FILE_MATE_2, - FILE_ORIENTATION_ISF_1, - FILE_ORIENTATION_ISF_2, - FILE_ORIENTATION_ISR_1, - FILE_ORIENTATION_ISR_2, FILE_ORIENTATION_IU_1, FILE_ORIENTATION_IU_2, - FILE_ORIENTATION_SF, - FILE_ORIENTATION_SR, - FILE_ORIENTATION_U, FILE_TRANSCRIPTS, - FILE_UNMAPPED_PAIRED_1, - FILE_UNMAPPED_PAIRED_2, - FILE_UNMAPPED_SINGLE, CONFIG, MAPPING, RaiseError, @@ -211,27 +195,6 @@ def test_prepare_star_alignment_commands(self, tmpdir): ) assert ' '.join(list(results.values())[0]) == cmd - # def test_generate_star_alignments_problem(self, monkeypatch, tmpdir): - # """Force raising exception to simulate problem.""" - # CONFIG.results.library_source = ResultsSource( - # file_1=SOURCE_HUMAN, - # file_2=SOURCE_FRUIT_FLY, - # ) - # CONFIG.args.path_1_processed = FILE_ORIENTATION_IU_1 - # CONFIG.args.path_2_processed = FILE_ORIENTATION_IU_2 - # CONFIG.results.library_type = ResultsType( - # relationship=StatesTypeRelationship.not_mates, - # ) - # CONFIG.args.tmp_dir = tmpdir - # test_instance = Mapping(config=CONFIG) - # sub_method_name = 'htsinfer.mapping.Mapping.generate_star_alignments' - # monkeypatch.setattr( - # sub_method_name, - # lambda *args, **kwargs: StarProblem, - # ) - # with pytest.raises(StarProblem): - # test_instance.evaluate() - def test_generate_star_alignments_dummy_cmd(self, tmpdir): """Pass dummy cmd to force simulate star problem.""" CONFIG.args.path_2_processed = None