Removed unused imports

zavolanlab · Jul 17, 2023 · e691fa1 · e691fa1
1 parent 00b0c2a
commit e691fa1
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Showing 2 changed files with 0 additions and 47 deletions.
diff --git 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
@@ -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