text: class Test_AE_Config:
  
      def test_config(self, dropConfig):
          assert dropConfig.AE.getWorkdir() == "Scripts/AberrantExpression/pipeline"
          dict_ = {
              'groups': ['outrider', 'import_exp'],
              'fpkmCutoff': 1,
              'implementation': 'autoencoder',
              'padjCutoff': 1,
              'zScoreCutoff': 0,
              'maxTestedDimensionProportion': 3
          }
          print(dropConfig.AE.dict_.items())
          assert dict_.items() <= dropConfig.AE.dict_.items()
  
      def test_getCountsFiles(self, demo_dir, dropConfig):
          counts_dir = f"{demo_dir}/Output/processed_data/aberrant_expression/v29/counts"
          counts_files = [
              'HG00103.4.M_120208_3.Rds',
              'HG00096.1.M_111124_6.Rds',
              'HG00106.4.M_120208_5.Rds',
              'HG00116.2.M_120131_1.Rds',
              'HG00111.2.M_111215_4.Rds',
              'HG00149.1.M_111124_6.Rds',
              'HG00176.4.M_120208_2.Rds',
              'HG00150.4.M_120208_7.Rds',
              'HG00126.1.M_111124_8.Rds',
              'HG00132.2.M_111215_4.Rds'
          ]
          counts_files_true = [f"{counts_dir}/{f}" for f in counts_files]
          counts_files_true.sort()
          counts_files_test = dropConfig.AE.getCountFiles(annotation="v29", group="outrider")
          counts_files_test.sort()
          assert counts_files_true == counts_files_test
  
          # import count
          counts_files_true = counts_files_true[2:]
          counts_files_true.append(f"{demo_dir}/Data/external_geneCounts.tsv.gz")
          counts_files_true.sort()
          counts_files_test = dropConfig.AE.getCountFiles(annotation="v29", group="import_exp")
          counts_files_test.sort()
          assert counts_files_true == counts_files_test
  
      def test_getCountParams(self, dropConfig):
          params = {
              'STRAND': 'no',
              'COUNT_MODE': 'IntersectionStrict',
              'PAIRED_END': True,
              'COUNT_OVERLAPS': True
          }
          assert params == dropConfig.AE.getCountParams("HG00103.4.M_120208_3")
  
  
  