Remove tests related to mitochondrial gene detection from filter_with…

…_counts
openpipelines-bio · Oct 16, 2023 · 17180b6 · 17180b6
1 parent 1836e92
commit 17180b6
Showing 1 changed file with 0 additions and 83 deletions.
diff --git a/src/filter/filter_with_counts/test.py b/src/filter/filter_with_counts/test.py
@@ -90,9 +90,6 @@ def test_filtering_a_little(run_component, input_path,
         "--min_genes_per_cell", "200",
         "--max_genes_per_cell", "1500000",
         "--min_cells_per_gene", "10",
-        "--min_fraction_mito", "0",
-        "--max_fraction_mito", "0.2",
-        "--var_gene_names", "gene_symbol",
         "--do_subset"])
     assert Path("output-2.h5mu").is_file()
     mu_out = mu.read_h5mu("output-2.h5mu")
@@ -122,85 +119,5 @@ def test_filter_cells_without_counts(run_component, input_h5mu, tmp_path):
     assert "mitochondrial" not in mu_out.mod['rna'].var
 
 
-def test_filter_mitochondrial(run_component, input_path,
-                              input_n_rna_obs, input_n_prot_obs,
-                              input_n_rna_vars, input_n_prot_vars):
-    run_component([
-        "--input", input_path,
-        "--output", "output-4.h5mu",
-        "--var_gene_names", "gene_symbol",
-        "--max_fraction_mito", "0.2",
-        "--do_subset"
-        ])
-    assert Path("output-4.h5mu").is_file()
-    mu_out = mu.read_h5mu("output-4.h5mu")
-    new_obs = mu_out.mod['rna'].n_obs
-    new_vars = mu_out.mod['rna'].n_vars
-    assert new_obs < input_n_rna_obs
-    assert new_vars == input_n_rna_vars
-    assert mu_out.mod['prot'].n_obs == input_n_prot_obs
-    assert mu_out.mod['prot'].n_vars == input_n_prot_vars
-    assert list(mu_out.mod['rna'].var['feature_types'].cat.categories) == ["Gene Expression"]
-    assert list(mu_out.mod['prot'].var['feature_types'].cat.categories) == ["Antibody Capture"]
-    assert "mitochondrial" not in mu_out.mod['rna'].var
-
-def test_filter_mitochondrial_regex(run_component, input_path,
-                                    input_n_rna_obs, input_n_prot_obs,
-                                    input_n_rna_vars, input_n_prot_vars):
-    run_component([
-        "--input", input_path,
-        "--output", "output-5.h5mu",
-        "--var_gene_names", "gene_symbol",
-        "--max_fraction_mito", "0.2",
-        "--mitochondrial_gene_regex", "^[M][T]-",
-        "--do_subset"
-        ])
-    assert Path("output-5.h5mu").is_file()
-    mu_out = mu.read_h5mu("output-5.h5mu")
-    new_obs = mu_out.mod['rna'].n_obs
-    new_vars = mu_out.mod['rna'].n_vars
-    assert new_obs < input_n_rna_obs
-    assert new_vars == input_n_rna_vars
-    assert mu_out.mod['prot'].n_obs == input_n_prot_obs
-    assert mu_out.mod['prot'].n_vars == input_n_prot_vars
-    assert list(mu_out.mod['rna'].var['feature_types'].cat.categories) == ["Gene Expression"]
-    assert list(mu_out.mod['prot'].var['feature_types'].cat.categories) == ["Antibody Capture"]
-    assert "mitochondrial" not in mu_out.mod['rna'].var
-
-
-def test_filter_mitochondrial_column_not_set(run_component, input_path,
-                                             input_n_rna_obs, input_n_prot_obs,
-                                             input_n_rna_vars, input_n_prot_vars):
-    run_component([
-        "--input", input_path,
-        "--output", "output-6.h5mu",
-        "--max_fraction_mito", "0.2",
-        "--mitochondrial_gene_regex", "^[mM][tT]-",
-        "--do_subset"
-        ])
-    assert Path("output-6.h5mu").is_file()
-    mu_out = mu.read_h5mu("output-6.h5mu")
-    new_obs = mu_out.mod['rna'].n_obs
-    new_vars = mu_out.mod['rna'].n_vars
-    assert new_obs == input_n_rna_obs # Stays the same because filtering on the wrong column
-    assert new_vars == input_n_rna_vars
-    assert mu_out.mod['prot'].n_obs == input_n_prot_obs
-    assert mu_out.mod['prot'].n_vars == input_n_prot_vars
-    assert list(mu_out.mod['rna'].var['feature_types'].cat.categories) == ["Gene Expression"]
-    assert list(mu_out.mod['prot'].var['feature_types'].cat.categories) == ["Antibody Capture"]
-    assert "mitochondrial" not in mu_out.mod['rna'].var.columns
-
-def test_var_name_mitochondrial_genes(run_component, input_path):
-    run_component([
-        "--input", input_path,
-        "--output", "output-4.h5mu",
-        "--var_gene_names", "gene_symbol",
-        "--max_fraction_mito", "0.2",
-        "--var_name_mitochondrial_genes", "mitochondrial"
-        ])
-    assert Path("output-6.h5mu").is_file()
-    mu_out = mu.read_h5mu("output-4.h5mu")
-    assert "mitochondrial" in mu_out.mod['rna'].var.columns
-
 if __name__ == "__main__":
     exit(pytest.main([__file__]))