diff --git a/tests/test_amr_mutation_parsing.py b/tests/test_amr_mutation_parsing.py index dcdb8ad..76b48fa 100644 --- a/tests/test_amr_mutation_parsing.py +++ b/tests/test_amr_mutation_parsing.py @@ -5,12 +5,19 @@ import pandas as pd from workflow.scripts.compare_aa_mutations import ( - create_locus_tag_gene_dict, filter_for_known_mutations, - filter_for_resistance_genes, merge_resistance_genes_with_ref, - read_input_file, rename_df_resistance_with_impact) + create_locus_tag_gene_dict, + filter_for_known_mutations, + filter_for_resistance_genes, + merge_resistance_genes_with_ref, + read_input_file, + rename_df_resistance_with_impact, +) from workflow.scripts.compare_nt_mutations import ( - combine_exact_matches_and_possible_cnvs, find_exact_matches, - find_large_indels, screen_for_possible_cnv_in_known_regions) + combine_exact_matches_and_possible_cnvs, + find_exact_matches, + find_large_indels, + screen_for_possible_cnv_in_known_regions, +) # init df_mutations with missense SNP and synonymous SNP in the same genetic element, and a large intergenic INDEL (promoter mutation) df_mutations = pd.read_csv("tests/test_files/df_mutations.tsv", sep="\t") @@ -210,13 +217,15 @@ def test_merge_resistance_genes_with_ref(self): resistance_variants_csv=df_aa_resistance_variants, ) df_resistance_with_impact_correct = pd.read_csv( - "tests/test_files/df_resistance_with_impact_correct.tsv", sep="\t", dtype={"AF": str} + "tests/test_files/df_resistance_with_impact_correct.tsv", + sep="\t", + dtype={"AF": str}, ) self.assertEqual(df_resistance_with_impact.shape[0], 2) self.assertEqual(df_resistance_with_impact.shape[1], 14) df_resistance_with_impact.reset_index(drop=True, inplace=True) df_resistance_with_impact_correct.reset_index(drop=True, inplace=True) - + self.assertTrue( df_resistance_with_impact.equals(df_resistance_with_impact_correct) )