diff --git a/gget/gget_mutate.py b/gget/gget_mutate.py index 52e98647..be1ee34f 100644 --- a/gget/gget_mutate.py +++ b/gget/gget_mutate.py @@ -324,8 +324,8 @@ def mutate( if isinstance(mutation_df, str): mutation_df = pd.read_csv(mutation_df) - logging.info("Extracting mutation types...") # Get all mutation types + tqdm.pandas(desc="Extracting mutation types") mutation_df["mutation_type"] = mutation_df[mut_column].progress_apply( extract_mutation_type ) @@ -367,6 +367,7 @@ def mutate( # Create mutated sequences logging.info("Mutating sequences...") if not mutation_dict["substitution"].empty: + tqdm.pandas(desc="Performing substitutions") mutation_dict["substitution"]["mutant_sequence_kmer"] = mutation_dict[ "substitution" ].progress_apply( @@ -378,6 +379,7 @@ def mutate( axis=1, ) if not mutation_dict["deletion"].empty: + tqdm.pandas(desc="Performing deletions") mutation_dict["deletion"]["mutant_sequence_kmer"] = mutation_dict[ "deletion" ].progress_apply( @@ -389,6 +391,7 @@ def mutate( axis=1, ) if not mutation_dict["delins"].empty: + tqdm.pandas(desc="Performing delins") mutation_dict["delins"]["mutant_sequence_kmer"] = mutation_dict[ "delins" ].progress_apply( @@ -400,6 +403,7 @@ def mutate( axis=1, ) if not mutation_dict["insertion"].empty: + tqdm.pandas(desc="Performing insertions") mutation_dict["insertion"]["mutant_sequence_kmer"] = mutation_dict[ "insertion" ].progress_apply( @@ -411,6 +415,7 @@ def mutate( axis=1, ) if not mutation_dict["duplication"].empty: + tqdm.pandas(desc="Performing duplications") mutation_dict["duplication"]["mutant_sequence_kmer"] = mutation_dict[ "duplication" ].progress_apply( @@ -422,6 +427,7 @@ def mutate( axis=1, ) if not mutation_dict["inversion"].empty: + tqdm.pandas(desc="Performing inversions") mutation_dict["inversion"]["mutant_sequence_kmer"] = mutation_dict[ "inversion" ].progress_apply( @@ -433,6 +439,7 @@ def mutate( axis=1, ) if not mutation_dict["unknown"].empty: + tqdm.pandas(desc="Performing unknown mutations") mutation_dict["unknown"]["mutant_sequence_kmer"] = mutation_dict[ "unknown" ].progress_apply(