diff --git a/lusSTR/wrappers/snps_convert.py b/lusSTR/wrappers/snps_convert.py index 4342936..ad73276 100644 --- a/lusSTR/wrappers/snps_convert.py +++ b/lusSTR/wrappers/snps_convert.py @@ -30,7 +30,6 @@ def kintelligence_filtering(input): def create_output_table(sample_df, orientation, separate, output_type, software): - allele_des = {"A": "1", "C": "2", "G": "3", "T": "4"} if orientation == "uas": allele_col = "UAS_Allele" else: @@ -41,7 +40,6 @@ def create_output_table(sample_df, orientation, separate, output_type, software) compiled_table = create_sample_df(indiv_df, output_type, allele_col) if software != "uas": compiled_table = check_allele_calls(compiled_table, output_type) - compiled_table = compiled_table.replace(allele_des) compiled_table.insert(0, "Sample.Name", sample) all_samples_df = pd.concat([all_samples_df, compiled_table]) if separate: @@ -187,11 +185,11 @@ def main(input, output, kit, strand, separate, refs, software, thresh): ref_samples = results[results["SampleID"].isin([refs])] if len(ref_samples) > 0: ref_table = create_output_table(ref_samples, strand, separate, "reference", software) - ref_table.to_csv(f"{output_name}_snp_reference.csv", index=False, sep="\t") + ref_table.to_csv(f"{output_name}_snp_reference.tsv", index=False, sep="\t") evid_samples = results[~results.SampleID.isin(ref_ids)] if len(evid_samples) > 0: evid_table = create_output_table(evid_samples, strand, separate, "evidence", software) - evid_table.to_csv(f"{output}_snp_evidence.csv", index=False, sep="\t") + evid_table.to_csv(f"{output}_snp_evidence.tsv", index=False, sep="\t") if __name__ == "__main__":