diff --git a/process.py b/process.py index 6abf15d..68d4152 100644 --- a/process.py +++ b/process.py @@ -86,6 +86,7 @@ def get_config(config_file, database): if type(config_dict) is dict: try: config_dict = config_dict['Submission'] + return config_dict except: print("Error: there is no Submission information in the config file.", file=sys.stderr) sys.exit(1) @@ -274,7 +275,7 @@ def process_fasta_samples(metadata, fasta_file): # Check duplicates in fasta_df duplicated_df = fasta_df[fasta_df.duplicated(subset = ["fasta_name_orig"], keep = False)] if not duplicated_df.empty: - print("Error: Sequences in fasta file must be unique at: " + fasta_file + "\nDuplicate Sequences\n" + df["fasta_sequence_orig"].to_string(index=False), file=sys.stderr) + print("Error: Sequences in fasta file must be unique at: " + fasta_file + "\nDuplicate Sequences\n" + fasta_df["fasta_name_orig"].to_string(index=False), file=sys.stderr) sys.exit(1) # Validate duplicates don't appear on merge try: