diff --git a/recognizer.py b/recognizer.py index cde2dd5..8cc5513 100644 --- a/recognizer.py +++ b/recognizer.py @@ -379,10 +379,9 @@ def main(): for db_group in database_groups: # run annotation with rps-blast and database timed_message('Running annotation with RPS-BLAST and {} database as reference.'.format(db_group[0])) - ''' run_rpsblast(args.file, '{}/{}_aligned.blast'.format(args.output, db_group[0]), ' '.join(db_group[1]), threads=args.threads, max_target_seqs=args.max_target_seqs) - ''' + if inputted_db: exit() @@ -452,7 +451,7 @@ def main(): ).reset_index().rename(columns={0: 'count'}) cog_quantification.to_excel('{}/COG_quantification.xlsx'.format(args.output)) cog_quantification[['count'] + cog_quantification.columns.tolist()[:-1]].to_csv( - '{}/COG_quantification.tsv'.format(args.output), sep='\t') + '{}/COG_quantification.tsv'.format(args.output), sep='\t', index=False, header=None) create_krona_plot('{}/krona.tsv'.format(args.output), '{}/cog_quantification.html'.format(args.output)) cols += blast_cols