| ''' | |
| Converts tblout outputs from hmmer to csv. | |
| ''' | |
| import argparse | |
| import pandas as pd | |
| if __name__ == '__main__': | |
| parser = argparse.ArgumentParser() | |
| parser.add_argument('input_file', type=str) | |
| parser.add_argument('output_file', type=str) | |
| args = parser.parse_args() | |
| column_names=['target', 'accession', 'query_name', 'accession_1', | |
| 'E-value_full', 'score_full', 'bias_full', 'E-value_domain', | |
| 'score_domain', 'bias_domain', 'exp', 'reg', 'clu', 'ov', 'env', 'dom', | |
| 'rep', 'inc', 'target_description'] | |
| df = pd.read_csv(args.input_file, delim_whitespace=True, comment='#', | |
| index_col=False, names=column_names) | |
| df.to_csv(args.output_file, index=False) | |