| ''' |
| 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) |
|
|
