Mercurial > repos > recetox > matchms_formatter
diff formatter.py @ 1:364976b9aba6 draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 67040e686204e86c07ec46ca90129e50e40eb737"
| author | recetox |
|---|---|
| date | Tue, 11 Jan 2022 15:13:57 +0000 |
| parents | 0a08bed94964 |
| children | 4ca9807c56e6 |
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--- a/formatter.py Sat Oct 30 13:48:25 2021 +0000 +++ b/formatter.py Tue Jan 11 15:13:57 2022 +0000 @@ -73,8 +73,8 @@ Returns: DataFrame: Joined dataframe on compounds containing scores an matches in long format. """ - matches = read_csv(matches_filename, sep='\t', index_col=0) - scores = read_csv(scores_filename, sep='\t', index_col=0) + matches = read_csv(matches_filename, sep=None, index_col=0) + scores = read_csv(scores_filename, sep=None, index_col=0) scores_long = create_long_table(scores, 'score') matches_long = create_long_table(matches, 'matches') @@ -113,8 +113,11 @@ @cli.resultcallback() def write_output(result: DataFrame, scores_filename, matches_filename, output_filename): + input_file = read_csv(scores_filename, sep=None, iterator=True) + sep = input_file._engine.data.dialect.delimiter + result = result.reset_index().rename(columns={'level_0': 'query', 'compound': 'reference'}) - result.to_csv(output_filename, sep="\t", index=False) + result.to_csv(output_filename, sep=sep, index=False) if __name__ == '__main__':