Mercurial > repos > bgruening > ctb_rdkit_descriptors
diff sdf_to_tab.py @ 8:a1c53f0533b0 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 4d0bfcf37bfbedafc7ff0672dfe452766ca8a606"
| author | bgruening |
|---|---|
| date | Wed, 17 Feb 2021 12:59:43 +0000 |
| parents | d68bf44e1f5c |
| children | 0993ac4f4a23 |
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--- a/sdf_to_tab.py Tue Jul 28 08:43:19 2020 -0400 +++ b/sdf_to_tab.py Wed Feb 17 12:59:43 2021 +0000 @@ -1,8 +1,10 @@ #!/usr/bin/env python3 import argparse + import pandas as pd from rdkit import Chem + def sdf_to_tab(vars): mols = Chem.SDMolSupplier(vars.inp, sanitize=False) df = pd.DataFrame() # for output @@ -29,6 +31,7 @@ sorted_cols = sorted(df.columns.values.tolist()) df.to_csv(vars.out, sep='\t', header=vars.header, columns=sorted_cols) + def main(): parser = argparse.ArgumentParser(description="Convert SDF to tabular") parser.add_argument('--inp', '-i', help="The input file", required=True) @@ -41,7 +44,7 @@ parser.add_argument('--name', '-n', action='store_true', help="Include molecule name in output.") sdf_to_tab(parser.parse_args()) - + if __name__ == "__main__": main()