Mercurial > repos > bgruening > sdf_to_tab

comparison sdf_to_tab.py @ 3:71bc02c59d3a draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a03b1b7b283901a1510562f1e6eba41f70afaac4"
author bgruening
date Mon, 23 Mar 2020 15:57:35 -0400
parents 40ff81f67f5e
children 351fbd750a6d
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2:40ff81f67f5e 3:71bc02c59d3a
24 df = df.append(d, ignore_index=True) 24 df = df.append(d, ignore_index=True)
25 else: 25 else:
26 print("Molecule could not be read - skipped.") 26 print("Molecule could not be read - skipped.")
27 27
28 df = df.astype({'Index': int}).set_index('Index') 28 df = df.astype({'Index': int}).set_index('Index')
29 df.to_csv(vars.out, sep='\t', header=vars.header) 29 sorted_cols = sorted(df.columns.values.tolist())
30 df.to_csv(vars.out, sep='\t', header=vars.header, columns=sorted_cols)
30 31
31 def main(): 32 def main():
32 parser = argparse.ArgumentParser(description="Convert SDF to tabular") 33 parser = argparse.ArgumentParser(description="Convert SDF to tabular")
33 parser.add_argument('--inp', '-i', help="The input file", required=True) 34 parser.add_argument('--inp', '-i', help="The input file", required=True)
34 parser.add_argument('--out', '-o', help="The output file", required=True) 35 parser.add_argument('--out', '-o', help="The output file", required=True)