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annotate sdf_to_tab.py @ 0:5c501eb8d56c draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
author bgruening
date Sat, 04 Dec 2021 16:39:31 +0000
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5c501eb8d56c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"
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1 #!/usr/bin/env python3
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2 import argparse
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4 import pandas as pd
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5 from rdkit import Chem
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8 def sdf_to_tab(vars):
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9 mols = Chem.SDMolSupplier(vars.inp, sanitize=False)
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10 df = pd.DataFrame() # for output
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11
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12 for n in range(len(mols)):
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13 if mols[n]:
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14 d = mols[n].GetPropsAsDict()
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15 # filter dict for desired props
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16 if vars.props.strip() == "": # none specified, return all
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17 d = {
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18 prop: val
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19 for (prop, val) in d.items()
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20 if not any(x in str(val) for x in ["\n", "\t"])
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21 } # remove items containing newlines or tabs
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22 else:
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23 d = {
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24 prop: val
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25 for (prop, val) in d.items()
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26 if prop in vars.props.replace(" ", "").split(",")
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27 } # remove items not requested via CLI
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28 if vars.name:
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29 d["SDFMoleculeName"] = mols[n].GetProp("_Name")
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30 if vars.smiles:
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31 d["SMILES"] = Chem.MolToSmiles(mols[n], isomericSmiles=False)
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32 d["Index"] = int(n)
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34 df = df.append(d, ignore_index=True)
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35 else:
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36 print("Molecule could not be read - skipped.")
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37
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38 df = df.astype({"Index": int}).set_index("Index")
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39 sorted_cols = sorted(df.columns.values.tolist())
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40 df.to_csv(vars.out, sep="\t", header=vars.header, columns=sorted_cols)
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43 def main():
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44 parser = argparse.ArgumentParser(description="Convert SDF to tabular")
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45 parser.add_argument("--inp", "-i", help="The input file", required=True)
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46 parser.add_argument("--out", "-o", help="The output file", required=True)
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47 parser.add_argument(
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48 "--props",
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49 "-p",
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50 help="Properties to filter (leave blank for all)",
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51 required=True,
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52 )
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53 parser.add_argument(
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54 "--header",
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55 "-t",
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56 action="store_true",
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57 help="Write property name as the first row.",
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58 )
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59 parser.add_argument(
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60 "--smiles", "-s", action="store_true", help="Include SMILES in output."
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61 )
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62 parser.add_argument(
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63 "--name", "-n", action="store_true", help="Include molecule name in output."
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64 )
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65 sdf_to_tab(parser.parse_args())
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66
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67
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68 if __name__ == "__main__":
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69 main()