diff rem_complex.py @ 0:a0e07a0bc047 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex commit 833f7671d1e1b713d52ba5c7e59d28be38b92b1e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rem_complex.py	Mon Nov 27 09:04:04 2023 +0000
@@ -0,0 +1,62 @@
+import argparse
+
+import pandas as pd
+from openbabel import openbabel, pybel
+openbabel.obErrorLog.SetOutputLevel(1)  # 0: suppress warnings; 1: warnings
+
+
+def parse_arguments() -> argparse.Namespace:
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-iformat', '--input_format', help='Input file format')
+    parser.add_argument('-i', '--input_filename', type=str, required=True, help='Input file name')
+    parser.add_argument('-o', '--output_filename', type=str, required=True, help='Outout file name')
+    args = parser.parse_args()
+    return args
+
+
+def filter_csv_molecules(file_name: str, output_file_name: str) -> None:
+    """Removes molecules with '.' in SMILES string from csv file.
+
+    Args:
+        file_name (str): Path to csv file that contains metadata.
+        output_file_name (str): Path to destination file, in csv format.
+    """
+    df = pd.read_csv(file_name)
+    mask = df['smiles'].str.contains(".", na=False, regex=False)
+    mask = mask.apply(lambda x: not x)
+    df[mask].to_csv(output_file_name, index=False)
+
+
+def filter_other_format_molecules(file_name: str, output_file_name: str, input_format: str) -> None:
+    """Removes molecules with '.' in SMILES string from smi or inchi files.
+
+    Args:
+        file_name (str): Path to smi or inchi files.
+        output_file_name (str): Path to destination files, in smi or inchi formats.
+        input_format (str): Input file format.
+    """
+    molecules = list(pybel.readfile(input_format, file_name))
+    filtered_molecules = [mol for mol in molecules if "." not in mol.write('smi').strip()]
+
+    with open(output_file_name, 'w') as f:
+        for mol in filtered_molecules:
+            f.write(mol.write(input_format))
+
+
+def filter_complex_molecules(file_name: str, output_file_name: str, input_format: str) -> None:
+    """Removes molecular complexes depending on the input format.
+
+    Args:
+        file_name (str): Path to csv, smi or inchi files
+        output_file_name (str): Path to destination files, in csv. smi or inchi formats.
+        input_format (str): Input file formats.
+    """
+    if input_format == 'csv':
+        filter_csv_molecules(file_name, output_file_name)
+    else:
+        filter_other_format_molecules(file_name, output_file_name, input_format)
+
+
+if __name__ == "__main__":
+    args = parse_arguments()
+    filter_complex_molecules(args.input_filename, args.output_filename, args.input_format)