diff table_pandas_arithmetics.py @ 0:0112f08c95ed draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/tables commit d0ff40eb2b536fec6c973c3a9ea8e7f31cd9a0d6
author recetox
date Wed, 29 Jan 2025 15:36:02 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/table_pandas_arithmetics.py	Wed Jan 29 15:36:02 2025 +0000
@@ -0,0 +1,106 @@
+import argparse
+import logging
+from typing import List, Tuple
+
+
+import numpy as np
+import pandas as pd
+from utils import LoadDataAction, SplitColumnIndicesAction, StoreOutputAction
+
+
+# Constants for operations
+OPERATIONS = {
+    "mul": np.multiply,
+    "sub": np.subtract,
+    "div": np.divide,
+    "add": np.add,
+    "pow": np.power,
+}
+
+
+def perform_operation(df: pd.DataFrame, column_indices: List[int], operation: str, operand: float):
+    """
+    Perform the specified arithmetic operation on the given columns of the dataframe.
+
+    Parameters:
+    df (pd.DataFrame): The input dataframe.
+    column_indices (list): The 0-based indices of the columns to perform the operation on.
+    operation (str): The arithmetic operation to perform.
+    operand (float): The operand for the arithmetic operation.
+
+    Returns:
+    pd.DataFrame: The dataframe with the operation applied.
+    """
+    for column_index in column_indices:
+        column_name = df.columns[column_index]
+        df[column_name] = OPERATIONS[operation](df[column_name], operand)
+    return df
+
+
+def main(input_dataset: pd.DataFrame, column_indices: List[int], operation: str, operand: float, output_dataset: Tuple[callable, str]):
+    """
+    Main function to load the dataset, perform the operation, and save the result.
+
+    Parameters:
+    input_dataset (tuple): The input dataset and its file extension.
+    column_indices (list): The 0-based indices of the columns to perform the operation on.
+    operation (str): The arithmetic operation to perform.
+    operand (float): The operand for the arithmetic operation.
+    output_dataset (tuple): The output dataset and its file extension.
+    """
+    try:
+        df = perform_operation(input_dataset, column_indices, operation, operand)
+        write_func, file_path = output_dataset
+        write_func(df, file_path)
+    except Exception as e:
+        logging.error(f"Error in main function: {e}")
+        raise
+
+
+if __name__ == "__main__":
+    logging.basicConfig(level=logging.INFO)
+    parser = argparse.ArgumentParser(
+        description="Perform arithmetic operations on dataframe columns."
+    )
+    parser.add_argument(
+        "--input_dataset",
+        nargs=2,
+        action=LoadDataAction,
+        required=True,
+        help="Path to the input dataset and its file extension (csv, tsv, parquet)",
+    )
+    parser.add_argument(
+        "--columns",
+        action=SplitColumnIndicesAction,
+        required=True,
+        help="Comma-separated list of 1-based indices of the columns to perform the operation on",
+    )
+    parser.add_argument(
+        "--operation",
+        type=str,
+        choices=OPERATIONS.keys(),
+        required=True,
+        help="Arithmetic operation to perform",
+    )
+    parser.add_argument(
+        "--operand",
+        type=float,
+        required=True,
+        help="Operand for the arithmetic operation",
+    )
+    parser.add_argument(
+        "--output_dataset",
+        nargs=2,
+        action=StoreOutputAction,
+        required=True,
+        help="Path to the output dataset and its file extension (csv, tsv, parquet)",
+    )
+
+    args = parser.parse_args()
+    main(
+        args.input_dataset,
+        args.columns,
+        args.operation,
+        args.operand,
+        args.output_dataset,
+    )