diff fitted_model_eval.py @ 0:af2624d5ab32 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fitted_model_eval.py	Sat May 01 01:24:32 2021 +0000
@@ -0,0 +1,183 @@
+import argparse
+import json
+import warnings
+
+import pandas as pd
+from galaxy_ml.utils import get_scoring, load_model, read_columns
+from scipy.io import mmread
+from sklearn.metrics.scorer import _check_multimetric_scoring
+from sklearn.model_selection._validation import _score
+from sklearn.pipeline import Pipeline
+
+
+def _get_X_y(params, infile1, infile2):
+    """read from inputs and output X and y
+
+    Parameters
+    ----------
+    params : dict
+        Tool inputs parameter
+    infile1 : str
+        File path to dataset containing features
+    infile2 : str
+        File path to dataset containing target values
+
+    """
+    # store read dataframe object
+    loaded_df = {}
+
+    input_type = params["input_options"]["selected_input"]
+    # tabular input
+    if input_type == "tabular":
+        header = "infer" if params["input_options"]["header1"] else None
+        column_option = params["input_options"]["column_selector_options_1"][
+            "selected_column_selector_option"
+        ]
+        if column_option in [
+            "by_index_number",
+            "all_but_by_index_number",
+            "by_header_name",
+            "all_but_by_header_name",
+        ]:
+            c = params["input_options"]["column_selector_options_1"]["col1"]
+        else:
+            c = None
+
+        df_key = infile1 + repr(header)
+        df = pd.read_csv(infile1, sep="\t", header=header, parse_dates=True)
+        loaded_df[df_key] = df
+
+        X = read_columns(df, c=c, c_option=column_option).astype(float)
+    # sparse input
+    elif input_type == "sparse":
+        X = mmread(open(infile1, "r"))
+
+    # Get target y
+    header = "infer" if params["input_options"]["header2"] else None
+    column_option = params["input_options"]["column_selector_options_2"][
+        "selected_column_selector_option2"
+    ]
+    if column_option in [
+        "by_index_number",
+        "all_but_by_index_number",
+        "by_header_name",
+        "all_but_by_header_name",
+    ]:
+        c = params["input_options"]["column_selector_options_2"]["col2"]
+    else:
+        c = None
+
+    df_key = infile2 + repr(header)
+    if df_key in loaded_df:
+        infile2 = loaded_df[df_key]
+    else:
+        infile2 = pd.read_csv(infile2, sep="\t", header=header, parse_dates=True)
+        loaded_df[df_key] = infile2
+
+    y = read_columns(
+        infile2, c=c, c_option=column_option, sep="\t", header=header, parse_dates=True
+    )
+    if len(y.shape) == 2 and y.shape[1] == 1:
+        y = y.ravel()
+
+    return X, y
+
+
+def main(
+    inputs,
+    infile_estimator,
+    outfile_eval,
+    infile_weights=None,
+    infile1=None,
+    infile2=None,
+):
+    """
+    Parameter
+    ---------
+    inputs : str
+        File path to galaxy tool parameter
+
+    infile_estimator : strgit
+        File path to trained estimator input
+
+    outfile_eval : str
+        File path to save the evalulation results, tabular
+
+    infile_weights : str
+        File path to weights input
+
+    infile1 : str
+        File path to dataset containing features
+
+    infile2 : str
+        File path to dataset containing target values
+    """
+    warnings.filterwarnings("ignore")
+
+    with open(inputs, "r") as param_handler:
+        params = json.load(param_handler)
+
+    X_test, y_test = _get_X_y(params, infile1, infile2)
+
+    # load model
+    with open(infile_estimator, "rb") as est_handler:
+        estimator = load_model(est_handler)
+
+    main_est = estimator
+    if isinstance(estimator, Pipeline):
+        main_est = estimator.steps[-1][-1]
+    if hasattr(main_est, "config") and hasattr(main_est, "load_weights"):
+        if not infile_weights or infile_weights == "None":
+            raise ValueError(
+                "The selected model skeleton asks for weights, "
+                "but no dataset for weights was provided!"
+            )
+        main_est.load_weights(infile_weights)
+
+    # handle scorer, convert to scorer dict
+    # Check if scoring is specified
+    scoring = params["scoring"]
+    if scoring is not None:
+        # get_scoring() expects secondary_scoring to be a comma separated string (not a list)
+        # Check if secondary_scoring is specified
+        secondary_scoring = scoring.get("secondary_scoring", None)
+        if secondary_scoring is not None:
+            # If secondary_scoring is specified, convert the list into comman separated string
+            scoring["secondary_scoring"] = ",".join(scoring["secondary_scoring"])
+
+    scorer = get_scoring(scoring)
+    scorer, _ = _check_multimetric_scoring(estimator, scoring=scorer)
+
+    if hasattr(estimator, "evaluate"):
+        scores = estimator.evaluate(
+            X_test, y_test=y_test, scorer=scorer, is_multimetric=True
+        )
+    else:
+        scores = _score(estimator, X_test, y_test, scorer, is_multimetric=True)
+
+    # handle output
+    for name, score in scores.items():
+        scores[name] = [score]
+    df = pd.DataFrame(scores)
+    df = df[sorted(df.columns)]
+    df.to_csv(path_or_buf=outfile_eval, sep="\t", header=True, index=False)
+
+
+if __name__ == "__main__":
+    aparser = argparse.ArgumentParser()
+    aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
+    aparser.add_argument("-e", "--infile_estimator", dest="infile_estimator")
+    aparser.add_argument("-w", "--infile_weights", dest="infile_weights")
+    aparser.add_argument("-X", "--infile1", dest="infile1")
+    aparser.add_argument("-y", "--infile2", dest="infile2")
+    aparser.add_argument("-O", "--outfile_eval", dest="outfile_eval")
+    args = aparser.parse_args()
+
+    main(
+        args.inputs,
+        args.infile_estimator,
+        args.outfile_eval,
+        infile_weights=args.infile_weights,
+        infile1=args.infile1,
+        infile2=args.infile2,
+    )