diff train_test_split.py @ 0:59e8b4328c82 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/train_test_split.py	Tue Apr 13 22:40:10 2021 +0000
@@ -0,0 +1,166 @@
+import argparse
+import json
+import warnings
+
+import pandas as pd
+from galaxy_ml.model_validations import train_test_split
+from galaxy_ml.utils import get_cv, read_columns
+
+
+def _get_single_cv_split(params, array, infile_labels=None, infile_groups=None):
+    """output (train, test) subset from a cv splitter
+
+    Parameters
+    ----------
+    params : dict
+        Galaxy tool inputs
+    array : pandas DataFrame object
+        The target dataset to split
+    infile_labels : str
+        File path to dataset containing target values
+    infile_groups : str
+        File path to dataset containing group values
+    """
+    y = None
+    groups = None
+
+    nth_split = params["mode_selection"]["nth_split"]
+
+    # read groups
+    if infile_groups:
+        header = "infer" if (params["mode_selection"]["cv_selector"]["groups_selector"]["header_g"]) else None
+        column_option = params["mode_selection"]["cv_selector"]["groups_selector"]["column_selector_options_g"][
+            "selected_column_selector_option_g"
+        ]
+        if column_option in [
+            "by_index_number",
+            "all_but_by_index_number",
+            "by_header_name",
+            "all_but_by_header_name",
+        ]:
+            c = params["mode_selection"]["cv_selector"]["groups_selector"]["column_selector_options_g"]["col_g"]
+        else:
+            c = None
+
+        groups = read_columns(
+            infile_groups,
+            c=c,
+            c_option=column_option,
+            sep="\t",
+            header=header,
+            parse_dates=True,
+        )
+        groups = groups.ravel()
+
+        params["mode_selection"]["cv_selector"]["groups_selector"] = groups
+
+    # read labels
+    if infile_labels:
+        target_input = params["mode_selection"]["cv_selector"].pop("target_input")
+        header = "infer" if target_input["header1"] else None
+        col_index = target_input["col"][0] - 1
+        df = pd.read_csv(infile_labels, sep="\t", header=header, parse_dates=True)
+        y = df.iloc[:, col_index].values
+
+    # construct the cv splitter object
+    splitter, groups = get_cv(params["mode_selection"]["cv_selector"])
+
+    total_n_splits = splitter.get_n_splits(array.values, y=y, groups=groups)
+    if nth_split > total_n_splits:
+        raise ValueError("Total number of splits is {}, but got `nth_split` " "= {}".format(total_n_splits, nth_split))
+
+    i = 1
+    for train_index, test_index in splitter.split(array.values, y=y, groups=groups):
+        # suppose nth_split >= 1
+        if i == nth_split:
+            break
+        else:
+            i += 1
+
+    train = array.iloc[train_index, :]
+    test = array.iloc[test_index, :]
+
+    return train, test
+
+
+def main(
+    inputs,
+    infile_array,
+    outfile_train,
+    outfile_test,
+    infile_labels=None,
+    infile_groups=None,
+):
+    """
+    Parameter
+    ---------
+    inputs : str
+        File path to galaxy tool parameter
+
+    infile_array : str
+        File paths of input arrays separated by comma
+
+    infile_labels : str
+        File path to dataset containing labels
+
+    infile_groups : str
+        File path to dataset containing groups
+
+    outfile_train : str
+        File path to dataset containing train split
+
+    outfile_test : str
+        File path to dataset containing test split
+    """
+    warnings.simplefilter("ignore")
+
+    with open(inputs, "r") as param_handler:
+        params = json.load(param_handler)
+
+    input_header = params["header0"]
+    header = "infer" if input_header else None
+    array = pd.read_csv(infile_array, sep="\t", header=header, parse_dates=True)
+
+    # train test split
+    if params["mode_selection"]["selected_mode"] == "train_test_split":
+        options = params["mode_selection"]["options"]
+        shuffle_selection = options.pop("shuffle_selection")
+        options["shuffle"] = shuffle_selection["shuffle"]
+        if infile_labels:
+            header = "infer" if shuffle_selection["header1"] else None
+            col_index = shuffle_selection["col"][0] - 1
+            df = pd.read_csv(infile_labels, sep="\t", header=header, parse_dates=True)
+            labels = df.iloc[:, col_index].values
+            options["labels"] = labels
+
+        train, test = train_test_split(array, **options)
+
+    # cv splitter
+    else:
+        train, test = _get_single_cv_split(params, array, infile_labels=infile_labels, infile_groups=infile_groups)
+
+    print("Input shape: %s" % repr(array.shape))
+    print("Train shape: %s" % repr(train.shape))
+    print("Test shape: %s" % repr(test.shape))
+    train.to_csv(outfile_train, sep="\t", header=input_header, index=False)
+    test.to_csv(outfile_test, sep="\t", header=input_header, index=False)
+
+
+if __name__ == "__main__":
+    aparser = argparse.ArgumentParser()
+    aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
+    aparser.add_argument("-X", "--infile_array", dest="infile_array")
+    aparser.add_argument("-y", "--infile_labels", dest="infile_labels")
+    aparser.add_argument("-g", "--infile_groups", dest="infile_groups")
+    aparser.add_argument("-o", "--outfile_train", dest="outfile_train")
+    aparser.add_argument("-t", "--outfile_test", dest="outfile_test")
+    args = aparser.parse_args()
+
+    main(
+        args.inputs,
+        args.infile_array,
+        args.outfile_train,
+        args.outfile_test,
+        args.infile_labels,
+        args.infile_groups,
+    )