annotate train_test_split.py @ 12:f903c8cf1455 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb

import argparse
import json
import warnings
from distutils.version import LooseVersion as Version

import pandas as pd
from galaxy_ml import __version__ as galaxy_ml_version
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
    cv_selector = params["mode_selection"]["cv_selector"]
    if Version(galaxy_ml_version) < Version("0.8.3"):
        cv_selector.pop("n_stratification_bins", None)
    splitter, groups = get_cv(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,
    )