annotate stacking_ensembles.py @ 0:0985b0dd6f1a draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"

import argparse
import ast
import json
import mlxtend.regressor
import mlxtend.classifier
import pandas as pd
import pickle
import sklearn
import sys
import warnings
from sklearn import ensemble

from galaxy_ml.utils import (load_model, get_cv, get_estimator,
                             get_search_params)


warnings.filterwarnings('ignore')

N_JOBS = int(__import__('os').environ.get('GALAXY_SLOTS', 1))


def main(inputs_path, output_obj, base_paths=None, meta_path=None,
         outfile_params=None):
    """
    Parameter
    ---------
    inputs_path : str
        File path for Galaxy parameters

    output_obj : str
        File path for ensemble estimator ouput

    base_paths : str
        File path or paths concatenated by comma.

    meta_path : str
        File path

    outfile_params : str
        File path for params output
    """
    with open(inputs_path, 'r') as param_handler:
        params = json.load(param_handler)

    estimator_type = params['algo_selection']['estimator_type']
    # get base estimators
    base_estimators = []
    for idx, base_file in enumerate(base_paths.split(',')):
        if base_file and base_file != 'None':
            with open(base_file, 'rb') as handler:
                model = load_model(handler)
        else:
            estimator_json = (params['base_est_builder'][idx]
                              ['estimator_selector'])
            model = get_estimator(estimator_json)

        if estimator_type.startswith('sklearn'):
            named = model.__class__.__name__.lower()
            named = 'base_%d_%s' % (idx, named)
            base_estimators.append((named, model))
        else:
            base_estimators.append(model)

    # get meta estimator, if applicable
    if estimator_type.startswith('mlxtend'):
        if meta_path:
            with open(meta_path, 'rb') as f:
                meta_estimator = load_model(f)
        else:
            estimator_json = (params['algo_selection']
                              ['meta_estimator']['estimator_selector'])
            meta_estimator = get_estimator(estimator_json)

    options = params['algo_selection']['options']

    cv_selector = options.pop('cv_selector', None)
    if cv_selector:
        splitter, groups = get_cv(cv_selector)
        options['cv'] = splitter
        # set n_jobs
        options['n_jobs'] = N_JOBS

    weights = options.pop('weights', None)
    if weights:
        weights = ast.literal_eval(weights)
        if weights:
            options['weights'] = weights

    mod_and_name = estimator_type.split('_')
    mod = sys.modules[mod_and_name[0]]
    klass = getattr(mod, mod_and_name[1])

    if estimator_type.startswith('sklearn'):
        options['n_jobs'] = N_JOBS
        ensemble_estimator = klass(base_estimators, **options)

    elif mod == mlxtend.classifier:
        ensemble_estimator = klass(
            classifiers=base_estimators,
            meta_classifier=meta_estimator,
            **options)

    else:
        ensemble_estimator = klass(
            regressors=base_estimators,
            meta_regressor=meta_estimator,
            **options)

    print(ensemble_estimator)
    for base_est in base_estimators:
        print(base_est)

    with open(output_obj, 'wb') as out_handler:
        pickle.dump(ensemble_estimator, out_handler, pickle.HIGHEST_PROTOCOL)

    if params['get_params'] and outfile_params:
        results = get_search_params(ensemble_estimator)
        df = pd.DataFrame(results, columns=['', 'Parameter', 'Value'])
        df.to_csv(outfile_params, sep='\t', index=False)


if __name__ == '__main__':
    aparser = argparse.ArgumentParser()
    aparser.add_argument("-b", "--bases", dest="bases")
    aparser.add_argument("-m", "--meta", dest="meta")
    aparser.add_argument("-i", "--inputs", dest="inputs")
    aparser.add_argument("-o", "--outfile", dest="outfile")
    aparser.add_argument("-p", "--outfile_params", dest="outfile_params")
    args = aparser.parse_args()

    main(args.inputs, args.outfile, base_paths=args.bases,
         meta_path=args.meta, outfile_params=args.outfile_params)