sklearn_pairwise_metrics: stacking

annotate stacking_ensembles.py @ 32:3afb10806f52 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"

author	bgruening
date	Wed, 02 Oct 2019 03:23:25 -0400
parents	ccba8508142e
children	65ce373f4d4b

rev	line source
28 a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	1 import argparse
30 ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	2 import ast
28 a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	3 import json
30 ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	4 import mlxtend.regressor
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	5 import mlxtend.classifier
28 a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	6 import pandas as pd
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	7 import pickle
30 ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	8 import sklearn
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	9 import sys
28 a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	10 import warnings
30 ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	11 from sklearn import ensemble
28 a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	12
30 ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	13 from galaxy_ml.utils import (load_model, get_cv, get_estimator,
32 3afb10806f52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty" bgruening parents: 30 diff changeset	14 get_search_params)
28 a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	15
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	16
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	17 warnings.filterwarnings('ignore')
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	18
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	19 N_JOBS = int(__import__('os').environ.get('GALAXY_SLOTS', 1))
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	20
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	21
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	22 def main(inputs_path, output_obj, base_paths=None, meta_path=None,
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	23 outfile_params=None):
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	24 """
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	25 Parameter
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	26 ---------
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	27 inputs_path : str
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	28 File path for Galaxy parameters
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	29
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	30 output_obj : str
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	31 File path for ensemble estimator ouput
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	32
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	33 base_paths : str
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	34 File path or paths concatenated by comma.
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	35
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	36 meta_path : str
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	37 File path
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	38
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	39 outfile_params : str
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	40 File path for params output
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	41 """
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	42 with open(inputs_path, 'r') as param_handler:
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	43 params = json.load(param_handler)
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	44
30 ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	45 estimator_type = params['algo_selection']['estimator_type']
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	46 # get base estimators
28 a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	47 base_estimators = []
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	48 for idx, base_file in enumerate(base_paths.split(',')):
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	49 if base_file and base_file != 'None':
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	50 with open(base_file, 'rb') as handler:
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	51 model = load_model(handler)
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	52 else:
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	53 estimator_json = (params['base_est_builder'][idx]
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	54 ['estimator_selector'])
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	55 model = get_estimator(estimator_json)
30 ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	56
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	57 if estimator_type.startswith('sklearn'):
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	58 named = model.__class__.__name__.lower()
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	59 named = 'base_%d_%s' % (idx, named)
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	60 base_estimators.append((named, model))
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	61 else:
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	62 base_estimators.append(model)
28 a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	63
30 ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	64 # get meta estimator, if applicable
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	65 if estimator_type.startswith('mlxtend'):
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	66 if meta_path:
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	67 with open(meta_path, 'rb') as f:
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	68 meta_estimator = load_model(f)
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	69 else:
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	70 estimator_json = (params['algo_selection']
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	71 ['meta_estimator']['estimator_selector'])
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	72 meta_estimator = get_estimator(estimator_json)
28 a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	73
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	74 options = params['algo_selection']['options']
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	75
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	76 cv_selector = options.pop('cv_selector', None)
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	77 if cv_selector:
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	78 splitter, groups = get_cv(cv_selector)
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	79 options['cv'] = splitter
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	80 # set n_jobs
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	81 options['n_jobs'] = N_JOBS
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	82
30 ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	83 weights = options.pop('weights', None)
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	84 if weights:
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	85 options['weights'] = ast.literal_eval(weights)
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	86
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	87 mod_and_name = estimator_type.split('_')
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	88 mod = sys.modules[mod_and_name[0]]
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	89 klass = getattr(mod, mod_and_name[1])
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	90
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	91 if estimator_type.startswith('sklearn'):
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	92 options['n_jobs'] = N_JOBS
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	93 ensemble_estimator = klass(base_estimators, **options)
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	94
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	95 elif mod == mlxtend.classifier:
ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	96 ensemble_estimator = klass(
28 a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	97 classifiers=base_estimators,
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	98 meta_classifier=meta_estimator,
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	99 **options)
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	100
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	101 else:
30 ccba8508142e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty bgruening parents: 28 diff changeset	102 ensemble_estimator = klass(
28 a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	103 regressors=base_estimators,
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	104 meta_regressor=meta_estimator,
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	105 **options)
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	106
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	107 print(ensemble_estimator)
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	108 for base_est in base_estimators:
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	109 print(base_est)
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	110
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	111 with open(output_obj, 'wb') as out_handler:
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	112 pickle.dump(ensemble_estimator, out_handler, pickle.HIGHEST_PROTOCOL)
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	113
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	114 if params['get_params'] and outfile_params:
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	115 results = get_search_params(ensemble_estimator)
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	116 df = pd.DataFrame(results, columns=['', 'Parameter', 'Value'])
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	117 df.to_csv(outfile_params, sep='\t', index=False)
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	118
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	119
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	120 if __name__ == '__main__':
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	121 aparser = argparse.ArgumentParser()
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	122 aparser.add_argument("-b", "--bases", dest="bases")
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	123 aparser.add_argument("-m", "--meta", dest="meta")
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	124 aparser.add_argument("-i", "--inputs", dest="inputs")
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	125 aparser.add_argument("-o", "--outfile", dest="outfile")
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	126 aparser.add_argument("-p", "--outfile_params", dest="outfile_params")
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	127 args = aparser.parse_args()
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	128
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	129 main(args.inputs, args.outfile, base_paths=args.bases,
a30fa9604c09 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7 bgruening parents: diff changeset	130 meta_path=args.meta, outfile_params=args.outfile_params)

Mercurial > repos > bgruening > sklearn_pairwise_metrics

annotate stacking_ensembles.py @ 32:3afb10806f52 draft