annotate stacking_ensembles.py @ 39:78a60f884ac9 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8850f42c2c3763e614f7454c9c006f3d2ff572c0
author bgruening
date Fri, 27 May 2022 11:47:11 +0000
parents e76f6dfea5c9
children d769d83ec796
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
1 import argparse
26
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
2 import ast
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
3 import json
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
4 import pickle
26
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
5 import sys
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
6 import warnings
36
420a4bf99244 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 35
diff changeset
7
420a4bf99244 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 35
diff changeset
8 import mlxtend.classifier
420a4bf99244 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 35
diff changeset
9 import mlxtend.regressor
420a4bf99244 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 35
diff changeset
10 import pandas as pd
37
e76f6dfea5c9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
11 from galaxy_ml.utils import (get_cv, get_estimator, get_search_params,
e76f6dfea5c9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
12 load_model)
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
13
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
14 warnings.filterwarnings("ignore")
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
15
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
16 N_JOBS = int(__import__("os").environ.get("GALAXY_SLOTS", 1))
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
17
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
18
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
19 def main(inputs_path, output_obj, base_paths=None, meta_path=None, outfile_params=None):
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
20 """
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
21 Parameter
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
22 ---------
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
23 inputs_path : str
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
24 File path for Galaxy parameters
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
25
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
26 output_obj : str
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
27 File path for ensemble estimator ouput
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
28
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
29 base_paths : str
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
30 File path or paths concatenated by comma.
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
31
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
32 meta_path : str
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
33 File path
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
34
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
35 outfile_params : str
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
36 File path for params output
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
37 """
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
38 with open(inputs_path, "r") as param_handler:
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
39 params = json.load(param_handler)
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
40
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
41 estimator_type = params["algo_selection"]["estimator_type"]
26
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
42 # get base estimators
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
43 base_estimators = []
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
44 for idx, base_file in enumerate(base_paths.split(",")):
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
45 if base_file and base_file != "None":
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
46 with open(base_file, "rb") as handler:
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
47 model = load_model(handler)
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
48 else:
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
49 estimator_json = params["base_est_builder"][idx]["estimator_selector"]
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
50 model = get_estimator(estimator_json)
26
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
51
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
52 if estimator_type.startswith("sklearn"):
26
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
53 named = model.__class__.__name__.lower()
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
54 named = "base_%d_%s" % (idx, named)
26
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
55 base_estimators.append((named, model))
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
56 else:
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
57 base_estimators.append(model)
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
58
26
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
59 # get meta estimator, if applicable
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
60 if estimator_type.startswith("mlxtend"):
26
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
61 if meta_path:
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
62 with open(meta_path, "rb") as f:
26
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
63 meta_estimator = load_model(f)
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
64 else:
37
e76f6dfea5c9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
65 estimator_json = params["algo_selection"]["meta_estimator"][
e76f6dfea5c9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
66 "estimator_selector"
e76f6dfea5c9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
67 ]
26
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
68 meta_estimator = get_estimator(estimator_json)
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
69
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
70 options = params["algo_selection"]["options"]
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
71
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
72 cv_selector = options.pop("cv_selector", None)
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
73 if cv_selector:
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
74 splitter, _groups = get_cv(cv_selector)
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
75 options["cv"] = splitter
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
76 # set n_jobs
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
77 options["n_jobs"] = N_JOBS
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
78
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
79 weights = options.pop("weights", None)
26
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
80 if weights:
29
95d0f81e46e8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents: 28
diff changeset
81 weights = ast.literal_eval(weights)
95d0f81e46e8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents: 28
diff changeset
82 if weights:
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
83 options["weights"] = weights
26
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
84
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
85 mod_and_name = estimator_type.split("_")
26
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
86 mod = sys.modules[mod_and_name[0]]
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
87 klass = getattr(mod, mod_and_name[1])
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
88
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
89 if estimator_type.startswith("sklearn"):
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
90 options["n_jobs"] = N_JOBS
26
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
91 ensemble_estimator = klass(base_estimators, **options)
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
92
9bb505eafac9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
93 elif mod == mlxtend.classifier:
37
e76f6dfea5c9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
94 ensemble_estimator = klass(
e76f6dfea5c9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
95 classifiers=base_estimators, meta_classifier=meta_estimator, **options
e76f6dfea5c9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
96 )
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
97
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
98 else:
37
e76f6dfea5c9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
99 ensemble_estimator = klass(
e76f6dfea5c9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
100 regressors=base_estimators, meta_regressor=meta_estimator, **options
e76f6dfea5c9 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
101 )
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
102
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
103 print(ensemble_estimator)
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
104 for base_est in base_estimators:
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
105 print(base_est)
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
106
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
107 with open(output_obj, "wb") as out_handler:
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
108 pickle.dump(ensemble_estimator, out_handler, pickle.HIGHEST_PROTOCOL)
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
109
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
110 if params["get_params"] and outfile_params:
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
111 results = get_search_params(ensemble_estimator)
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
112 df = pd.DataFrame(results, columns=["", "Parameter", "Value"])
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
113 df.to_csv(outfile_params, sep="\t", index=False)
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
114
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
115
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
116 if __name__ == "__main__":
24
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
117 aparser = argparse.ArgumentParser()
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
118 aparser.add_argument("-b", "--bases", dest="bases")
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
119 aparser.add_argument("-m", "--meta", dest="meta")
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
120 aparser.add_argument("-i", "--inputs", dest="inputs")
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
121 aparser.add_argument("-o", "--outfile", dest="outfile")
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
122 aparser.add_argument("-p", "--outfile_params", dest="outfile_params")
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
123 args = aparser.parse_args()
5552eda109bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
124
35
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
125 main(
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
126 args.inputs,
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
127 args.outfile,
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
128 base_paths=args.bases,
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
129 meta_path=args.meta,
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
130 outfile_params=args.outfile_params,
eeaf989f1024 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 29
diff changeset
131 )