Mercurial > repos > bgruening > sklearn_model_validation
annotate stacking_ensembles.py @ 38:61e76fb65daf draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
author | bgruening |
---|---|
date | Mon, 02 Oct 2023 09:21:02 +0000 |
parents | 1fe00785190d |
children |
rev | line source |
---|---|
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
1 import argparse |
19
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
2 import ast |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
3 import json |
19
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
4 import sys |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
5 import warnings |
34
1fe00785190d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
30
diff
changeset
|
6 from distutils.version import LooseVersion as Version |
29
de360b57a5ab
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents:
28
diff
changeset
|
7 |
de360b57a5ab
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents:
28
diff
changeset
|
8 import mlxtend.classifier |
de360b57a5ab
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents:
28
diff
changeset
|
9 import mlxtend.regressor |
34
1fe00785190d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
30
diff
changeset
|
10 from galaxy_ml import __version__ as galaxy_ml_version |
1fe00785190d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
30
diff
changeset
|
11 from galaxy_ml.model_persist import dump_model_to_h5, load_model_from_h5 |
1fe00785190d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
30
diff
changeset
|
12 from galaxy_ml.utils import get_cv, get_estimator |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
13 |
28
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
14 warnings.filterwarnings("ignore") |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
15 |
28
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
16 N_JOBS = int(__import__("os").environ.get("GALAXY_SLOTS", 1)) |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
17 |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
18 |
34
1fe00785190d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
30
diff
changeset
|
19 def main(inputs_path, output_obj, base_paths=None, meta_path=None): |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
20 """ |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
21 Parameter |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
22 --------- |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
23 inputs_path : str |
cf9aa11b91c8
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 |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
25 |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
26 output_obj : str |
cf9aa11b91c8
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 |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
28 |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
29 base_paths : str |
cf9aa11b91c8
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. |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
31 |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
32 meta_path : str |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
33 File path |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
34 """ |
28
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
35 with open(inputs_path, "r") as param_handler: |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
36 params = json.load(param_handler) |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
37 |
28
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
38 estimator_type = params["algo_selection"]["estimator_type"] |
19
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
39 # get base estimators |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
40 base_estimators = [] |
28
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
41 for idx, base_file in enumerate(base_paths.split(",")): |
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
42 if base_file and base_file != "None": |
34
1fe00785190d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
30
diff
changeset
|
43 model = load_model_from_h5(base_file) |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
44 else: |
28
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
45 estimator_json = params["base_est_builder"][idx]["estimator_selector"] |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
46 model = get_estimator(estimator_json) |
19
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
47 |
28
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
48 if estimator_type.startswith("sklearn"): |
19
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
49 named = model.__class__.__name__.lower() |
28
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
50 named = "base_%d_%s" % (idx, named) |
19
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
51 base_estimators.append((named, model)) |
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
52 else: |
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
53 base_estimators.append(model) |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
54 |
19
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
55 # get meta estimator, if applicable |
28
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
56 if estimator_type.startswith("mlxtend"): |
19
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
57 if meta_path: |
34
1fe00785190d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
30
diff
changeset
|
58 meta_estimator = load_model_from_h5(meta_path) |
19
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
59 else: |
30
4b359039f09f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
29
diff
changeset
|
60 estimator_json = params["algo_selection"]["meta_estimator"][ |
4b359039f09f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
29
diff
changeset
|
61 "estimator_selector" |
4b359039f09f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
29
diff
changeset
|
62 ] |
19
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
63 meta_estimator = get_estimator(estimator_json) |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
64 |
28
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
65 options = params["algo_selection"]["options"] |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
66 |
28
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
67 cv_selector = options.pop("cv_selector", None) |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
68 if cv_selector: |
34
1fe00785190d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
30
diff
changeset
|
69 if Version(galaxy_ml_version) < Version("0.8.3"): |
1fe00785190d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
30
diff
changeset
|
70 cv_selector.pop("n_stratification_bins", None) |
1fe00785190d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
30
diff
changeset
|
71 splitter, groups = get_cv(cv_selector) |
28
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
72 options["cv"] = splitter |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
73 # set n_jobs |
28
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
74 options["n_jobs"] = N_JOBS |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
75 |
28
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
76 weights = options.pop("weights", None) |
19
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
77 if weights: |
22
95b04e086576
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
21
diff
changeset
|
78 weights = ast.literal_eval(weights) |
95b04e086576
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
21
diff
changeset
|
79 if weights: |
28
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
80 options["weights"] = weights |
19
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
81 |
28
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
82 mod_and_name = estimator_type.split("_") |
19
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
83 mod = sys.modules[mod_and_name[0]] |
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
84 klass = getattr(mod, mod_and_name[1]) |
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
85 |
28
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
86 if estimator_type.startswith("sklearn"): |
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
87 options["n_jobs"] = N_JOBS |
19
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
88 ensemble_estimator = klass(base_estimators, **options) |
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
89 |
efbec977a47d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
17
diff
changeset
|
90 elif mod == mlxtend.classifier: |
30
4b359039f09f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
29
diff
changeset
|
91 ensemble_estimator = klass( |
4b359039f09f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
29
diff
changeset
|
92 classifiers=base_estimators, meta_classifier=meta_estimator, **options |
4b359039f09f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
29
diff
changeset
|
93 ) |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
94 |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
95 else: |
30
4b359039f09f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
29
diff
changeset
|
96 ensemble_estimator = klass( |
4b359039f09f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
29
diff
changeset
|
97 regressors=base_estimators, meta_regressor=meta_estimator, **options |
4b359039f09f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
29
diff
changeset
|
98 ) |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
99 |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
100 print(ensemble_estimator) |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
101 for base_est in base_estimators: |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
102 print(base_est) |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
103 |
34
1fe00785190d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
30
diff
changeset
|
104 dump_model_to_h5(ensemble_estimator, output_obj) |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
105 |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
106 |
28
9b017b0da56e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
22
diff
changeset
|
107 if __name__ == "__main__": |
17
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
108 aparser = argparse.ArgumentParser() |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
109 aparser.add_argument("-b", "--bases", dest="bases") |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
110 aparser.add_argument("-m", "--meta", dest="meta") |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
111 aparser.add_argument("-i", "--inputs", dest="inputs") |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
112 aparser.add_argument("-o", "--outfile", dest="outfile") |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
113 args = aparser.parse_args() |
cf9aa11b91c8
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff
changeset
|
114 |
34
1fe00785190d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
30
diff
changeset
|
115 main(args.inputs, args.outfile, base_paths=args.bases, meta_path=args.meta) |