Mercurial > repos > bgruening > sklearn_data_preprocess

annotate keras_train_and_eval.py @ 46:761269451e98 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sun, 05 Nov 2023 15:52:21 +0000
parents 29e863d1491e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
1 import argparse
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
2 import json
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
3 import os
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
4 import warnings
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
5 from itertools import chain
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
6
36
b75cae00f980 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 35
diff changeset
7 import joblib
b75cae00f980 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 35
diff changeset
8 import numpy as np
b75cae00f980 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 35
diff changeset
9 import pandas as pd
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
10 from galaxy_ml.keras_galaxy_models import (
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
11 _predict_generator,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
12 KerasGBatchClassifier,
45
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
13 KerasGClassifier,
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
14 KerasGRegressor
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
15 )
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
16 from galaxy_ml.model_persist import dump_model_to_h5, load_model_from_h5
36
b75cae00f980 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 35
diff changeset
17 from galaxy_ml.model_validations import train_test_split
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
18 from galaxy_ml.utils import (
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
19 clean_params,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
20 gen_compute_scores,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
21 get_main_estimator,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
22 get_module,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
23 get_scoring,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
24 read_columns,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
25 SafeEval
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
26 )
36
b75cae00f980 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 35
diff changeset
27 from scipy.io import mmread
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
28 from sklearn.metrics._scorer import _check_multimetric_scoring
36
b75cae00f980 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 35
diff changeset
29 from sklearn.model_selection._validation import _score
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
30 from sklearn.utils import _safe_indexing, indexable
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
31
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
32 N_JOBS = int(os.environ.get("GALAXY_SLOTS", 1))
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
33 CACHE_DIR = os.path.join(os.getcwd(), "cached")
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
34 NON_SEARCHABLE = (
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
35 "n_jobs",
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
36 "pre_dispatch",
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
37 "memory",
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
38 "_path",
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
39 "_dir",
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
40 "nthread",
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
41 "callbacks",
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
42 )
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
43 ALLOWED_CALLBACKS = (
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
44 "EarlyStopping",
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
45 "TerminateOnNaN",
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
46 "ReduceLROnPlateau",
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
47 "CSVLogger",
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
48 "None",
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
49 )
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
50
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
51
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
52 def _eval_swap_params(params_builder):
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
53 swap_params = {}
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
54
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
55 for p in params_builder["param_set"]:
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
56 swap_value = p["sp_value"].strip()
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
57 if swap_value == "":
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
58 continue
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
59
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
60 param_name = p["sp_name"]
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
61 if param_name.lower().endswith(NON_SEARCHABLE):
37
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
62 warnings.warn(
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
63 "Warning: `%s` is not eligible for search and was "
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
64 "omitted!" % param_name
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
65 )
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
66 continue
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
67
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
68 if not swap_value.startswith(":"):
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
69 safe_eval = SafeEval(load_scipy=True, load_numpy=True)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
70 ev = safe_eval(swap_value)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
71 else:
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
72 # Have `:` before search list, asks for estimator evaluatio
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
73 safe_eval_es = SafeEval(load_estimators=True)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
74 swap_value = swap_value[1:].strip()
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
75 # TODO maybe add regular express check
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
76 ev = safe_eval_es(swap_value)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
77
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
78 swap_params[param_name] = ev
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
79
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
80 return swap_params
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
81
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
82
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
83 def train_test_split_none(*arrays, **kwargs):
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
84 """extend train_test_split to take None arrays
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
85 and support split by group names.
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
86 """
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
87 nones = []
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
88 new_arrays = []
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
89 for idx, arr in enumerate(arrays):
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
90 if arr is None:
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
91 nones.append(idx)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
92 else:
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
93 new_arrays.append(arr)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
94
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
95 if kwargs["shuffle"] == "None":
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
96 kwargs["shuffle"] = None
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
97
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
98 group_names = kwargs.pop("group_names", None)
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
99
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
100 if group_names is not None and group_names.strip():
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
101 group_names = [name.strip() for name in group_names.split(",")]
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
102 new_arrays = indexable(*new_arrays)
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
103 groups = kwargs["labels"]
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
104 n_samples = new_arrays[0].shape[0]
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
105 index_arr = np.arange(n_samples)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
106 test = index_arr[np.isin(groups, group_names)]
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
107 train = index_arr[~np.isin(groups, group_names)]
37
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
108 rval = list(
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
109 chain.from_iterable(
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
110 (_safe_indexing(a, train), _safe_indexing(a, test)) for a in new_arrays
37
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
111 )
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
112 )
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
113 else:
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
114 rval = train_test_split(*new_arrays, **kwargs)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
115
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
116 for pos in nones:
36
b75cae00f980 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 35
diff changeset
117 rval[pos * 2: 2] = [None, None]
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
118
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
119 return rval
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
120
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
121
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
122 def _evaluate_keras_and_sklearn_scores(
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
123 estimator,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
124 data_generator,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
125 X,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
126 y=None,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
127 sk_scoring=None,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
128 steps=None,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
129 batch_size=32,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
130 return_predictions=False,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
131 ):
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
132 """output scores for bother keras and sklearn metrics
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
133
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
134 Parameters
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
135 -----------
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
136 estimator : object
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
137 Fitted `galaxy_ml.keras_galaxy_models.KerasGBatchClassifier`.
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
138 data_generator : object
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
139 From `galaxy_ml.preprocessors.ImageDataFrameBatchGenerator`.
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
140 X : 2-D array
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
141 Contains indecies of images that need to be evaluated.
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
142 y : None
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
143 Target value.
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
144 sk_scoring : dict
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
145 Galaxy tool input parameters.
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
146 steps : integer or None
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
147 Evaluation/prediction steps before stop.
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
148 batch_size : integer
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
149 Number of samples in a batch
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
150 return_predictions : bool, default is False
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
151 Whether to return predictions and true labels.
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
152 """
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
153 scores = {}
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
154
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
155 generator = data_generator.flow(X, y=y, batch_size=batch_size)
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
156 # keras metrics evaluation
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
157 # handle scorer, convert to scorer dict
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
158 generator.reset()
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
159 score_results = estimator.model_.evaluate_generator(generator, steps=steps)
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
160 metrics_names = estimator.model_.metrics_names
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
161 if not isinstance(metrics_names, list):
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
162 scores[metrics_names] = score_results
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
163 else:
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
164 scores = dict(zip(metrics_names, score_results))
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
165
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
166 if sk_scoring["primary_scoring"] == "default" and not return_predictions:
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
167 return scores
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
168
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
169 generator.reset()
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
170 predictions, y_true = _predict_generator(estimator.model_, generator, steps=steps)
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
171
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
172 # for sklearn metrics
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
173 if sk_scoring["primary_scoring"] != "default":
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
174 scorer = get_scoring(sk_scoring)
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
175 if not isinstance(scorer, (dict, list)):
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
176 scorer = [sk_scoring["primary_scoring"]]
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
177 scorer = _check_multimetric_scoring(estimator, scoring=scorer)
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
178 sk_scores = gen_compute_scores(y_true, predictions, scorer)
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
179 scores.update(sk_scores)
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
180
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
181 if return_predictions:
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
182 return scores, predictions, y_true
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
183 else:
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
184 return scores, None, None
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
185
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
186
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
187 def main(
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
188 inputs,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
189 infile_estimator,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
190 infile1,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
191 infile2,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
192 outfile_result,
44
6c030fe29722 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 41
diff changeset
193 outfile_history=None,
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
194 outfile_object=None,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
195 outfile_y_true=None,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
196 outfile_y_preds=None,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
197 groups=None,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
198 ref_seq=None,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
199 intervals=None,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
200 targets=None,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
201 fasta_path=None,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
202 ):
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
203 """
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
204 Parameter
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
205 ---------
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
206 inputs : str
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
207 File path to galaxy tool parameter.
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
208
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
209 infile_estimator : str
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
210 File path to estimator.
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
211
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
212 infile1 : str
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
213 File path to dataset containing features.
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
214
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
215 infile2 : str
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
216 File path to dataset containing target values.
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
217
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
218 outfile_result : str
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
219 File path to save the results, either cv_results or test result.
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
220
44
6c030fe29722 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 41
diff changeset
221 outfile_history : str, optional
6c030fe29722 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 41
diff changeset
222 File path to save the training history.
6c030fe29722 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 41
diff changeset
223
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
224 outfile_object : str, optional
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
225 File path to save searchCV object.
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
226
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
227 outfile_y_true : str, optional
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
228 File path to target values for prediction.
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
229
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
230 outfile_y_preds : str, optional
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
231 File path to save predictions.
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
232
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
233 groups : str
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
234 File path to dataset containing groups labels.
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
235
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
236 ref_seq : str
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
237 File path to dataset containing genome sequence file.
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
238
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
239 intervals : str
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
240 File path to dataset containing interval file.
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
241
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
242 targets : str
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
243 File path to dataset compressed target bed file.
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
244
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
245 fasta_path : str
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
246 File path to dataset containing fasta file.
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
247 """
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
248 warnings.simplefilter("ignore")
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
249
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
250 with open(inputs, "r") as param_handler:
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
251 params = json.load(param_handler)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
252
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
253 # load estimator
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
254 estimator = load_model_from_h5(infile_estimator)
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
255
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
256 estimator = clean_params(estimator)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
257
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
258 # swap hyperparameter
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
259 swapping = params["experiment_schemes"]["hyperparams_swapping"]
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
260 swap_params = _eval_swap_params(swapping)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
261 estimator.set_params(**swap_params)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
262 estimator_params = estimator.get_params()
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
263 # store read dataframe object
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
264 loaded_df = {}
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
265
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
266 input_type = params["input_options"]["selected_input"]
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
267 # tabular input
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
268 if input_type == "tabular":
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
269 header = "infer" if params["input_options"]["header1"] else None
37
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
270 column_option = params["input_options"]["column_selector_options_1"][
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
271 "selected_column_selector_option"
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
272 ]
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
273 if column_option in [
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
274 "by_index_number",
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
275 "all_but_by_index_number",
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
276 "by_header_name",
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
277 "all_but_by_header_name",
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
278 ]:
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
279 c = params["input_options"]["column_selector_options_1"]["col1"]
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
280 else:
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
281 c = None
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
282
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
283 df_key = infile1 + repr(header)
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
284 df = pd.read_csv(infile1, sep="\t", header=header, parse_dates=True)
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
285 loaded_df[df_key] = df
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
286
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
287 X = read_columns(df, c=c, c_option=column_option).astype(float)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
288 # sparse input
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
289 elif input_type == "sparse":
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
290 X = mmread(open(infile1, "r"))
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
291
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
292 # fasta_file input
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
293 elif input_type == "seq_fasta":
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
294 pyfaidx = get_module("pyfaidx")
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
295 sequences = pyfaidx.Fasta(fasta_path)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
296 n_seqs = len(sequences.keys())
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
297 X = np.arange(n_seqs)[:, np.newaxis]
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
298 for param in estimator_params.keys():
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
299 if param.endswith("fasta_path"):
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
300 estimator.set_params(**{param: fasta_path})
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
301 break
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
302 else:
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
303 raise ValueError(
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
304 "The selected estimator doesn't support "
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
305 "fasta file input! Please consider using "
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
306 "KerasGBatchClassifier with "
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
307 "FastaDNABatchGenerator/FastaProteinBatchGenerator "
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
308 "or having GenomeOneHotEncoder/ProteinOneHotEncoder "
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
309 "in pipeline!"
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
310 )
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
311
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
312 elif input_type == "refseq_and_interval":
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
313 path_params = {
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
314 "data_batch_generator__ref_genome_path": ref_seq,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
315 "data_batch_generator__intervals_path": intervals,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
316 "data_batch_generator__target_path": targets,
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
317 }
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
318 estimator.set_params(**path_params)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
319 n_intervals = sum(1 for line in open(intervals))
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
320 X = np.arange(n_intervals)[:, np.newaxis]
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
321
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
322 # Get target y
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
323 header = "infer" if params["input_options"]["header2"] else None
37
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
324 column_option = params["input_options"]["column_selector_options_2"][
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
325 "selected_column_selector_option2"
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
326 ]
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
327 if column_option in [
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
328 "by_index_number",
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
329 "all_but_by_index_number",
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
330 "by_header_name",
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
331 "all_but_by_header_name",
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
332 ]:
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
333 c = params["input_options"]["column_selector_options_2"]["col2"]
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
334 else:
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
335 c = None
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
336
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
337 df_key = infile2 + repr(header)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
338 if df_key in loaded_df:
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
339 infile2 = loaded_df[df_key]
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
340 else:
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
341 infile2 = pd.read_csv(infile2, sep="\t", header=header, parse_dates=True)
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
342 loaded_df[df_key] = infile2
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
343
37
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
344 y = read_columns(
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
345 infile2,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
346 c=c,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
347 c_option=column_option,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
348 sep="\t",
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
349 header=header,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
350 parse_dates=True,
37
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
351 )
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
352 if len(y.shape) == 2 and y.shape[1] == 1:
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
353 y = y.ravel()
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
354 if input_type == "refseq_and_interval":
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
355 estimator.set_params(data_batch_generator__features=y.ravel().tolist())
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
356 y = None
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
357 # end y
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
358
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
359 # load groups
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
360 if groups:
37
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
361 groups_selector = (
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
362 params["experiment_schemes"]["test_split"]["split_algos"]
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
363 ).pop("groups_selector")
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
364
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
365 header = "infer" if groups_selector["header_g"] else None
37
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
366 column_option = groups_selector["column_selector_options_g"][
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
367 "selected_column_selector_option_g"
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
368 ]
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
369 if column_option in [
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
370 "by_index_number",
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
371 "all_but_by_index_number",
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
372 "by_header_name",
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
373 "all_but_by_header_name",
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
374 ]:
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
375 c = groups_selector["column_selector_options_g"]["col_g"]
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
376 else:
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
377 c = None
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
378
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
379 df_key = groups + repr(header)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
380 if df_key in loaded_df:
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
381 groups = loaded_df[df_key]
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
382
37
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
383 groups = read_columns(
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
384 groups,
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
385 c=c,
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
386 c_option=column_option,
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
387 sep="\t",
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
388 header=header,
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
389 parse_dates=True,
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
390 )
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
391 groups = groups.ravel()
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
392
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
393 # del loaded_df
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
394 del loaded_df
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
395
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
396 # cache iraps_core fits could increase search speed significantly
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
397 memory = joblib.Memory(location=CACHE_DIR, verbose=0)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
398 main_est = get_main_estimator(estimator)
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
399 if main_est.__class__.__name__ == "IRAPSClassifier":
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
400 main_est.set_params(memory=memory)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
401
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
402 # handle scorer, convert to scorer dict
37
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
403 scoring = params["experiment_schemes"]["metrics"]["scoring"]
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
404 scorer = get_scoring(scoring)
45
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
405
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
406 # We get 'None' back from the call to 'get_scoring()' if
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
407 # the primary scoring is 'default'. Replace 'default' with
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
408 # the default scoring for classification/regression (accuracy/r2)
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
409 if scorer is None:
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
410 if isinstance(estimator, KerasGClassifier):
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
411 scorer = ['accuracy']
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
412 if isinstance(estimator, KerasGRegressor):
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
413 scorer = ['r2']
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
414
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
415 scorer = _check_multimetric_scoring(estimator, scoring=scorer)
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
416
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
417 # handle test (first) split
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
418 test_split_options = params["experiment_schemes"]["test_split"]["split_algos"]
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
419
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
420 if test_split_options["shuffle"] == "group":
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
421 test_split_options["labels"] = groups
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
422 if test_split_options["shuffle"] == "stratified":
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
423 if y is not None:
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
424 test_split_options["labels"] = y
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
425 else:
37
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
426 raise ValueError(
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
427 "Stratified shuffle split is not " "applicable on empty target values!"
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
428 )
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
429
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
430 X_train, X_test, y_train, y_test, groups_train, groups_test = train_test_split_none(
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
431 X, y, groups, **test_split_options
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
432 )
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
433
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
434 exp_scheme = params["experiment_schemes"]["selected_exp_scheme"]
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
435
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
436 # handle validation (second) split
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
437 if exp_scheme == "train_val_test":
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
438 val_split_options = params["experiment_schemes"]["val_split"]["split_algos"]
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
439
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
440 if val_split_options["shuffle"] == "group":
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
441 val_split_options["labels"] = groups_train
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
442 if val_split_options["shuffle"] == "stratified":
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
443 if y_train is not None:
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
444 val_split_options["labels"] = y_train
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
445 else:
37
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
446 raise ValueError(
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
447 "Stratified shuffle split is not "
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
448 "applicable on empty target values!"
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
449 )
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
450
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
451 (
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
452 X_train,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
453 X_val,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
454 y_train,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
455 y_val,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
456 groups_train,
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
457 groups_val,
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
458 ) = train_test_split_none(X_train, y_train, groups_train, **val_split_options)
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
459
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
460 # train and eval
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
461 if hasattr(estimator, "config") and hasattr(estimator, "model_type"):
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
462 if exp_scheme == "train_val_test":
44
6c030fe29722 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 41
diff changeset
463 history = estimator.fit(X_train, y_train, validation_data=(X_val, y_val))
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
464 else:
44
6c030fe29722 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 41
diff changeset
465 history = estimator.fit(X_train, y_train, validation_data=(X_test, y_test))
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
466 else:
44
6c030fe29722 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 41
diff changeset
467 history = estimator.fit(X_train, y_train)
6c030fe29722 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 41
diff changeset
468 if "callbacks" in estimator_params:
6c030fe29722 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 41
diff changeset
469 for cb in estimator_params["callbacks"]:
6c030fe29722 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 41
diff changeset
470 if cb["callback_selection"]["callback_type"] == "CSVLogger":
6c030fe29722 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 41
diff changeset
471 hist_df = pd.DataFrame(history.history)
6c030fe29722 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 41
diff changeset
472 hist_df["epoch"] = np.arange(1, estimator_params["epochs"] + 1)
6c030fe29722 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 41
diff changeset
473 epo_col = hist_df.pop('epoch')
6c030fe29722 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 41
diff changeset
474 hist_df.insert(0, 'epoch', epo_col)
6c030fe29722 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 41
diff changeset
475 hist_df.to_csv(path_or_buf=outfile_history, sep="\t", header=True, index=False)
6c030fe29722 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 41
diff changeset
476 break
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
477 if isinstance(estimator, KerasGBatchClassifier):
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
478 scores = {}
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
479 steps = estimator.prediction_steps
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
480 batch_size = estimator.batch_size
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
481 data_generator = estimator.data_generator_
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
482
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
483 scores, predictions, y_true = _evaluate_keras_and_sklearn_scores(
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
484 estimator,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
485 data_generator,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
486 X_test,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
487 y=y_test,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
488 sk_scoring=scoring,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
489 steps=steps,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
490 batch_size=batch_size,
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
491 return_predictions=bool(outfile_y_true),
37
1bef885255e0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 36
diff changeset
492 )
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
493
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
494 else:
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
495 scores = {}
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
496 if hasattr(estimator, "model_") and hasattr(estimator.model_, "metrics_names"):
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
497 batch_size = estimator.batch_size
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
498 score_results = estimator.model_.evaluate(
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
499 X_test, y=y_test, batch_size=batch_size, verbose=0
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
500 )
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
501 metrics_names = estimator.model_.metrics_names
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
502 if not isinstance(metrics_names, list):
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
503 scores[metrics_names] = score_results
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
504 else:
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
505 scores = dict(zip(metrics_names, score_results))
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
506
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
507 if hasattr(estimator, "predict_proba"):
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
508 predictions = estimator.predict_proba(X_test)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
509 else:
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
510 predictions = estimator.predict(X_test)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
511
45
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
512 # Un-do OHE of the validation labels
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
513 if len(y_test.shape) == 2:
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
514 rounded_test_labels = np.argmax(y_test, axis=1)
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
515 y_true = rounded_test_labels
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
516 sk_scores = _score(estimator, X_test, rounded_test_labels, scorer)
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
517 else:
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
518 y_true = y_test
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
519 sk_scores = _score(estimator, X_test, y_true, scorer)
29e863d1491e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
bgruening
parents: 44
diff changeset
520
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
521 scores.update(sk_scores)
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
522
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
523 # handle output
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
524 if outfile_y_true:
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
525 try:
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
526 pd.DataFrame(y_true).to_csv(outfile_y_true, sep="\t", index=False)
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
527 pd.DataFrame(predictions).astype(np.float32).to_csv(
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
528 outfile_y_preds,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
529 sep="\t",
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
530 index=False,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
531 float_format="%g",
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
532 chunksize=10000,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
533 )
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
534 except Exception as e:
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
535 print("Error in saving predictions: %s" % e)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
536 # handle output
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
537 for name, score in scores.items():
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
538 scores[name] = [score]
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
539 df = pd.DataFrame(scores)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
540 df = df[sorted(df.columns)]
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
541 df.to_csv(path_or_buf=outfile_result, sep="\t", header=True, index=False)
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
542
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
543 memory.clear(warn=False)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
544
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
545 if outfile_object:
41
a16f33c6ca64 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 37
diff changeset
546 dump_model_to_h5(estimator, outfile_object)
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
547
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
548
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
549 if __name__ == "__main__":
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
550 aparser = argparse.ArgumentParser()
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
551 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
552 aparser.add_argument("-e", "--estimator", dest="infile_estimator")
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
553 aparser.add_argument("-X", "--infile1", dest="infile1")
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
554 aparser.add_argument("-y", "--infile2", dest="infile2")
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
555 aparser.add_argument("-O", "--outfile_result", dest="outfile_result")
44
6c030fe29722 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 41
diff changeset
556 aparser.add_argument("-hi", "--outfile_history", dest="outfile_history")
31
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
557 aparser.add_argument("-o", "--outfile_object", dest="outfile_object")
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
558 aparser.add_argument("-l", "--outfile_y_true", dest="outfile_y_true")
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
559 aparser.add_argument("-p", "--outfile_y_preds", dest="outfile_y_preds")
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
560 aparser.add_argument("-g", "--groups", dest="groups")
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
561 aparser.add_argument("-r", "--ref_seq", dest="ref_seq")
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
562 aparser.add_argument("-b", "--intervals", dest="intervals")
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
563 aparser.add_argument("-t", "--targets", dest="targets")
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
564 aparser.add_argument("-f", "--fasta_path", dest="fasta_path")
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
565 args = aparser.parse_args()
eb79bde99328 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
566
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
567 main(
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
568 args.inputs,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
569 args.infile_estimator,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
570 args.infile1,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
571 args.infile2,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
572 args.outfile_result,
44
6c030fe29722 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
bgruening
parents: 41
diff changeset
573 outfile_history=args.outfile_history,
35
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
574 outfile_object=args.outfile_object,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
575 outfile_y_true=args.outfile_y_true,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
576 outfile_y_preds=args.outfile_y_preds,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
577 groups=args.groups,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
578 ref_seq=args.ref_seq,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
579 intervals=args.intervals,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
580 targets=args.targets,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
581 fasta_path=args.fasta_path,
0e5fcf7ddc75 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
582 )