annotate fitted_model_eval.py @ 17:a01fa4e8fe4f draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
author bgruening
date Wed, 09 Aug 2023 12:54:40 +0000
parents c9ddd20d25d0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
1 import argparse
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
2 import json
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
3 import warnings
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
4
12
74de84506e74 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents: 11
diff changeset
5 import pandas as pd
17
a01fa4e8fe4f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 13
diff changeset
6 from galaxy_ml.model_persist import load_model_from_h5
a01fa4e8fe4f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 13
diff changeset
7 from galaxy_ml.utils import clean_params, get_scoring, read_columns
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
8 from scipy.io import mmread
17
a01fa4e8fe4f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 13
diff changeset
9 from sklearn.metrics._scorer import _check_multimetric_scoring
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
10 from sklearn.model_selection._validation import _score
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
11
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
12
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
13 def _get_X_y(params, infile1, infile2):
11
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
14 """read from inputs and output X and y
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
15
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
16 Parameters
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
17 ----------
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
18 params : dict
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
19 Tool inputs parameter
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
20 infile1 : str
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
21 File path to dataset containing features
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
22 infile2 : str
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
23 File path to dataset containing target values
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
24
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
25 """
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
26 # store read dataframe object
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
27 loaded_df = {}
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
28
11
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
29 input_type = params["input_options"]["selected_input"]
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
30 # tabular input
11
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
31 if input_type == "tabular":
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
32 header = "infer" if params["input_options"]["header1"] else None
13
c9ddd20d25d0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 12
diff changeset
33 column_option = params["input_options"]["column_selector_options_1"][
c9ddd20d25d0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 12
diff changeset
34 "selected_column_selector_option"
c9ddd20d25d0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 12
diff changeset
35 ]
11
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
36 if column_option in [
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
37 "by_index_number",
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
38 "all_but_by_index_number",
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
39 "by_header_name",
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
40 "all_but_by_header_name",
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
41 ]:
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
42 c = params["input_options"]["column_selector_options_1"]["col1"]
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
43 else:
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
44 c = None
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
45
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
46 df_key = infile1 + repr(header)
11
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
47 df = pd.read_csv(infile1, sep="\t", header=header, parse_dates=True)
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
48 loaded_df[df_key] = df
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
49
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
50 X = read_columns(df, c=c, c_option=column_option).astype(float)
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
51 # sparse input
11
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
52 elif input_type == "sparse":
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
53 X = mmread(open(infile1, "r"))
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
54
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
55 # Get target y
11
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
56 header = "infer" if params["input_options"]["header2"] else None
13
c9ddd20d25d0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 12
diff changeset
57 column_option = params["input_options"]["column_selector_options_2"][
c9ddd20d25d0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 12
diff changeset
58 "selected_column_selector_option2"
c9ddd20d25d0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 12
diff changeset
59 ]
11
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
60 if column_option in [
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
61 "by_index_number",
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
62 "all_but_by_index_number",
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
63 "by_header_name",
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
64 "all_but_by_header_name",
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
65 ]:
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
66 c = params["input_options"]["column_selector_options_2"]["col2"]
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
67 else:
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
68 c = None
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
69
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
70 df_key = infile2 + repr(header)
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
71 if df_key in loaded_df:
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
72 infile2 = loaded_df[df_key]
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
73 else:
11
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
74 infile2 = pd.read_csv(infile2, sep="\t", header=header, parse_dates=True)
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
75 loaded_df[df_key] = infile2
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
76
13
c9ddd20d25d0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 12
diff changeset
77 y = read_columns(
17
a01fa4e8fe4f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 13
diff changeset
78 infile2,
a01fa4e8fe4f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 13
diff changeset
79 c=c,
a01fa4e8fe4f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 13
diff changeset
80 c_option=column_option,
a01fa4e8fe4f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 13
diff changeset
81 sep="\t",
a01fa4e8fe4f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 13
diff changeset
82 header=header,
a01fa4e8fe4f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 13
diff changeset
83 parse_dates=True,
13
c9ddd20d25d0 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 12
diff changeset
84 )
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
85 if len(y.shape) == 2 and y.shape[1] == 1:
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
86 y = y.ravel()
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
87
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
88 return X, y
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
89
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
90
17
a01fa4e8fe4f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 13
diff changeset
91 def main(inputs, infile_estimator, outfile_eval, infile1=None, infile2=None):
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
92 """
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
93 Parameter
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
94 ---------
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
95 inputs : str
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
96 File path to galaxy tool parameter
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
97
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
98 infile_estimator : strgit
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
99 File path to trained estimator input
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
100
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
101 outfile_eval : str
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
102 File path to save the evalulation results, tabular
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
103
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
104 infile1 : str
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
105 File path to dataset containing features
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
106
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
107 infile2 : str
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
108 File path to dataset containing target values
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
109 """
11
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
110 warnings.filterwarnings("ignore")
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
111
11
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
112 with open(inputs, "r") as param_handler:
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
113 params = json.load(param_handler)
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
114
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
115 X_test, y_test = _get_X_y(params, infile1, infile2)
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
116
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
117 # load model
17
a01fa4e8fe4f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 13
diff changeset
118 estimator = load_model_from_h5(infile_estimator)
a01fa4e8fe4f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 13
diff changeset
119 estimator = clean_params(estimator)
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
120
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
121 # handle scorer, convert to scorer dict
11
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
122 scoring = params["scoring"]
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
123 scorer = get_scoring(scoring)
17
a01fa4e8fe4f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 13
diff changeset
124 if not isinstance(scorer, (dict, list)):
a01fa4e8fe4f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 13
diff changeset
125 scorer = [scoring["primary_scoring"]]
a01fa4e8fe4f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 13
diff changeset
126 scorer = _check_multimetric_scoring(estimator, scoring=scorer)
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
127
11
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
128 if hasattr(estimator, "evaluate"):
17
a01fa4e8fe4f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 13
diff changeset
129 scores = estimator.evaluate(X_test, y_test=y_test, scorer=scorer)
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
130 else:
17
a01fa4e8fe4f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 13
diff changeset
131 scores = _score(estimator, X_test, y_test, scorer)
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
132
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
133 # handle output
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
134 for name, score in scores.items():
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
135 scores[name] = [score]
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
136 df = pd.DataFrame(scores)
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
137 df = df[sorted(df.columns)]
11
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
138 df.to_csv(path_or_buf=outfile_eval, sep="\t", header=True, index=False)
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
139
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
140
11
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
141 if __name__ == "__main__":
5
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
142 aparser = argparse.ArgumentParser()
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
143 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
144 aparser.add_argument("-e", "--infile_estimator", dest="infile_estimator")
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
145 aparser.add_argument("-X", "--infile1", dest="infile1")
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
146 aparser.add_argument("-y", "--infile2", dest="infile2")
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
147 aparser.add_argument("-O", "--outfile_eval", dest="outfile_eval")
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
148 args = aparser.parse_args()
f4a7c3aa1e10 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
149
11
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
150 main(
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
151 args.inputs,
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
152 args.infile_estimator,
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
153 args.outfile_eval,
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
154 infile1=args.infile1,
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
155 infile2=args.infile2,
27fabe5feedc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 5
diff changeset
156 )