annotate train_test_split.py @ 32:1a53edc4b438 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
author bgruening
date Wed, 22 Jan 2020 08:06:22 -0500
parents 172365bc2b5f
children 19d6c2745d34
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
29
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
1 import argparse
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
2 import json
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
3 import pandas as pd
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
4 import warnings
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
5
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
6 from galaxy_ml.model_validations import train_test_split
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
7 from galaxy_ml.utils import get_cv, read_columns
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
8
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
9
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
10 def _get_single_cv_split(params, array, infile_labels=None,
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
11 infile_groups=None):
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
12 """ output (train, test) subset from a cv splitter
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
13
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
14 Parameters
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
15 ----------
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
16 params : dict
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
17 Galaxy tool inputs
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
18 array : pandas DataFrame object
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
19 The target dataset to split
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
20 infile_labels : str
172365bc2b5f "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 target values
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
22 infile_groups : str
172365bc2b5f "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 group values
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
24 """
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
25 y = None
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
26 groups = None
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
27
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
28 nth_split = params['mode_selection']['nth_split']
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
29
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
30 # read groups
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
31 if infile_groups:
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
32 header = 'infer' if (params['mode_selection']['cv_selector']
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
33 ['groups_selector']['header_g']) else None
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
34 column_option = (params['mode_selection']['cv_selector']
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
35 ['groups_selector']['column_selector_options_g']
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
36 ['selected_column_selector_option_g'])
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
37 if column_option in ['by_index_number', 'all_but_by_index_number',
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
38 'by_header_name', 'all_but_by_header_name']:
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
39 c = (params['mode_selection']['cv_selector']['groups_selector']
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
40 ['column_selector_options_g']['col_g'])
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
41 else:
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
42 c = None
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
43
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
44 groups = read_columns(infile_groups, c=c, c_option=column_option,
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
45 sep='\t', header=header, parse_dates=True)
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
46 groups = groups.ravel()
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
47
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
48 params['mode_selection']['cv_selector']['groups_selector'] = groups
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
49
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
50 # read labels
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
51 if infile_labels:
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
52 target_input = (params['mode_selection']
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
53 ['cv_selector'].pop('target_input'))
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
54 header = 'infer' if target_input['header1'] else None
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
55 col_index = target_input['col'][0] - 1
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
56 df = pd.read_csv(infile_labels, sep='\t', header=header,
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
57 parse_dates=True)
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
58 y = df.iloc[:, col_index].values
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
59
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
60 # construct the cv splitter object
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
61 splitter, groups = get_cv(params['mode_selection']['cv_selector'])
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
62
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
63 total_n_splits = splitter.get_n_splits(array.values, y=y, groups=groups)
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
64 if nth_split > total_n_splits:
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
65 raise ValueError("Total number of splits is {}, but got `nth_split` "
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
66 "= {}".format(total_n_splits, nth_split))
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
67
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
68 i = 1
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
69 for train_index, test_index in splitter.split(array.values, y=y, groups=groups):
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
70 # suppose nth_split >= 1
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
71 if i == nth_split:
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
72 break
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
73 else:
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
74 i += 1
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
75
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
76 train = array.iloc[train_index, :]
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
77 test = array.iloc[test_index, :]
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
78
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
79 return train, test
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
80
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
81
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
82 def main(inputs, infile_array, outfile_train, outfile_test,
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
83 infile_labels=None, infile_groups=None):
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
84 """
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
85 Parameter
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
86 ---------
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
87 inputs : str
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
88 File path to galaxy tool parameter
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
89
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
90 infile_array : str
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
91 File paths of input arrays separated by comma
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
92
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
93 infile_labels : str
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
94 File path to dataset containing labels
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
95
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
96 infile_groups : str
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
97 File path to dataset containing groups
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
98
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
99 outfile_train : str
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
100 File path to dataset containing train split
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
101
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
102 outfile_test : str
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
103 File path to dataset containing test split
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
104 """
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
105 warnings.simplefilter('ignore')
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
106
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
107 with open(inputs, 'r') as param_handler:
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
108 params = json.load(param_handler)
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
109
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
110 input_header = params['header0']
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
111 header = 'infer' if input_header else None
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
112 array = pd.read_csv(infile_array, sep='\t', header=header,
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
113 parse_dates=True)
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
114
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
115 # train test split
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
116 if params['mode_selection']['selected_mode'] == 'train_test_split':
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
117 options = params['mode_selection']['options']
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
118 shuffle_selection = options.pop('shuffle_selection')
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
119 options['shuffle'] = shuffle_selection['shuffle']
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
120 if infile_labels:
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
121 header = 'infer' if shuffle_selection['header1'] else None
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
122 col_index = shuffle_selection['col'][0] - 1
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
123 df = pd.read_csv(infile_labels, sep='\t', header=header,
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
124 parse_dates=True)
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
125 labels = df.iloc[:, col_index].values
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
126 options['labels'] = labels
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
127
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
128 train, test = train_test_split(array, **options)
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
129
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
130 # cv splitter
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
131 else:
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
132 train, test = _get_single_cv_split(params, array,
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
133 infile_labels=infile_labels,
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
134 infile_groups=infile_groups)
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
135
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
136 print("Input shape: %s" % repr(array.shape))
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
137 print("Train shape: %s" % repr(train.shape))
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
138 print("Test shape: %s" % repr(test.shape))
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
139 train.to_csv(outfile_train, sep='\t', header=input_header, index=False)
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
140 test.to_csv(outfile_test, sep='\t', header=input_header, index=False)
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
141
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
142
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
143 if __name__ == '__main__':
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
144 aparser = argparse.ArgumentParser()
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
145 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
146 aparser.add_argument("-X", "--infile_array", dest="infile_array")
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
147 aparser.add_argument("-y", "--infile_labels", dest="infile_labels")
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
148 aparser.add_argument("-g", "--infile_groups", dest="infile_groups")
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
149 aparser.add_argument("-o", "--outfile_train", dest="outfile_train")
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
150 aparser.add_argument("-t", "--outfile_test", dest="outfile_test")
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
151 args = aparser.parse_args()
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
152
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
153 main(args.inputs, args.infile_array, args.outfile_train,
172365bc2b5f "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
diff changeset
154 args.outfile_test, args.infile_labels, args.infile_groups)