Mercurial > repos > bgruening > sklearn_numeric_clustering

annotate utils.py @ 29:c156b85a6389 draft

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 57f4407e278a615f47a377a3328782b1d8e0b54d
author bgruening
date Sun, 30 Dec 2018 01:39:27 -0500
parents a62c8c1f2ef7
children 60d80322e1e9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
1 import json
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
2 import numpy as np
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
3 import os
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
4 import pandas
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
5 import pickle
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
6 import re
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
7 import scipy
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
8 import sklearn
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
9 import sys
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
10 import warnings
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
11 import xgboost
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
12
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
13 from asteval import Interpreter, make_symbol_table
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
14 from sklearn import (cluster, compose, decomposition, ensemble, feature_extraction,
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
15 feature_selection, gaussian_process, kernel_approximation, metrics,
26
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
16 model_selection, naive_bayes, neighbors, pipeline, preprocessing,
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
17 svm, linear_model, tree, discriminant_analysis)
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
18
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
19 try:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
20 import skrebate
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
21 except ModuleNotFoundError:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
22 pass
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
23
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
24
27
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
25 N_JOBS = int(os.environ.get('GALAXY_SLOTS', 1))
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
26
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
27 try:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
28 sk_whitelist
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
29 except NameError:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
30 sk_whitelist = None
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
31
27
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
32
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
33 class SafePickler(pickle.Unpickler):
26
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
34 """
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
35 Used to safely deserialize scikit-learn model objects serialized by cPickle.dump
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
36 Usage:
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
37 eg.: SafePickler.load(pickled_file_object)
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
38 """
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
39 def find_class(self, module, name):
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
40
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
41 # sk_whitelist could be read from tool
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
42 global sk_whitelist
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
43 if not sk_whitelist:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
44 whitelist_file = os.path.join(os.path.dirname(__file__), 'sk_whitelist.json')
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
45 with open(whitelist_file, 'r') as f:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
46 sk_whitelist = json.load(f)
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
47
26
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
48 bad_names = ('and', 'as', 'assert', 'break', 'class', 'continue',
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
49 'def', 'del', 'elif', 'else', 'except', 'exec',
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
50 'finally', 'for', 'from', 'global', 'if', 'import',
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
51 'in', 'is', 'lambda', 'not', 'or', 'pass', 'print',
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
52 'raise', 'return', 'try', 'system', 'while', 'with',
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
53 'True', 'False', 'None', 'eval', 'execfile', '__import__',
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
54 '__package__', '__subclasses__', '__bases__', '__globals__',
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
55 '__code__', '__closure__', '__func__', '__self__', '__module__',
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
56 '__dict__', '__class__', '__call__', '__get__',
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
57 '__getattribute__', '__subclasshook__', '__new__',
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
58 '__init__', 'func_globals', 'func_code', 'func_closure',
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
59 'im_class', 'im_func', 'im_self', 'gi_code', 'gi_frame',
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
60 '__asteval__', 'f_locals', '__mro__')
27
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
61 good_names = ['copy_reg._reconstructor', '__builtin__.object']
26
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
62
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
63 if re.match(r'^[a-zA-Z_][a-zA-Z0-9_]*$', name):
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
64 fullname = module + '.' + name
27
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
65 if (fullname in good_names)\
26
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
66 or ( ( module.startswith('sklearn.')
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
67 or module.startswith('xgboost.')
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
68 or module.startswith('skrebate.')
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
69 or module.startswith('imblearn')
26
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
70 or module.startswith('numpy.')
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
71 or module == 'numpy'
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
72 )
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
73 and (name not in bad_names)
27
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
74 ):
26
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
75 # TODO: replace with a whitelist checker
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
76 if fullname not in sk_whitelist['SK_NAMES'] + sk_whitelist['SKR_NAMES'] + sk_whitelist['XGB_NAMES'] + sk_whitelist['NUMPY_NAMES'] + sk_whitelist['IMBLEARN_NAMES'] + good_names:
26
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
77 print("Warning: global %s is not in pickler whitelist yet and will loss support soon. Contact tool author or leave a message at github.com" % fullname)
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
78 mod = sys.modules[module]
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
79 return getattr(mod, name)
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
80
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
81 raise pickle.UnpicklingError("global '%s' is forbidden" % fullname)
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
82
27
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
83
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
84 def load_model(file):
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
85 return SafePickler(file).load()
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
86
26
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
87
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
88 def read_columns(f, c=None, c_option='by_index_number', return_df=False, **args):
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
89 data = pandas.read_csv(f, **args)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
90 if c_option == 'by_index_number':
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
91 cols = list(map(lambda x: x - 1, c))
27
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
92 data = data.iloc[:, cols]
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
93 if c_option == 'all_but_by_index_number':
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
94 cols = list(map(lambda x: x - 1, c))
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
95 data.drop(data.columns[cols], axis=1, inplace=True)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
96 if c_option == 'by_header_name':
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
97 cols = [e.strip() for e in c.split(',')]
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
98 data = data[cols]
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
99 if c_option == 'all_but_by_header_name':
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
100 cols = [e.strip() for e in c.split(',')]
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
101 data.drop(cols, axis=1, inplace=True)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
102 y = data.values
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
103 if return_df:
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
104 return y, data
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
105 else:
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
106 return y
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
107
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
108
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
109 ## generate an instance for one of sklearn.feature_selection classes
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
110 def feature_selector(inputs):
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
111 selector = inputs['selected_algorithm']
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
112 selector = getattr(sklearn.feature_selection, selector)
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
113 options = inputs['options']
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
114
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
115 if inputs['selected_algorithm'] == 'SelectFromModel':
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
116 if not options['threshold'] or options['threshold'] == 'None':
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
117 options['threshold'] = None
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
118 else:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
119 try:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
120 options['threshold'] = float(options['threshold'])
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
121 except ValueError:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
122 pass
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
123 if inputs['model_inputter']['input_mode'] == 'prefitted':
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
124 model_file = inputs['model_inputter']['fitted_estimator']
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
125 with open(model_file, 'rb') as model_handler:
27
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
126 fitted_estimator = load_model(model_handler)
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
127 new_selector = selector(fitted_estimator, prefit=True, **options)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
128 else:
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
129 estimator_json = inputs['model_inputter']['estimator_selector']
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
130 estimator = get_estimator(estimator_json)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
131 new_selector = selector(estimator, **options)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
132
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
133 elif inputs['selected_algorithm'] == 'RFE':
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
134 estimator = get_estimator(inputs['estimator_selector'])
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
135 step = options.get('step', None)
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
136 if step and step >= 1.0:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
137 options['step'] = int(step)
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
138 new_selector = selector(estimator, **options)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
139
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
140 elif inputs['selected_algorithm'] == 'RFECV':
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
141 options['scoring'] = get_scoring(options['scoring'])
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
142 options['n_jobs'] = N_JOBS
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
143 splitter, groups = get_cv(options.pop('cv_selector'))
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
144 # TODO support group cv splitters
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
145 options['cv'] = splitter
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
146 step = options.get('step', None)
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
147 if step and step >= 1.0:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
148 options['step'] = int(step)
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
149 estimator = get_estimator(inputs['estimator_selector'])
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
150 new_selector = selector(estimator, **options)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
151
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
152 elif inputs['selected_algorithm'] == 'VarianceThreshold':
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
153 new_selector = selector(**options)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
154
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
155 else:
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
156 score_func = inputs['score_func']
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
157 score_func = getattr(sklearn.feature_selection, score_func)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
158 new_selector = selector(score_func, **options)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
159
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
160 return new_selector
27
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
161
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
162
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
163 def get_X_y(params, file1, file2):
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
164 input_type = params['selected_tasks']['selected_algorithms']['input_options']['selected_input']
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
165 if input_type == 'tabular':
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
166 header = 'infer' if params['selected_tasks']['selected_algorithms']['input_options']['header1'] else None
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
167 column_option = params['selected_tasks']['selected_algorithms']['input_options']['column_selector_options_1']['selected_column_selector_option']
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
168 if column_option in ['by_index_number', 'all_but_by_index_number', 'by_header_name', 'all_but_by_header_name']:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
169 c = params['selected_tasks']['selected_algorithms']['input_options']['column_selector_options_1']['col1']
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
170 else:
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
171 c = None
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
172 X = read_columns(
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
173 file1,
27
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
174 c=c,
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
175 c_option=column_option,
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
176 sep='\t',
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
177 header=header,
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
178 parse_dates=True
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
179 )
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
180 else:
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
181 X = mmread(file1)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
182
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
183 header = 'infer' if params['selected_tasks']['selected_algorithms']['input_options']['header2'] else None
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
184 column_option = params['selected_tasks']['selected_algorithms']['input_options']['column_selector_options_2']['selected_column_selector_option2']
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
185 if column_option in ['by_index_number', 'all_but_by_index_number', 'by_header_name', 'all_but_by_header_name']:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
186 c = params['selected_tasks']['selected_algorithms']['input_options']['column_selector_options_2']['col2']
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
187 else:
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
188 c = None
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
189 y = read_columns(
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
190 file2,
27
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
191 c=c,
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
192 c_option=column_option,
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
193 sep='\t',
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
194 header=header,
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
195 parse_dates=True
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
196 )
27
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
197 y = y.ravel()
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
198 return X, y
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
199
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
200
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
201 class SafeEval(Interpreter):
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
202
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
203 def __init__(self, load_scipy=False, load_numpy=False, load_estimators=False):
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
204
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
205 # File opening and other unneeded functions could be dropped
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
206 unwanted = ['open', 'type', 'dir', 'id', 'str', 'repr']
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
207
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
208 # Allowed symbol table. Add more if needed.
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
209 new_syms = {
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
210 'np_arange': getattr(np, 'arange'),
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
211 'ensemble_ExtraTreesClassifier': getattr(ensemble, 'ExtraTreesClassifier')
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
212 }
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
213
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
214 syms = make_symbol_table(use_numpy=False, **new_syms)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
215
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
216 if load_scipy:
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
217 scipy_distributions = scipy.stats.distributions.__dict__
26
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
218 for k, v in scipy_distributions.items():
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
219 if isinstance(v, (scipy.stats.rv_continuous, scipy.stats.rv_discrete)):
6bebd53612d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
bgruening
parents: 25
diff changeset
220 syms['scipy_stats_' + k] = v
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
221
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
222 if load_numpy:
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
223 from_numpy_random = ['beta', 'binomial', 'bytes', 'chisquare', 'choice', 'dirichlet', 'division',
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
224 'exponential', 'f', 'gamma', 'geometric', 'gumbel', 'hypergeometric',
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
225 'laplace', 'logistic', 'lognormal', 'logseries', 'mtrand', 'multinomial',
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
226 'multivariate_normal', 'negative_binomial', 'noncentral_chisquare', 'noncentral_f',
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
227 'normal', 'pareto', 'permutation', 'poisson', 'power', 'rand', 'randint',
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
228 'randn', 'random', 'random_integers', 'random_sample', 'ranf', 'rayleigh',
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
229 'sample', 'seed', 'set_state', 'shuffle', 'standard_cauchy', 'standard_exponential',
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
230 'standard_gamma', 'standard_normal', 'standard_t', 'triangular', 'uniform',
27
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
231 'vonmises', 'wald', 'weibull', 'zipf']
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
232 for f in from_numpy_random:
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
233 syms['np_random_' + f] = getattr(np.random, f)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
234
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
235 if load_estimators:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
236 estimator_table = {
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
237 'sklearn_svm' : getattr(sklearn, 'svm'),
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
238 'sklearn_tree' : getattr(sklearn, 'tree'),
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
239 'sklearn_ensemble' : getattr(sklearn, 'ensemble'),
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
240 'sklearn_neighbors' : getattr(sklearn, 'neighbors'),
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
241 'sklearn_naive_bayes' : getattr(sklearn, 'naive_bayes'),
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
242 'sklearn_linear_model' : getattr(sklearn, 'linear_model'),
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
243 'sklearn_cluster' : getattr(sklearn, 'cluster'),
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
244 'sklearn_decomposition' : getattr(sklearn, 'decomposition'),
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
245 'sklearn_preprocessing' : getattr(sklearn, 'preprocessing'),
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
246 'sklearn_feature_selection' : getattr(sklearn, 'feature_selection'),
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
247 'sklearn_kernel_approximation' : getattr(sklearn, 'kernel_approximation'),
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
248 'skrebate_ReliefF': getattr(skrebate, 'ReliefF'),
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
249 'skrebate_SURF': getattr(skrebate, 'SURF'),
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
250 'skrebate_SURFstar': getattr(skrebate, 'SURFstar'),
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
251 'skrebate_MultiSURF': getattr(skrebate, 'MultiSURF'),
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
252 'skrebate_MultiSURFstar': getattr(skrebate, 'MultiSURFstar'),
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
253 'skrebate_TuRF': getattr(skrebate, 'TuRF'),
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
254 'xgboost_XGBClassifier' : getattr(xgboost, 'XGBClassifier'),
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
255 'xgboost_XGBRegressor' : getattr(xgboost, 'XGBRegressor')
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
256 }
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
257 syms.update(estimator_table)
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
258
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
259 for key in unwanted:
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
260 syms.pop(key, None)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
261
27
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
262 super(SafeEval, self).__init__(symtable=syms, use_numpy=False, minimal=False,
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
263 no_if=True, no_for=True, no_while=True, no_try=True,
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
264 no_functiondef=True, no_ifexp=True, no_listcomp=False,
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
265 no_augassign=False, no_assert=True, no_delete=True,
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
266 no_raise=True, no_print=True)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
267
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
268
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
269
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
270 def get_estimator(estimator_json):
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
271
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
272 estimator_module = estimator_json['selected_module']
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
273
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
274 if estimator_module == 'customer_estimator':
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
275 c_estimator = estimator_json['c_estimator']
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
276 with open(c_estimator, 'rb') as model_handler:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
277 new_model = load_model(model_handler)
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
278 return new_model
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
279
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
280 estimator_cls = estimator_json['selected_estimator']
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
281
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
282 if estimator_module == 'xgboost':
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
283 cls = getattr(xgboost, estimator_cls)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
284 else:
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
285 module = getattr(sklearn, estimator_module)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
286 cls = getattr(module, estimator_cls)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
287
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
288 estimator = cls()
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
289
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
290 estimator_params = estimator_json['text_params'].strip()
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
291 if estimator_params != '':
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
292 try:
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
293 params = safe_eval('dict(' + estimator_params + ')')
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
294 except ValueError:
27
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
295 sys.exit("Unsupported parameter input: `%s`" % estimator_params)
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
296 estimator.set_params(**params)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
297 if 'n_jobs' in estimator.get_params():
27
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
298 estimator.set_params(n_jobs=N_JOBS)
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
299
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
300 return estimator
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
301
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
302
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
303 def get_cv(cv_json):
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
304 """
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
305 cv_json:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
306 e.g.:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
307 {
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
308 'selected_cv': 'StratifiedKFold',
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
309 'n_splits': 3,
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
310 'shuffle': True,
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
311 'random_state': 0
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
312 }
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
313 """
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
314 cv = cv_json.pop('selected_cv')
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
315 if cv == 'default':
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
316 return cv_json['n_splits'], None
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
317
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
318 groups = cv_json.pop('groups', None)
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
319 if groups:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
320 groups = groups.strip()
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
321 if groups != '':
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
322 if groups.startswith('__ob__'):
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
323 groups = groups[6:]
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
324 if groups.endswith('__cb__'):
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
325 groups = groups[:-6]
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
326 groups = [int(x.strip()) for x in groups.split(',')]
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
327
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
328 for k, v in cv_json.items():
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
329 if v == '':
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
330 cv_json[k] = None
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
331
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
332 test_fold = cv_json.get('test_fold', None)
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
333 if test_fold:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
334 if test_fold.startswith('__ob__'):
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
335 test_fold = test_fold[6:]
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
336 if test_fold.endswith('__cb__'):
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
337 test_fold = test_fold[:-6]
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
338 cv_json['test_fold'] = [int(x.strip()) for x in test_fold.split(',')]
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
339
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
340 test_size = cv_json.get('test_size', None)
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
341 if test_size and test_size > 1.0:
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
342 cv_json['test_size'] = int(test_size)
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
343
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
344 cv_class = getattr(model_selection, cv)
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
345 splitter = cv_class(**cv_json)
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
346
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
347 return splitter, groups
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
348
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
349
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
350 # needed when sklearn < v0.20
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
351 def balanced_accuracy_score(y_true, y_pred):
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
352 C = metrics.confusion_matrix(y_true, y_pred)
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
353 with np.errstate(divide='ignore', invalid='ignore'):
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
354 per_class = np.diag(C) / C.sum(axis=1)
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
355 if np.any(np.isnan(per_class)):
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
356 warnings.warn('y_pred contains classes not in y_true')
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
357 per_class = per_class[~np.isnan(per_class)]
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
358 score = np.mean(per_class)
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
359 return score
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
360
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
361
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
362 def get_scoring(scoring_json):
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
363
29
c156b85a6389 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 27
diff changeset
364 if scoring_json['primary_scoring'] == 'default':
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
365 return None
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
366
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
367 my_scorers = metrics.SCORERS
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
368 if 'balanced_accuracy' not in my_scorers:
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
369 my_scorers['balanced_accuracy'] = metrics.make_scorer(balanced_accuracy_score)
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
370
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
371 if scoring_json['secondary_scoring'] != 'None'\
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
372 and scoring_json['secondary_scoring'] != scoring_json['primary_scoring']:
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
373 scoring = {}
27
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
374 scoring['primary'] = my_scorers[scoring_json['primary_scoring']]
25
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
375 for scorer in scoring_json['secondary_scoring'].split(','):
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
376 if scorer != scoring_json['primary_scoring']:
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
377 scoring[scorer] = my_scorers[scorer]
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
378 return scoring
64200dc3d769 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents:
diff changeset
379
27
a62c8c1f2ef7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2a058459e6daf0486871f93845f00fdb4a4eaca1
bgruening
parents: 26
diff changeset
380 return my_scorers[scoring_json['primary_scoring']]