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annotate search_model_validation.py @ 14:2fc88dc854ee draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit f031d8ddfb73cec24572648666ac44ee47f08aad
author bgruening
date Thu, 11 Aug 2022 07:49:08 +0000
parents 0380f10c4e04
children
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47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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1 import argparse
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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2 import collections
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3 import json
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4 import os
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5 import pickle
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6 import sys
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7 import warnings
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8
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47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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9 import imblearn
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10 import joblib
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47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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11 import numpy as np
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12 import pandas as pd
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13 import skrebate
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14 from galaxy_ml.utils import (clean_params, get_cv,
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15 get_main_estimator, get_module, get_scoring,
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16 load_model, read_columns, SafeEval, try_get_attr)
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17 from scipy.io import mmread
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18 from sklearn import (cluster, decomposition, feature_selection,
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19 kernel_approximation, model_selection, preprocessing)
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20 from sklearn.exceptions import FitFailedWarning
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21 from sklearn.model_selection import _search, _validation
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22 from sklearn.model_selection._validation import _score, cross_validate
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23
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24 _fit_and_score = try_get_attr("galaxy_ml.model_validations", "_fit_and_score")
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25 setattr(_search, "_fit_and_score", _fit_and_score)
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26 setattr(_validation, "_fit_and_score", _fit_and_score)
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27
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28 N_JOBS = int(os.environ.get("GALAXY_SLOTS", 1))
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29 # handle disk cache
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30 CACHE_DIR = os.path.join(os.getcwd(), "cached")
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31 del os
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32 NON_SEARCHABLE = ("n_jobs", "pre_dispatch", "memory", "_path", "nthread", "callbacks")
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35 def _eval_search_params(params_builder):
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36 search_params = {}
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37
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38 for p in params_builder["param_set"]:
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39 search_list = p["sp_list"].strip()
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40 if search_list == "":
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41 continue
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42
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43 param_name = p["sp_name"]
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44 if param_name.lower().endswith(NON_SEARCHABLE):
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45 print(
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46 "Warning: `%s` is not eligible for search and was "
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47 "omitted!" % param_name
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48 )
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49 continue
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50
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51 if not search_list.startswith(":"):
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52 safe_eval = SafeEval(load_scipy=True, load_numpy=True)
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53 ev = safe_eval(search_list)
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54 search_params[param_name] = ev
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55 else:
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56 # Have `:` before search list, asks for estimator evaluatio
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57 safe_eval_es = SafeEval(load_estimators=True)
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58 search_list = search_list[1:].strip()
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59 # TODO maybe add regular express check
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60 ev = safe_eval_es(search_list)
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61 preprocessings = (
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62 preprocessing.StandardScaler(),
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63 preprocessing.Binarizer(),
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64 preprocessing.MaxAbsScaler(),
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65 preprocessing.Normalizer(),
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66 preprocessing.MinMaxScaler(),
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67 preprocessing.PolynomialFeatures(),
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68 preprocessing.RobustScaler(),
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69 feature_selection.SelectKBest(),
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70 feature_selection.GenericUnivariateSelect(),
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71 feature_selection.SelectPercentile(),
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72 feature_selection.SelectFpr(),
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73 feature_selection.SelectFdr(),
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74 feature_selection.SelectFwe(),
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75 feature_selection.VarianceThreshold(),
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76 decomposition.FactorAnalysis(random_state=0),
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77 decomposition.FastICA(random_state=0),
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78 decomposition.IncrementalPCA(),
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79 decomposition.KernelPCA(random_state=0, n_jobs=N_JOBS),
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80 decomposition.LatentDirichletAllocation(random_state=0, n_jobs=N_JOBS),
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81 decomposition.MiniBatchDictionaryLearning(
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82 random_state=0, n_jobs=N_JOBS
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83 ),
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84 decomposition.MiniBatchSparsePCA(random_state=0, n_jobs=N_JOBS),
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85 decomposition.NMF(random_state=0),
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86 decomposition.PCA(random_state=0),
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87 decomposition.SparsePCA(random_state=0, n_jobs=N_JOBS),
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88 decomposition.TruncatedSVD(random_state=0),
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89 kernel_approximation.Nystroem(random_state=0),
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90 kernel_approximation.RBFSampler(random_state=0),
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91 kernel_approximation.AdditiveChi2Sampler(),
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92 kernel_approximation.SkewedChi2Sampler(random_state=0),
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93 cluster.FeatureAgglomeration(),
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94 skrebate.ReliefF(n_jobs=N_JOBS),
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95 skrebate.SURF(n_jobs=N_JOBS),
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96 skrebate.SURFstar(n_jobs=N_JOBS),
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97 skrebate.MultiSURF(n_jobs=N_JOBS),
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98 skrebate.MultiSURFstar(n_jobs=N_JOBS),
9
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99 imblearn.under_sampling.ClusterCentroids(random_state=0, n_jobs=N_JOBS),
11
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100 imblearn.under_sampling.CondensedNearestNeighbour(
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101 random_state=0, n_jobs=N_JOBS
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102 ),
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103 imblearn.under_sampling.EditedNearestNeighbours(
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104 random_state=0, n_jobs=N_JOBS
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105 ),
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106 imblearn.under_sampling.RepeatedEditedNearestNeighbours(
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107 random_state=0, n_jobs=N_JOBS
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108 ),
0
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109 imblearn.under_sampling.AllKNN(random_state=0, n_jobs=N_JOBS),
11
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110 imblearn.under_sampling.InstanceHardnessThreshold(
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111 random_state=0, n_jobs=N_JOBS
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112 ),
9
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113 imblearn.under_sampling.NearMiss(random_state=0, n_jobs=N_JOBS),
11
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114 imblearn.under_sampling.NeighbourhoodCleaningRule(
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115 random_state=0, n_jobs=N_JOBS
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116 ),
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117 imblearn.under_sampling.OneSidedSelection(
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118 random_state=0, n_jobs=N_JOBS
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119 ),
9
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120 imblearn.under_sampling.RandomUnderSampler(random_state=0),
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121 imblearn.under_sampling.TomekLinks(random_state=0, n_jobs=N_JOBS),
0
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122 imblearn.over_sampling.ADASYN(random_state=0, n_jobs=N_JOBS),
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123 imblearn.over_sampling.RandomOverSampler(random_state=0),
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124 imblearn.over_sampling.SMOTE(random_state=0, n_jobs=N_JOBS),
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125 imblearn.over_sampling.SVMSMOTE(random_state=0, n_jobs=N_JOBS),
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126 imblearn.over_sampling.BorderlineSMOTE(random_state=0, n_jobs=N_JOBS),
11
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127 imblearn.over_sampling.SMOTENC(
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128 categorical_features=[], random_state=0, n_jobs=N_JOBS
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129 ),
0
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130 imblearn.combine.SMOTEENN(random_state=0),
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131 imblearn.combine.SMOTETomek(random_state=0),
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132 )
0
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133 newlist = []
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134 for obj in ev:
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135 if obj is None:
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136 newlist.append(None)
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137 elif obj == "all_0":
2
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138 newlist.extend(preprocessings[0:35])
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139 elif obj == "sk_prep_all": # no KernalCenter()
2
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140 newlist.extend(preprocessings[0:7])
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141 elif obj == "fs_all":
2
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142 newlist.extend(preprocessings[7:14])
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143 elif obj == "decomp_all":
2
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144 newlist.extend(preprocessings[14:25])
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145 elif obj == "k_appr_all":
2
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146 newlist.extend(preprocessings[25:29])
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147 elif obj == "reb_all":
2
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148 newlist.extend(preprocessings[30:35])
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149 elif obj == "imb_all":
2
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150 newlist.extend(preprocessings[35:54])
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151 elif type(obj) is int and -1 < obj < len(preprocessings):
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152 newlist.append(preprocessings[obj])
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153 elif hasattr(obj, "get_params"): # user uploaded object
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154 if "n_jobs" in obj.get_params():
0
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155 newlist.append(obj.set_params(n_jobs=N_JOBS))
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156 else:
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157 newlist.append(obj)
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158 else:
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159 sys.exit("Unsupported estimator type: %r" % (obj))
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160
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161 search_params[param_name] = newlist
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162
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163 return search_params
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164
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165
9
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166 def _handle_X_y(
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167 estimator,
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168 params,
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169 infile1,
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170 infile2,
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171 loaded_df={},
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172 ref_seq=None,
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173 intervals=None,
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174 targets=None,
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175 fasta_path=None,
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176 ):
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177 """read inputs
0
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178
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179 Params
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180 -------
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181 estimator : estimator object
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182 params : dict
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183 Galaxy tool parameter inputs
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184 infile1 : str
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185 File path to dataset containing features
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186 infile2 : str
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187 File path to dataset containing target values
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188 loaded_df : dict
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189 Contains loaded DataFrame objects with file path as keys
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190 ref_seq : str
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191 File path to dataset containing genome sequence file
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192 interval : str
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193 File path to dataset containing interval file
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194 targets : str
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195 File path to dataset compressed target bed file
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196 fasta_path : str
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197 File path to dataset containing fasta file
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198
3
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199
7
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200 Returns
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201 -------
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202 estimator : estimator object after setting new attributes
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203 X : numpy array
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204 y : numpy array
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205 """
2
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206 estimator_params = estimator.get_params()
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207
9
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208 input_type = params["input_options"]["selected_input"]
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209 # tabular input
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210 if input_type == "tabular":
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211 header = "infer" if params["input_options"]["header1"] else None
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212 column_option = params["input_options"]["column_selector_options_1"][
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213 "selected_column_selector_option"
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214 ]
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215 if column_option in [
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216 "by_index_number",
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217 "all_but_by_index_number",
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218 "by_header_name",
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219 "all_but_by_header_name",
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220 ]:
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221 c = params["input_options"]["column_selector_options_1"]["col1"]
0
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222 else:
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223 c = None
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224
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225 df_key = infile1 + repr(header)
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226
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227 if df_key in loaded_df:
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228 infile1 = loaded_df[df_key]
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229
9
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230 df = pd.read_csv(infile1, sep="\t", header=header, parse_dates=True)
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231 loaded_df[df_key] = df
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232
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233 X = read_columns(df, c=c, c_option=column_option).astype(float)
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234 # sparse input
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235 elif input_type == "sparse":
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236 X = mmread(open(infile1, "r"))
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237
2
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238 # fasta_file input
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239 elif input_type == "seq_fasta":
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240 pyfaidx = get_module("pyfaidx")
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241 sequences = pyfaidx.Fasta(fasta_path)
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242 n_seqs = len(sequences.keys())
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243 X = np.arange(n_seqs)[:, np.newaxis]
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244 for param in estimator_params.keys():
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245 if param.endswith("fasta_path"):
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246 estimator.set_params(**{param: fasta_path})
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247 break
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248 else:
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249 raise ValueError(
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250 "The selected estimator doesn't support "
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251 "fasta file input! Please consider using "
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252 "KerasGBatchClassifier with "
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253 "FastaDNABatchGenerator/FastaProteinBatchGenerator "
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254 "or having GenomeOneHotEncoder/ProteinOneHotEncoder "
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255 "in pipeline!"
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256 )
2
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257
9
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258 elif input_type == "refseq_and_interval":
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259 path_params = {
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260 "data_batch_generator__ref_genome_path": ref_seq,
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261 "data_batch_generator__intervals_path": intervals,
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262 "data_batch_generator__target_path": targets,
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263 }
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264 estimator.set_params(**path_params)
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265 n_intervals = sum(1 for line in open(intervals))
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266 X = np.arange(n_intervals)[:, np.newaxis]
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267
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268 # Get target y
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269 header = "infer" if params["input_options"]["header2"] else None
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270 column_option = params["input_options"]["column_selector_options_2"][
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271 "selected_column_selector_option2"
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272 ]
9
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273 if column_option in [
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274 "by_index_number",
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275 "all_but_by_index_number",
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276 "by_header_name",
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277 "all_but_by_header_name",
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278 ]:
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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279 c = params["input_options"]["column_selector_options_2"]["col2"]
0
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280 else:
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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281 c = None
2
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282
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283 df_key = infile2 + repr(header)
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284 if df_key in loaded_df:
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285 infile2 = loaded_df[df_key]
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286 else:
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287 infile2 = pd.read_csv(infile2, sep="\t", header=header, parse_dates=True)
2
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288 loaded_df[df_key] = infile2
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289
11
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290 y = read_columns(
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291 infile2, c=c, c_option=column_option, sep="\t", header=header, parse_dates=True
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292 )
2
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293 if len(y.shape) == 2 and y.shape[1] == 1:
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294 y = y.ravel()
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295 if input_type == "refseq_and_interval":
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296 estimator.set_params(data_batch_generator__features=y.ravel().tolist())
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297 y = None
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298 # end y
0
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299
7
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300 return estimator, X, y
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301
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302
9
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303 def _do_outer_cv(searcher, X, y, outer_cv, scoring, error_score="raise", outfile=None):
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304 """Do outer cross-validation for nested CV
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305
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
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306 Parameters
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307 ----------
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
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308 searcher : object
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309 SearchCV object
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310 X : numpy array
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311 Containing features
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312 y : numpy array
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313 Target values or labels
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314 outer_cv : int or CV splitter
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315 Control the cv splitting
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316 scoring : object
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317 Scorer
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318 error_score: str, float or numpy float
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319 Whether to raise fit error or return an value
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320 outfile : str
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321 File path to store the restuls
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322 """
9
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323 if error_score == "raise":
7
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324 rval = cross_validate(
9
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325 searcher,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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326 X,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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327 y,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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328 scoring=scoring,
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329 cv=outer_cv,
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330 n_jobs=N_JOBS,
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331 verbose=0,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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332 error_score=error_score,
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333 )
7
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334 else:
9
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335 warnings.simplefilter("always", FitFailedWarning)
7
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336 with warnings.catch_warnings(record=True) as w:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
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337 try:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
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338 rval = cross_validate(
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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339 searcher,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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340 X,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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341 y,
7
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342 scoring=scoring,
9
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343 cv=outer_cv,
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344 n_jobs=N_JOBS,
7
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345 verbose=0,
9
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346 error_score=error_score,
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347 )
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
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348 except ValueError:
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349 pass
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
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350 for warning in w:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
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351 print(repr(warning.message))
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
352
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
353 keys = list(rval.keys())
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
354 for k in keys:
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
355 if k.startswith("test"):
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
356 rval["mean_" + k] = np.mean(rval[k])
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
357 rval["std_" + k] = np.std(rval[k])
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
358 if k.endswith("time"):
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
359 rval.pop(k)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
360 rval = pd.DataFrame(rval)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
361 rval = rval[sorted(rval.columns)]
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
362 rval.to_csv(path_or_buf=outfile, sep="\t", header=True, index=False)
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
363
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
364
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
365 def _do_train_test_split_val(
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
366 searcher,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
367 X,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
368 y,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
369 params,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
370 error_score="raise",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
371 primary_scoring=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
372 groups=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
373 outfile=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
374 ):
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
375 """do train test split, searchCV validates on the train and then use
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
376 the best_estimator_ to evaluate on the test
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
377
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
378 Returns
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
379 --------
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
380 Fitted SearchCV object
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
381 """
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
382 train_test_split = try_get_attr("galaxy_ml.model_validations", "train_test_split")
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
383 split_options = params["outer_split"]
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
384
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
385 # splits
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
386 if split_options["shuffle"] == "stratified":
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
387 split_options["labels"] = y
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
388 X, X_test, y, y_test = train_test_split(X, y, **split_options)
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
389 elif split_options["shuffle"] == "group":
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
390 if groups is None:
11
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
391 raise ValueError(
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
392 "No group based CV option was choosen for " "group shuffle!"
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
393 )
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
394 split_options["labels"] = groups
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
395 if y is None:
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
396 X, X_test, groups, _ = train_test_split(X, groups, **split_options)
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
397 else:
11
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
398 X, X_test, y, y_test, groups, _ = train_test_split(
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
399 X, y, groups, **split_options
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
400 )
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
401 else:
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
402 if split_options["shuffle"] == "None":
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
403 split_options["shuffle"] = None
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
404 X, X_test, y, y_test = train_test_split(X, y, **split_options)
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
405
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
406 if error_score == "raise":
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
407 searcher.fit(X, y, groups=groups)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
408 else:
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
409 warnings.simplefilter("always", FitFailedWarning)
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
410 with warnings.catch_warnings(record=True) as w:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
411 try:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
412 searcher.fit(X, y, groups=groups)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
413 except ValueError:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
414 pass
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
415 for warning in w:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
416 print(repr(warning.message))
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
417
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
418 scorer_ = searcher.scorer_
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
419 if isinstance(scorer_, collections.Mapping):
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
420 is_multimetric = True
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
421 else:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
422 is_multimetric = False
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
423
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
424 best_estimator_ = getattr(searcher, "best_estimator_")
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
425
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
426 # TODO Solve deep learning models in pipeline
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
427 if best_estimator_.__class__.__name__ == "KerasGBatchClassifier":
11
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
428 test_score = best_estimator_.evaluate(
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
429 X_test, scorer=scorer_, is_multimetric=is_multimetric
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
430 )
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
431 else:
11
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
432 test_score = _score(
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
433 best_estimator_, X_test, y_test, scorer_, is_multimetric=is_multimetric
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
434 )
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
435
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
436 if not is_multimetric:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
437 test_score = {primary_scoring: test_score}
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
438 for key, value in test_score.items():
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
439 test_score[key] = [value]
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
440 result_df = pd.DataFrame(test_score)
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
441 result_df.to_csv(path_or_buf=outfile, sep="\t", header=True, index=False)
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
442
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
443 return searcher
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
444
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
445
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
446 def main(
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
447 inputs,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
448 infile_estimator,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
449 infile1,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
450 infile2,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
451 outfile_result,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
452 outfile_object=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
453 outfile_weights=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
454 groups=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
455 ref_seq=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
456 intervals=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
457 targets=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
458 fasta_path=None,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
459 ):
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
460 """
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
461 Parameter
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
462 ---------
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
463 inputs : str
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
464 File path to galaxy tool parameter
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
465
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
466 infile_estimator : str
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
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diff changeset
467 File path to estimator
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
468
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
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diff changeset
469 infile1 : str
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
470 File path to dataset containing features
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
471
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
472 infile2 : str
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
473 File path to dataset containing target values
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
474
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
475 outfile_result : str
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
476 File path to save the results, either cv_results or test result
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
477
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
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diff changeset
478 outfile_object : str, optional
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
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diff changeset
479 File path to save searchCV object
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
480
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
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diff changeset
481 outfile_weights : str, optional
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
482 File path to save model weights
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
483
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
484 groups : str
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
485 File path to dataset containing groups labels
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
486
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
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diff changeset
487 ref_seq : str
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
488 File path to dataset containing genome sequence file
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
489
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
490 intervals : str
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
491 File path to dataset containing interval file
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
492
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
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diff changeset
493 targets : str
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
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diff changeset
494 File path to dataset compressed target bed file
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
495
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
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diff changeset
496 fasta_path : str
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
497 File path to dataset containing fasta file
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
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diff changeset
498 """
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
499 warnings.simplefilter("ignore")
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
500
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
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diff changeset
501 # store read dataframe object
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
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diff changeset
502 loaded_df = {}
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
503
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
504 with open(inputs, "r") as param_handler:
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
505 params = json.load(param_handler)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
506
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
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diff changeset
507 # Override the refit parameter
11
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
508 params["search_schemes"]["options"]["refit"] = (
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
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diff changeset
509 True if params["save"] != "nope" else False
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
510 )
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
511
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
512 with open(infile_estimator, "rb") as estimator_handler:
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
513 estimator = load_model(estimator_handler)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
514
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
515 optimizer = params["search_schemes"]["selected_search_scheme"]
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
516 optimizer = getattr(model_selection, optimizer)
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
517
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
518 # handle gridsearchcv options
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
519 options = params["search_schemes"]["options"]
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
520
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
521 if groups:
11
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
522 header = (
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
523 "infer" if (options["cv_selector"]["groups_selector"]["header_g"]) else None
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
524 )
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
525 column_option = options["cv_selector"]["groups_selector"][
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
526 "column_selector_options_g"
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
527 ]["selected_column_selector_option_g"]
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
528 if column_option in [
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
529 "by_index_number",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
530 "all_but_by_index_number",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
531 "by_header_name",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
532 "all_but_by_header_name",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
533 ]:
11
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
534 c = options["cv_selector"]["groups_selector"]["column_selector_options_g"][
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
535 "col_g"
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
536 ]
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
537 else:
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
538 c = None
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
539
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
540 df_key = groups + repr(header)
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
541
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
542 groups = pd.read_csv(groups, sep="\t", header=header, parse_dates=True)
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
543 loaded_df[df_key] = groups
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
544
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
545 groups = read_columns(
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
546 groups,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
547 c=c,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
548 c_option=column_option,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
549 sep="\t",
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
550 header=header,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
551 parse_dates=True,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
552 )
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
553 groups = groups.ravel()
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
554 options["cv_selector"]["groups_selector"] = groups
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
555
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
556 splitter, groups = get_cv(options.pop("cv_selector"))
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
557 options["cv"] = splitter
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
558 primary_scoring = options["scoring"]["primary_scoring"]
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
559 # get_scoring() expects secondary_scoring to be a comma separated string (not a list)
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
560 # Check if secondary_scoring is specified
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
561 secondary_scoring = options["scoring"].get("secondary_scoring", None)
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
562 if secondary_scoring is not None:
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
563 # If secondary_scoring is specified, convert the list into comman separated string
11
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
564 options["scoring"]["secondary_scoring"] = ",".join(
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
565 options["scoring"]["secondary_scoring"]
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
566 )
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
567 options["scoring"] = get_scoring(options["scoring"])
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
568 if options["error_score"]:
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
569 options["error_score"] = "raise"
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
570 else:
11
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
571 options["error_score"] = np.nan
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
572 if options["refit"] and isinstance(options["scoring"], dict):
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
573 options["refit"] = primary_scoring
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
574 if "pre_dispatch" in options and options["pre_dispatch"] == "":
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
575 options["pre_dispatch"] = None
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
576
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
577 params_builder = params["search_schemes"]["search_params_builder"]
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
578 param_grid = _eval_search_params(params_builder)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
579
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
580 estimator = clean_params(estimator)
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
581
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
582 # save the SearchCV object without fit
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
583 if params["save"] == "save_no_fit":
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
584 searcher = optimizer(estimator, param_grid, **options)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
585 print(searcher)
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
586 with open(outfile_object, "wb") as output_handler:
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
587 pickle.dump(searcher, output_handler, pickle.HIGHEST_PROTOCOL)
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
588 return 0
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
589
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
590 # read inputs and loads new attributes, like paths
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
591 estimator, X, y = _handle_X_y(
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
592 estimator,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
593 params,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
594 infile1,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
595 infile2,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
596 loaded_df=loaded_df,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
597 ref_seq=ref_seq,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
598 intervals=intervals,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
599 targets=targets,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
600 fasta_path=fasta_path,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
601 )
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
602
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
603 # cache iraps_core fits could increase search speed significantly
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
604 memory = joblib.Memory(location=CACHE_DIR, verbose=0)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
605 main_est = get_main_estimator(estimator)
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
606 if main_est.__class__.__name__ == "IRAPSClassifier":
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
607 main_est.set_params(memory=memory)
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
608
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
609 searcher = optimizer(estimator, param_grid, **options)
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
610
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
611 split_mode = params["outer_split"].pop("split_mode")
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
612
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
613 if split_mode == "nested_cv":
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
614 # make sure refit is choosen
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
615 # this could be True for sklearn models, but not the case for
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
616 # deep learning models
11
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
617 if not options["refit"] and not all(
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
618 hasattr(estimator, attr) for attr in ("config", "model_type")
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
619 ):
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
620 warnings.warn("Refit is change to `True` for nested validation!")
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
621 setattr(searcher, "refit", True)
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
622
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
623 outer_cv, _ = get_cv(params["outer_split"]["cv_selector"])
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
624 # nested CV, outer cv using cross_validate
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
625 if options["error_score"] == "raise":
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
626 rval = cross_validate(
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
627 searcher,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
628 X,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
629 y,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
630 scoring=options["scoring"],
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
631 cv=outer_cv,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
632 n_jobs=N_JOBS,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
633 verbose=options["verbose"],
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
634 return_estimator=(params["save"] == "save_estimator"),
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
635 error_score=options["error_score"],
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
636 return_train_score=True,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
637 )
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
638 else:
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
639 warnings.simplefilter("always", FitFailedWarning)
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
640 with warnings.catch_warnings(record=True) as w:
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
641 try:
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
642 rval = cross_validate(
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
643 searcher,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
644 X,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
645 y,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
646 scoring=options["scoring"],
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
647 cv=outer_cv,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
648 n_jobs=N_JOBS,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
649 verbose=options["verbose"],
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
650 return_estimator=(params["save"] == "save_estimator"),
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
651 error_score=options["error_score"],
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
652 return_train_score=True,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
653 )
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
654 except ValueError:
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
655 pass
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
656 for warning in w:
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
657 print(repr(warning.message))
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
658
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
659 fitted_searchers = rval.pop("estimator", [])
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
660 if fitted_searchers:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
661 import os
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
662
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
663 pwd = os.getcwd()
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
664 save_dir = os.path.join(pwd, "cv_results_in_folds")
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
665 try:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
666 os.mkdir(save_dir)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
667 for idx, obj in enumerate(fitted_searchers):
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
668 target_name = "cv_results_" + "_" + "split%d" % idx
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
669 target_path = os.path.join(pwd, save_dir, target_name)
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
670 cv_results_ = getattr(obj, "cv_results_", None)
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
671 if not cv_results_:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
672 print("%s is not available" % target_name)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
673 continue
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
674 cv_results_ = pd.DataFrame(cv_results_)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
675 cv_results_ = cv_results_[sorted(cv_results_.columns)]
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
676 cv_results_.to_csv(target_path, sep="\t", header=True, index=False)
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
677 except Exception as e:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
678 print(e)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
679 finally:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
680 del os
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
681
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
682 keys = list(rval.keys())
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
683 for k in keys:
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
684 if k.startswith("test"):
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
685 rval["mean_" + k] = np.mean(rval[k])
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
686 rval["std_" + k] = np.std(rval[k])
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
687 if k.endswith("time"):
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
688 rval.pop(k)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
689 rval = pd.DataFrame(rval)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
690 rval = rval[sorted(rval.columns)]
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
691 rval.to_csv(path_or_buf=outfile_result, sep="\t", header=True, index=False)
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
692 # deprecate train test split mode
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
693 """searcher = _do_train_test_split_val(
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
694 searcher, X, y, params,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
695 primary_scoring=primary_scoring,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
696 error_score=options['error_score'],
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
697 groups=groups,
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
698 outfile=outfile_result)"""
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
699 return 0
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
700
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
701 # no outer split
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
702 else:
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
703 searcher.set_params(n_jobs=N_JOBS)
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
704 if options["error_score"] == "raise":
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
705 searcher.fit(X, y, groups=groups)
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
706 else:
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
707 warnings.simplefilter("always", FitFailedWarning)
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
708 with warnings.catch_warnings(record=True) as w:
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
709 try:
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
710 searcher.fit(X, y, groups=groups)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
711 except ValueError:
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
712 pass
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
713 for warning in w:
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
714 print(repr(warning.message))
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
715
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
716 cv_results = pd.DataFrame(searcher.cv_results_)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
717 cv_results = cv_results[sorted(cv_results.columns)]
11
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
718 cv_results.to_csv(
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
719 path_or_buf=outfile_result, sep="\t", header=True, index=False
0380f10c4e04 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents: 10
diff changeset
720 )
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
721
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
722 memory.clear(warn=False)
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
723
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
724 # output best estimator, and weights if applicable
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
725 if outfile_object:
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
726 best_estimator_ = getattr(searcher, "best_estimator_", None)
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
727 if not best_estimator_:
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
728 warnings.warn(
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
729 "GridSearchCV object has no attribute "
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
730 "'best_estimator_', because either it's "
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
731 "nested gridsearch or `refit` is False!"
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
732 )
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
733 return
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
734
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
735 # clean prams
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
736 best_estimator_ = clean_params(best_estimator_)
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
737
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
738 main_est = get_main_estimator(best_estimator_)
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
739
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
740 if hasattr(main_est, "model_") and hasattr(main_est, "save_weights"):
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
741 if outfile_weights:
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
742 main_est.save_weights(outfile_weights)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
743 del main_est.model_
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
744 del main_est.fit_params
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
745 del main_est.model_class_
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
746 del main_est.validation_data
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
747 if getattr(main_est, "data_generator_", None):
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
748 del main_est.data_generator_
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
749
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
750 with open(outfile_object, "wb") as output_handler:
7
00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"
bgruening
parents: 3
diff changeset
751 print("Best estimator is saved: %s " % repr(best_estimator_))
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
752 pickle.dump(best_estimator_, output_handler, pickle.HIGHEST_PROTOCOL)
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
753
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
754
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
755 if __name__ == "__main__":
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
756 aparser = argparse.ArgumentParser()
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
757 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
758 aparser.add_argument("-e", "--estimator", dest="infile_estimator")
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
759 aparser.add_argument("-X", "--infile1", dest="infile1")
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
760 aparser.add_argument("-y", "--infile2", dest="infile2")
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
761 aparser.add_argument("-O", "--outfile_result", dest="outfile_result")
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
762 aparser.add_argument("-o", "--outfile_object", dest="outfile_object")
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
763 aparser.add_argument("-w", "--outfile_weights", dest="outfile_weights")
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
764 aparser.add_argument("-g", "--groups", dest="groups")
2
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
765 aparser.add_argument("-r", "--ref_seq", dest="ref_seq")
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
766 aparser.add_argument("-b", "--intervals", dest="intervals")
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
767 aparser.add_argument("-t", "--targets", dest="targets")
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e
bgruening
parents: 0
diff changeset
768 aparser.add_argument("-f", "--fasta_path", dest="fasta_path")
0
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
769 args = aparser.parse_args()
47467890f541 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents:
diff changeset
770
9
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
771 main(
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
772 args.inputs,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
773 args.infile_estimator,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
774 args.infile1,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
775 args.infile2,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
776 args.outfile_result,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
777 outfile_object=args.outfile_object,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
778 outfile_weights=args.outfile_weights,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
779 groups=args.groups,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
780 ref_seq=args.ref_seq,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
781 intervals=args.intervals,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
782 targets=args.targets,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
783 fasta_path=args.fasta_path,
b8c92e94ac1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 7
diff changeset
784 )