Mercurial > repos > bgruening > sklearn_nn_classifier

annotate search_model_validation.py @ 22:34d31bd995e9 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
author bgruening
date Tue, 13 Apr 2021 22:12:07 +0000
parents 1d3447c2203c
children 823ecc0bce45
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1 import argparse
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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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9 import imblearn
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10 import joblib
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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 (
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15 clean_params,
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16 get_cv,
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17 get_main_estimator,
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18 get_module,
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19 get_scoring,
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20 load_model,
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21 read_columns,
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22 SafeEval,
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23 try_get_attr
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24 )
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25 from scipy.io import mmread
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26 from sklearn import (
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27 cluster,
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28 decomposition,
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29 feature_selection,
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30 kernel_approximation,
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31 model_selection,
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32 preprocessing,
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33 )
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34 from sklearn.exceptions import FitFailedWarning
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35 from sklearn.model_selection import _search, _validation
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36 from sklearn.model_selection._validation import _score, cross_validate
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37
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38
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39 _fit_and_score = try_get_attr("galaxy_ml.model_validations", "_fit_and_score")
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40 setattr(_search, "_fit_and_score", _fit_and_score)
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41 setattr(_validation, "_fit_and_score", _fit_and_score)
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43 N_JOBS = int(os.environ.get("GALAXY_SLOTS", 1))
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44 # handle disk cache
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45 CACHE_DIR = os.path.join(os.getcwd(), "cached")
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46 del os
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47 NON_SEARCHABLE = ("n_jobs", "pre_dispatch", "memory", "_path", "nthread", "callbacks")
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49
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50 def _eval_search_params(params_builder):
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51 search_params = {}
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53 for p in params_builder["param_set"]:
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54 search_list = p["sp_list"].strip()
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55 if search_list == "":
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56 continue
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57
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58 param_name = p["sp_name"]
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59 if param_name.lower().endswith(NON_SEARCHABLE):
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60 print("Warning: `%s` is not eligible for search and was " "omitted!" % param_name)
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61 continue
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62
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63 if not search_list.startswith(":"):
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64 safe_eval = SafeEval(load_scipy=True, load_numpy=True)
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65 ev = safe_eval(search_list)
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66 search_params[param_name] = ev
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67 else:
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68 # Have `:` before search list, asks for estimator evaluatio
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69 safe_eval_es = SafeEval(load_estimators=True)
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70 search_list = search_list[1:].strip()
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71 # TODO maybe add regular express check
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72 ev = safe_eval_es(search_list)
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73 preprocessings = (
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74 preprocessing.StandardScaler(),
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75 preprocessing.Binarizer(),
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76 preprocessing.MaxAbsScaler(),
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77 preprocessing.Normalizer(),
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78 preprocessing.MinMaxScaler(),
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79 preprocessing.PolynomialFeatures(),
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80 preprocessing.RobustScaler(),
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81 feature_selection.SelectKBest(),
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82 feature_selection.GenericUnivariateSelect(),
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83 feature_selection.SelectPercentile(),
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84 feature_selection.SelectFpr(),
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85 feature_selection.SelectFdr(),
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86 feature_selection.SelectFwe(),
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87 feature_selection.VarianceThreshold(),
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88 decomposition.FactorAnalysis(random_state=0),
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89 decomposition.FastICA(random_state=0),
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90 decomposition.IncrementalPCA(),
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91 decomposition.KernelPCA(random_state=0, n_jobs=N_JOBS),
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92 decomposition.LatentDirichletAllocation(random_state=0, n_jobs=N_JOBS),
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93 decomposition.MiniBatchDictionaryLearning(random_state=0, n_jobs=N_JOBS),
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94 decomposition.MiniBatchSparsePCA(random_state=0, n_jobs=N_JOBS),
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95 decomposition.NMF(random_state=0),
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96 decomposition.PCA(random_state=0),
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97 decomposition.SparsePCA(random_state=0, n_jobs=N_JOBS),
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98 decomposition.TruncatedSVD(random_state=0),
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99 kernel_approximation.Nystroem(random_state=0),
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100 kernel_approximation.RBFSampler(random_state=0),
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101 kernel_approximation.AdditiveChi2Sampler(),
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102 kernel_approximation.SkewedChi2Sampler(random_state=0),
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103 cluster.FeatureAgglomeration(),
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104 skrebate.ReliefF(n_jobs=N_JOBS),
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105 skrebate.SURF(n_jobs=N_JOBS),
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106 skrebate.SURFstar(n_jobs=N_JOBS),
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107 skrebate.MultiSURF(n_jobs=N_JOBS),
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108 skrebate.MultiSURFstar(n_jobs=N_JOBS),
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109 imblearn.under_sampling.ClusterCentroids(random_state=0, n_jobs=N_JOBS),
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110 imblearn.under_sampling.CondensedNearestNeighbour(random_state=0, n_jobs=N_JOBS),
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111 imblearn.under_sampling.EditedNearestNeighbours(random_state=0, n_jobs=N_JOBS),
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112 imblearn.under_sampling.RepeatedEditedNearestNeighbours(random_state=0, n_jobs=N_JOBS),
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113 imblearn.under_sampling.AllKNN(random_state=0, n_jobs=N_JOBS),
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114 imblearn.under_sampling.InstanceHardnessThreshold(random_state=0, n_jobs=N_JOBS),
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115 imblearn.under_sampling.NearMiss(random_state=0, n_jobs=N_JOBS),
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116 imblearn.under_sampling.NeighbourhoodCleaningRule(random_state=0, n_jobs=N_JOBS),
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117 imblearn.under_sampling.OneSidedSelection(random_state=0, n_jobs=N_JOBS),
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118 imblearn.under_sampling.RandomUnderSampler(random_state=0),
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119 imblearn.under_sampling.TomekLinks(random_state=0, n_jobs=N_JOBS),
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120 imblearn.over_sampling.ADASYN(random_state=0, n_jobs=N_JOBS),
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121 imblearn.over_sampling.RandomOverSampler(random_state=0),
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122 imblearn.over_sampling.SMOTE(random_state=0, n_jobs=N_JOBS),
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123 imblearn.over_sampling.SVMSMOTE(random_state=0, n_jobs=N_JOBS),
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124 imblearn.over_sampling.BorderlineSMOTE(random_state=0, n_jobs=N_JOBS),
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125 imblearn.over_sampling.SMOTENC(categorical_features=[], random_state=0, n_jobs=N_JOBS),
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126 imblearn.combine.SMOTEENN(random_state=0),
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127 imblearn.combine.SMOTETomek(random_state=0),
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128 )
9
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129 newlist = []
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130 for obj in ev:
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131 if obj is None:
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132 newlist.append(None)
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133 elif obj == "all_0":
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134 newlist.extend(preprocessings[0:35])
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135 elif obj == "sk_prep_all": # no KernalCenter()
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136 newlist.extend(preprocessings[0:7])
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137 elif obj == "fs_all":
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138 newlist.extend(preprocessings[7:14])
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139 elif obj == "decomp_all":
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140 newlist.extend(preprocessings[14:25])
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141 elif obj == "k_appr_all":
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142 newlist.extend(preprocessings[25:29])
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143 elif obj == "reb_all":
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144 newlist.extend(preprocessings[30:35])
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145 elif obj == "imb_all":
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146 newlist.extend(preprocessings[35:54])
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147 elif type(obj) is int and -1 < obj < len(preprocessings):
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148 newlist.append(preprocessings[obj])
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149 elif hasattr(obj, "get_params"): # user uploaded object
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150 if "n_jobs" in obj.get_params():
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151 newlist.append(obj.set_params(n_jobs=N_JOBS))
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152 else:
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153 newlist.append(obj)
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154 else:
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155 sys.exit("Unsupported estimator type: %r" % (obj))
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156
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157 search_params[param_name] = newlist
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158
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159 return search_params
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160
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161
21
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162 def _handle_X_y(
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163 estimator,
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164 params,
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165 infile1,
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166 infile2,
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167 loaded_df={},
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168 ref_seq=None,
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169 intervals=None,
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170 targets=None,
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171 fasta_path=None,
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172 ):
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173 """read inputs
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174
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175 Params
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176 -------
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177 estimator : estimator object
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178 params : dict
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179 Galaxy tool parameter inputs
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180 infile1 : str
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181 File path to dataset containing features
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182 infile2 : str
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183 File path to dataset containing target values
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184 loaded_df : dict
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185 Contains loaded DataFrame objects with file path as keys
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186 ref_seq : str
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187 File path to dataset containing genome sequence file
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188 interval : str
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189 File path to dataset containing interval file
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190 targets : str
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191 File path to dataset compressed target bed file
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192 fasta_path : str
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193 File path to dataset containing fasta file
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194
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195
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196 Returns
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197 -------
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198 estimator : estimator object after setting new attributes
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199 X : numpy array
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200 y : numpy array
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201 """
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202 estimator_params = estimator.get_params()
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203
21
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204 input_type = params["input_options"]["selected_input"]
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205 # tabular input
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206 if input_type == "tabular":
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207 header = "infer" if params["input_options"]["header1"] else None
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208 column_option = params["input_options"]["column_selector_options_1"]["selected_column_selector_option"]
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209 if column_option in [
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210 "by_index_number",
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211 "all_but_by_index_number",
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212 "by_header_name",
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213 "all_but_by_header_name",
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214 ]:
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215 c = params["input_options"]["column_selector_options_1"]["col1"]
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216 else:
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217 c = None
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218
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219 df_key = infile1 + repr(header)
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220
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221 if df_key in loaded_df:
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222 infile1 = loaded_df[df_key]
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223
21
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224 df = pd.read_csv(infile1, sep="\t", header=header, parse_dates=True)
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225 loaded_df[df_key] = df
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226
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227 X = read_columns(df, c=c, c_option=column_option).astype(float)
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228 # sparse input
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229 elif input_type == "sparse":
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230 X = mmread(open(infile1, "r"))
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231
12
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232 # fasta_file input
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233 elif input_type == "seq_fasta":
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234 pyfaidx = get_module("pyfaidx")
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235 sequences = pyfaidx.Fasta(fasta_path)
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236 n_seqs = len(sequences.keys())
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237 X = np.arange(n_seqs)[:, np.newaxis]
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238 for param in estimator_params.keys():
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239 if param.endswith("fasta_path"):
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240 estimator.set_params(**{param: fasta_path})
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241 break
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242 else:
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243 raise ValueError(
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244 "The selected estimator doesn't support "
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245 "fasta file input! Please consider using "
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246 "KerasGBatchClassifier with "
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247 "FastaDNABatchGenerator/FastaProteinBatchGenerator "
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248 "or having GenomeOneHotEncoder/ProteinOneHotEncoder "
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249 "in pipeline!"
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250 )
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251
21
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252 elif input_type == "refseq_and_interval":
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253 path_params = {
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254 "data_batch_generator__ref_genome_path": ref_seq,
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255 "data_batch_generator__intervals_path": intervals,
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256 "data_batch_generator__target_path": targets,
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257 }
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258 estimator.set_params(**path_params)
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259 n_intervals = sum(1 for line in open(intervals))
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260 X = np.arange(n_intervals)[:, np.newaxis]
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261
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262 # Get target y
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263 header = "infer" if params["input_options"]["header2"] else None
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264 column_option = params["input_options"]["column_selector_options_2"]["selected_column_selector_option2"]
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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265 if column_option in [
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266 "by_index_number",
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267 "all_but_by_index_number",
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268 "by_header_name",
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269 "all_but_by_header_name",
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270 ]:
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271 c = params["input_options"]["column_selector_options_2"]["col2"]
9
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272 else:
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273 c = None
12
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274
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275 df_key = infile2 + repr(header)
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276 if df_key in loaded_df:
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277 infile2 = loaded_df[df_key]
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278 else:
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279 infile2 = pd.read_csv(infile2, sep="\t", header=header, parse_dates=True)
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280 loaded_df[df_key] = infile2
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281
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282 y = read_columns(infile2, c=c, c_option=column_option, sep="\t", header=header, parse_dates=True)
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283 if len(y.shape) == 2 and y.shape[1] == 1:
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284 y = y.ravel()
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285 if input_type == "refseq_and_interval":
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286 estimator.set_params(data_batch_generator__features=y.ravel().tolist())
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287 y = None
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288 # end y
9
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289
17
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290 return estimator, X, y
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291
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292
21
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293 def _do_outer_cv(searcher, X, y, outer_cv, scoring, error_score="raise", outfile=None):
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294 """Do outer cross-validation for nested CV
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295
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296 Parameters
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297 ----------
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298 searcher : object
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299 SearchCV object
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300 X : numpy array
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301 Containing features
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302 y : numpy array
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303 Target values or labels
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304 outer_cv : int or CV splitter
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305 Control the cv splitting
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306 scoring : object
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307 Scorer
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308 error_score: str, float or numpy float
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309 Whether to raise fit error or return an value
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310 outfile : str
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311 File path to store the restuls
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312 """
21
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313 if error_score == "raise":
17
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314 rval = cross_validate(
21
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315 searcher,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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316 X,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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317 y,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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318 scoring=scoring,
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319 cv=outer_cv,
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320 n_jobs=N_JOBS,
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321 verbose=0,
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322 error_score=error_score,
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323 )
17
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324 else:
21
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325 warnings.simplefilter("always", FitFailedWarning)
17
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326 with warnings.catch_warnings(record=True) as w:
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327 try:
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328 rval = cross_validate(
21
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329 searcher,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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330 X,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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331 y,
17
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332 scoring=scoring,
21
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333 cv=outer_cv,
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334 n_jobs=N_JOBS,
17
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335 verbose=0,
21
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336 error_score=error_score,
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337 )
17
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338 except ValueError:
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339 pass
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340 for warning in w:
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341 print(repr(warning.message))
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342
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343 keys = list(rval.keys())
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344 for k in keys:
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345 if k.startswith("test"):
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346 rval["mean_" + k] = np.mean(rval[k])
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347 rval["std_" + k] = np.std(rval[k])
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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348 if k.endswith("time"):
17
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349 rval.pop(k)
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350 rval = pd.DataFrame(rval)
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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351 rval = rval[sorted(rval.columns)]
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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352 rval.to_csv(path_or_buf=outfile, sep="\t", header=True, index=False)
17
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353
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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354
21
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355 def _do_train_test_split_val(
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
356 searcher,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
357 X,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
358 y,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
359 params,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
360 error_score="raise",
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
361 primary_scoring=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
362 groups=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
363 outfile=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
364 ):
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
365 """do train test split, searchCV validates on the train and then use
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
366 the best_estimator_ to evaluate on the test
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
367
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
368 Returns
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
369 --------
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
370 Fitted SearchCV object
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
371 """
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
372 train_test_split = try_get_attr("galaxy_ml.model_validations", "train_test_split")
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
373 split_options = params["outer_split"]
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
374
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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375 # splits
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
376 if split_options["shuffle"] == "stratified":
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
377 split_options["labels"] = y
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
378 X, X_test, y, y_test = train_test_split(X, y, **split_options)
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
379 elif split_options["shuffle"] == "group":
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
380 if groups is None:
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
381 raise ValueError("No group based CV option was choosen for " "group shuffle!")
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
382 split_options["labels"] = groups
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
383 if y is None:
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
384 X, X_test, groups, _ = train_test_split(X, groups, **split_options)
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
385 else:
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
386 X, X_test, y, y_test, groups, _ = train_test_split(X, y, groups, **split_options)
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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387 else:
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
388 if split_options["shuffle"] == "None":
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
389 split_options["shuffle"] = None
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
390 X, X_test, y, y_test = train_test_split(X, y, **split_options)
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
391
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
392 if error_score == "raise":
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
393 searcher.fit(X, y, groups=groups)
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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394 else:
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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395 warnings.simplefilter("always", FitFailedWarning)
17
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396 with warnings.catch_warnings(record=True) as w:
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
397 try:
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
398 searcher.fit(X, y, groups=groups)
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
399 except ValueError:
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
400 pass
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
401 for warning in w:
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
402 print(repr(warning.message))
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
403
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
404 scorer_ = searcher.scorer_
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
405 if isinstance(scorer_, collections.Mapping):
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
406 is_multimetric = True
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
407 else:
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
408 is_multimetric = False
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
409
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
410 best_estimator_ = getattr(searcher, "best_estimator_")
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
411
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
412 # TODO Solve deep learning models in pipeline
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
413 if best_estimator_.__class__.__name__ == "KerasGBatchClassifier":
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
414 test_score = best_estimator_.evaluate(X_test, scorer=scorer_, is_multimetric=is_multimetric)
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
415 else:
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
416 test_score = _score(best_estimator_, X_test, y_test, scorer_, is_multimetric=is_multimetric)
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
417
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
418 if not is_multimetric:
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
419 test_score = {primary_scoring: test_score}
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
420 for key, value in test_score.items():
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
421 test_score[key] = [value]
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
422 result_df = pd.DataFrame(test_score)
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
423 result_df.to_csv(path_or_buf=outfile, sep="\t", header=True, index=False)
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
424
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
425 return searcher
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
426
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
427
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
428 def main(
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
429 inputs,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
430 infile_estimator,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
431 infile1,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
432 infile2,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
433 outfile_result,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
434 outfile_object=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
435 outfile_weights=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
436 groups=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
437 ref_seq=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
438 intervals=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
439 targets=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
440 fasta_path=None,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
441 ):
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
442 """
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
443 Parameter
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
444 ---------
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
445 inputs : str
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
446 File path to galaxy tool parameter
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
447
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
448 infile_estimator : str
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
449 File path to estimator
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
450
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
451 infile1 : str
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
452 File path to dataset containing features
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
453
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
454 infile2 : str
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
455 File path to dataset containing target values
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
456
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
457 outfile_result : str
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
458 File path to save the results, either cv_results or test result
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
459
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
460 outfile_object : str, optional
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
461 File path to save searchCV object
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
462
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
463 outfile_weights : str, optional
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
464 File path to save model weights
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
465
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
466 groups : str
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
467 File path to dataset containing groups labels
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
468
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
469 ref_seq : str
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
470 File path to dataset containing genome sequence file
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
471
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
472 intervals : str
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
473 File path to dataset containing interval file
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
474
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
475 targets : str
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
476 File path to dataset compressed target bed file
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
477
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
478 fasta_path : str
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
479 File path to dataset containing fasta file
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
480 """
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
481 warnings.simplefilter("ignore")
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
482
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
483 # store read dataframe object
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
484 loaded_df = {}
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
485
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
486 with open(inputs, "r") as param_handler:
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
487 params = json.load(param_handler)
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
488
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
489 # Override the refit parameter
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
490 params["search_schemes"]["options"]["refit"] = True if params["save"] != "nope" else False
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
491
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
492 with open(infile_estimator, "rb") as estimator_handler:
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
493 estimator = load_model(estimator_handler)
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
494
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
495 optimizer = params["search_schemes"]["selected_search_scheme"]
9
ed7b1654e841 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
diff changeset
496 optimizer = getattr(model_selection, optimizer)
ed7b1654e841 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
diff changeset
497
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
498 # handle gridsearchcv options
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
499 options = params["search_schemes"]["options"]
10
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
500
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
501 if groups:
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
502 header = "infer" if (options["cv_selector"]["groups_selector"]["header_g"]) else None
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
503 column_option = options["cv_selector"]["groups_selector"]["column_selector_options_g"][
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
504 "selected_column_selector_option_g"
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
505 ]
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
506 if column_option in [
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
507 "by_index_number",
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
508 "all_but_by_index_number",
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
509 "by_header_name",
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
510 "all_but_by_header_name",
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
511 ]:
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
512 c = options["cv_selector"]["groups_selector"]["column_selector_options_g"]["col_g"]
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
513 else:
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
514 c = None
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
515
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
516 df_key = groups + repr(header)
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
517
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
518 groups = pd.read_csv(groups, sep="\t", header=header, parse_dates=True)
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
519 loaded_df[df_key] = groups
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
520
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
521 groups = read_columns(
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
522 groups,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
523 c=c,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
524 c_option=column_option,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
525 sep="\t",
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
526 header=header,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
527 parse_dates=True,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
528 )
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
529 groups = groups.ravel()
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
530 options["cv_selector"]["groups_selector"] = groups
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
531
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
532 splitter, groups = get_cv(options.pop("cv_selector"))
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
533 options["cv"] = splitter
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
534 primary_scoring = options["scoring"]["primary_scoring"]
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
535 # get_scoring() expects secondary_scoring to be a comma separated string (not a list)
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
536 # Check if secondary_scoring is specified
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
537 secondary_scoring = options["scoring"].get("secondary_scoring", None)
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
538 if secondary_scoring is not None:
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
539 # If secondary_scoring is specified, convert the list into comman separated string
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
540 options["scoring"]["secondary_scoring"] = ",".join(options["scoring"]["secondary_scoring"])
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
541 options["scoring"] = get_scoring(options["scoring"])
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
542 if options["error_score"]:
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
543 options["error_score"] = "raise"
9
ed7b1654e841 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
diff changeset
544 else:
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
545 options["error_score"] = np.NaN
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
546 if options["refit"] and isinstance(options["scoring"], dict):
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
547 options["refit"] = primary_scoring
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
548 if "pre_dispatch" in options and options["pre_dispatch"] == "":
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
549 options["pre_dispatch"] = None
9
ed7b1654e841 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
diff changeset
550
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
551 params_builder = params["search_schemes"]["search_params_builder"]
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
552 param_grid = _eval_search_params(params_builder)
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
553
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
554 estimator = clean_params(estimator)
10
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
555
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
556 # save the SearchCV object without fit
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
557 if params["save"] == "save_no_fit":
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
558 searcher = optimizer(estimator, param_grid, **options)
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
559 print(searcher)
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
560 with open(outfile_object, "wb") as output_handler:
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
561 pickle.dump(searcher, output_handler, pickle.HIGHEST_PROTOCOL)
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
562 return 0
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
563
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
564 # read inputs and loads new attributes, like paths
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
565 estimator, X, y = _handle_X_y(
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
566 estimator,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
567 params,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
568 infile1,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
569 infile2,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
570 loaded_df=loaded_df,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
571 ref_seq=ref_seq,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
572 intervals=intervals,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
573 targets=targets,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
574 fasta_path=fasta_path,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
575 )
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
576
10
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
577 # cache iraps_core fits could increase search speed significantly
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
578 memory = joblib.Memory(location=CACHE_DIR, verbose=0)
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
579 main_est = get_main_estimator(estimator)
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
580 if main_est.__class__.__name__ == "IRAPSClassifier":
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
581 main_est.set_params(memory=memory)
10
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
582
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
583 searcher = optimizer(estimator, param_grid, **options)
9
ed7b1654e841 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
diff changeset
584
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
585 split_mode = params["outer_split"].pop("split_mode")
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
586
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
587 if split_mode == "nested_cv":
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
588 # make sure refit is choosen
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
589 # this could be True for sklearn models, but not the case for
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
590 # deep learning models
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
591 if not options["refit"] and not all(hasattr(estimator, attr) for attr in ("config", "model_type")):
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
592 warnings.warn("Refit is change to `True` for nested validation!")
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
593 setattr(searcher, "refit", True)
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
594
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
595 outer_cv, _ = get_cv(params["outer_split"]["cv_selector"])
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
596 # nested CV, outer cv using cross_validate
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
597 if options["error_score"] == "raise":
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
598 rval = cross_validate(
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
599 searcher,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
600 X,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
601 y,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
602 scoring=options["scoring"],
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
603 cv=outer_cv,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
604 n_jobs=N_JOBS,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
605 verbose=options["verbose"],
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
606 return_estimator=(params["save"] == "save_estimator"),
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
607 error_score=options["error_score"],
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
608 return_train_score=True,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
609 )
10
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
610 else:
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
611 warnings.simplefilter("always", FitFailedWarning)
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
612 with warnings.catch_warnings(record=True) as w:
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
613 try:
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
614 rval = cross_validate(
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
615 searcher,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
616 X,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
617 y,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
618 scoring=options["scoring"],
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
619 cv=outer_cv,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
620 n_jobs=N_JOBS,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
621 verbose=options["verbose"],
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
622 return_estimator=(params["save"] == "save_estimator"),
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
623 error_score=options["error_score"],
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
624 return_train_score=True,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
625 )
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
626 except ValueError:
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
627 pass
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
628 for warning in w:
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
629 print(repr(warning.message))
9
ed7b1654e841 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
diff changeset
630
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
631 fitted_searchers = rval.pop("estimator", [])
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
632 if fitted_searchers:
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
633 import os
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
634
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
635 pwd = os.getcwd()
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
636 save_dir = os.path.join(pwd, "cv_results_in_folds")
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
637 try:
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
638 os.mkdir(save_dir)
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
639 for idx, obj in enumerate(fitted_searchers):
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
640 target_name = "cv_results_" + "_" + "split%d" % idx
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
641 target_path = os.path.join(pwd, save_dir, target_name)
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
642 cv_results_ = getattr(obj, "cv_results_", None)
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
643 if not cv_results_:
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
644 print("%s is not available" % target_name)
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
645 continue
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
646 cv_results_ = pd.DataFrame(cv_results_)
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
647 cv_results_ = cv_results_[sorted(cv_results_.columns)]
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
648 cv_results_.to_csv(target_path, sep="\t", header=True, index=False)
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
649 except Exception as e:
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
650 print(e)
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
651 finally:
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
652 del os
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
653
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
654 keys = list(rval.keys())
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
655 for k in keys:
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
656 if k.startswith("test"):
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
657 rval["mean_" + k] = np.mean(rval[k])
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
658 rval["std_" + k] = np.std(rval[k])
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
659 if k.endswith("time"):
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
660 rval.pop(k)
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
661 rval = pd.DataFrame(rval)
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
662 rval = rval[sorted(rval.columns)]
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
663 rval.to_csv(path_or_buf=outfile_result, sep="\t", header=True, index=False)
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
664 # deprecate train test split mode
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
665 """searcher = _do_train_test_split_val(
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
666 searcher, X, y, params,
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
667 primary_scoring=primary_scoring,
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
668 error_score=options['error_score'],
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
669 groups=groups,
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
670 outfile=outfile_result)"""
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
671 return 0
10
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
672
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
673 # no outer split
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
674 else:
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
675 searcher.set_params(n_jobs=N_JOBS)
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
676 if options["error_score"] == "raise":
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
677 searcher.fit(X, y, groups=groups)
10
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
678 else:
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
679 warnings.simplefilter("always", FitFailedWarning)
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
680 with warnings.catch_warnings(record=True) as w:
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
681 try:
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
682 searcher.fit(X, y, groups=groups)
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
683 except ValueError:
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
684 pass
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
685 for warning in w:
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
686 print(repr(warning.message))
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
687
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
688 cv_results = pd.DataFrame(searcher.cv_results_)
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
689 cv_results = cv_results[sorted(cv_results.columns)]
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
690 cv_results.to_csv(path_or_buf=outfile_result, sep="\t", header=True, index=False)
10
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
691
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
692 memory.clear(warn=False)
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
693
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
694 # output best estimator, and weights if applicable
10
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
695 if outfile_object:
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
696 best_estimator_ = getattr(searcher, "best_estimator_", None)
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
697 if not best_estimator_:
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
698 warnings.warn(
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
699 "GridSearchCV object has no attribute "
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
700 "'best_estimator_', because either it's "
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
701 "nested gridsearch or `refit` is False!"
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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702 )
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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diff changeset
703 return
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
704
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
705 # clean prams
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
706 best_estimator_ = clean_params(best_estimator_)
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
707
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
708 main_est = get_main_estimator(best_estimator_)
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
709
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
710 if hasattr(main_est, "model_") and hasattr(main_est, "save_weights"):
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
711 if outfile_weights:
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
712 main_est.save_weights(outfile_weights)
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
713 del main_est.model_
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
714 del main_est.fit_params
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
715 del main_est.model_class_
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
716 del main_est.validation_data
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
717 if getattr(main_est, "data_generator_", None):
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
718 del main_est.data_generator_
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
719
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
720 with open(outfile_object, "wb") as output_handler:
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 13
diff changeset
721 print("Best estimator is saved: %s " % repr(best_estimator_))
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
722 pickle.dump(best_estimator_, output_handler, pickle.HIGHEST_PROTOCOL)
10
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
723
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
724
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
725 if __name__ == "__main__":
10
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
726 aparser = argparse.ArgumentParser()
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
727 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
728 aparser.add_argument("-e", "--estimator", dest="infile_estimator")
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
729 aparser.add_argument("-X", "--infile1", dest="infile1")
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
730 aparser.add_argument("-y", "--infile2", dest="infile2")
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
731 aparser.add_argument("-O", "--outfile_result", dest="outfile_result")
10
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
732 aparser.add_argument("-o", "--outfile_object", dest="outfile_object")
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
733 aparser.add_argument("-w", "--outfile_weights", dest="outfile_weights")
10
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
734 aparser.add_argument("-g", "--groups", dest="groups")
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
735 aparser.add_argument("-r", "--ref_seq", dest="ref_seq")
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
736 aparser.add_argument("-b", "--intervals", dest="intervals")
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
737 aparser.add_argument("-t", "--targets", dest="targets")
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
738 aparser.add_argument("-f", "--fasta_path", dest="fasta_path")
10
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
739 args = aparser.parse_args()
e9ba818e7877 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 9
diff changeset
740
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
741 main(
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
742 args.inputs,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
743 args.infile_estimator,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
744 args.infile1,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
745 args.infile2,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
746 args.outfile_result,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
747 outfile_object=args.outfile_object,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
748 outfile_weights=args.outfile_weights,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
749 groups=args.groups,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
750 ref_seq=args.ref_seq,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
751 intervals=args.intervals,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
752 targets=args.targets,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
753 fasta_path=args.fasta_path,
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
754 )