Mercurial > repos > bgruening > sklearn_generalized_linear

annotate search_model_validation.py @ 35:602edec75e1d draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
author bgruening
date Tue, 13 Apr 2021 17:25:00 +0000
parents a8c7b9fa426c
children 616a241c5b37
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1 import argparse
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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2 import collections
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3 import imblearn
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4 import joblib
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5 import json
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6 import numpy as np
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7 import os
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8 import pandas as pd
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9 import pickle
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10 import skrebate
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11 import sys
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12 import warnings
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13 from scipy.io import mmread
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14 from sklearn import (
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15 cluster,
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16 decomposition,
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17 feature_selection,
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18 kernel_approximation,
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19 model_selection,
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20 preprocessing,
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21 )
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22 from sklearn.exceptions import FitFailedWarning
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23 from sklearn.model_selection._validation import _score, cross_validate
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24 from sklearn.model_selection import _search, _validation
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25 from sklearn.pipeline import Pipeline
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27 from galaxy_ml.utils import (
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28 SafeEval,
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29 get_cv,
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30 get_scoring,
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31 load_model,
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32 read_columns,
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33 try_get_attr,
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34 get_module,
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35 clean_params,
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36 get_main_estimator,
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37 )
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38
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39
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40 _fit_and_score = try_get_attr("galaxy_ml.model_validations", "_fit_and_score")
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41 setattr(_search, "_fit_and_score", _fit_and_score)
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42 setattr(_validation, "_fit_and_score", _fit_and_score)
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43
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44 N_JOBS = int(os.environ.get("GALAXY_SLOTS", 1))
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45 # handle disk cache
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46 CACHE_DIR = os.path.join(os.getcwd(), "cached")
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47 del os
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48 NON_SEARCHABLE = ("n_jobs", "pre_dispatch", "memory", "_path", "nthread", "callbacks")
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51 def _eval_search_params(params_builder):
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52 search_params = {}
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54 for p in params_builder["param_set"]:
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55 search_list = p["sp_list"].strip()
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56 if search_list == "":
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57 continue
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58
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59 param_name = p["sp_name"]
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60 if param_name.lower().endswith(NON_SEARCHABLE):
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61 print("Warning: `%s` is not eligible for search and was " "omitted!" % param_name)
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62 continue
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63
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64 if not search_list.startswith(":"):
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65 safe_eval = SafeEval(load_scipy=True, load_numpy=True)
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66 ev = safe_eval(search_list)
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67 search_params[param_name] = ev
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68 else:
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69 # Have `:` before search list, asks for estimator evaluatio
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70 safe_eval_es = SafeEval(load_estimators=True)
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71 search_list = search_list[1:].strip()
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72 # TODO maybe add regular express check
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73 ev = safe_eval_es(search_list)
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74 preprocessings = (
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75 preprocessing.StandardScaler(),
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76 preprocessing.Binarizer(),
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77 preprocessing.MaxAbsScaler(),
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78 preprocessing.Normalizer(),
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79 preprocessing.MinMaxScaler(),
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80 preprocessing.PolynomialFeatures(),
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81 preprocessing.RobustScaler(),
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82 feature_selection.SelectKBest(),
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83 feature_selection.GenericUnivariateSelect(),
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84 feature_selection.SelectPercentile(),
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85 feature_selection.SelectFpr(),
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86 feature_selection.SelectFdr(),
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87 feature_selection.SelectFwe(),
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88 feature_selection.VarianceThreshold(),
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89 decomposition.FactorAnalysis(random_state=0),
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90 decomposition.FastICA(random_state=0),
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91 decomposition.IncrementalPCA(),
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92 decomposition.KernelPCA(random_state=0, n_jobs=N_JOBS),
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93 decomposition.LatentDirichletAllocation(random_state=0, n_jobs=N_JOBS),
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94 decomposition.MiniBatchDictionaryLearning(random_state=0, n_jobs=N_JOBS),
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95 decomposition.MiniBatchSparsePCA(random_state=0, n_jobs=N_JOBS),
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96 decomposition.NMF(random_state=0),
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97 decomposition.PCA(random_state=0),
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98 decomposition.SparsePCA(random_state=0, n_jobs=N_JOBS),
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99 decomposition.TruncatedSVD(random_state=0),
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100 kernel_approximation.Nystroem(random_state=0),
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101 kernel_approximation.RBFSampler(random_state=0),
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102 kernel_approximation.AdditiveChi2Sampler(),
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103 kernel_approximation.SkewedChi2Sampler(random_state=0),
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104 cluster.FeatureAgglomeration(),
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105 skrebate.ReliefF(n_jobs=N_JOBS),
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106 skrebate.SURF(n_jobs=N_JOBS),
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107 skrebate.SURFstar(n_jobs=N_JOBS),
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108 skrebate.MultiSURF(n_jobs=N_JOBS),
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109 skrebate.MultiSURFstar(n_jobs=N_JOBS),
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110 imblearn.under_sampling.ClusterCentroids(random_state=0, n_jobs=N_JOBS),
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111 imblearn.under_sampling.CondensedNearestNeighbour(random_state=0, n_jobs=N_JOBS),
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112 imblearn.under_sampling.EditedNearestNeighbours(random_state=0, n_jobs=N_JOBS),
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113 imblearn.under_sampling.RepeatedEditedNearestNeighbours(random_state=0, n_jobs=N_JOBS),
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114 imblearn.under_sampling.AllKNN(random_state=0, n_jobs=N_JOBS),
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115 imblearn.under_sampling.InstanceHardnessThreshold(random_state=0, n_jobs=N_JOBS),
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116 imblearn.under_sampling.NearMiss(random_state=0, n_jobs=N_JOBS),
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117 imblearn.under_sampling.NeighbourhoodCleaningRule(random_state=0, n_jobs=N_JOBS),
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118 imblearn.under_sampling.OneSidedSelection(random_state=0, n_jobs=N_JOBS),
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119 imblearn.under_sampling.RandomUnderSampler(random_state=0),
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120 imblearn.under_sampling.TomekLinks(random_state=0, n_jobs=N_JOBS),
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121 imblearn.over_sampling.ADASYN(random_state=0, n_jobs=N_JOBS),
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122 imblearn.over_sampling.RandomOverSampler(random_state=0),
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123 imblearn.over_sampling.SMOTE(random_state=0, n_jobs=N_JOBS),
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124 imblearn.over_sampling.SVMSMOTE(random_state=0, n_jobs=N_JOBS),
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125 imblearn.over_sampling.BorderlineSMOTE(random_state=0, n_jobs=N_JOBS),
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126 imblearn.over_sampling.SMOTENC(categorical_features=[], random_state=0, n_jobs=N_JOBS),
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127 imblearn.combine.SMOTEENN(random_state=0),
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128 imblearn.combine.SMOTETomek(random_state=0),
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129 )
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130 newlist = []
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131 for obj in ev:
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132 if obj is None:
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133 newlist.append(None)
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134 elif obj == "all_0":
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135 newlist.extend(preprocessings[0:35])
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136 elif obj == "sk_prep_all": # no KernalCenter()
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137 newlist.extend(preprocessings[0:7])
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138 elif obj == "fs_all":
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139 newlist.extend(preprocessings[7:14])
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140 elif obj == "decomp_all":
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141 newlist.extend(preprocessings[14:25])
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142 elif obj == "k_appr_all":
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143 newlist.extend(preprocessings[25:29])
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144 elif obj == "reb_all":
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145 newlist.extend(preprocessings[30:35])
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146 elif obj == "imb_all":
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147 newlist.extend(preprocessings[35:54])
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148 elif type(obj) is int and -1 < obj < len(preprocessings):
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149 newlist.append(preprocessings[obj])
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150 elif hasattr(obj, "get_params"): # user uploaded object
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151 if "n_jobs" in obj.get_params():
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152 newlist.append(obj.set_params(n_jobs=N_JOBS))
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153 else:
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154 newlist.append(obj)
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155 else:
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156 sys.exit("Unsupported estimator type: %r" % (obj))
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157
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158 search_params[param_name] = newlist
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159
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160 return search_params
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161
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162
35
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163 def _handle_X_y(
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164 estimator,
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165 params,
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166 infile1,
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167 infile2,
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168 loaded_df={},
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169 ref_seq=None,
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170 intervals=None,
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171 targets=None,
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172 fasta_path=None,
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173 ):
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174 """read inputs
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175
31
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176 Params
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177 -------
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178 estimator : estimator object
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179 params : dict
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180 Galaxy tool parameter inputs
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181 infile1 : str
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182 File path to dataset containing features
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183 infile2 : str
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184 File path to dataset containing target values
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185 loaded_df : dict
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186 Contains loaded DataFrame objects with file path as keys
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187 ref_seq : str
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188 File path to dataset containing genome sequence file
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189 interval : str
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190 File path to dataset containing interval file
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191 targets : str
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192 File path to dataset compressed target bed file
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193 fasta_path : str
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194 File path to dataset containing fasta file
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195
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196
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197 Returns
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198 -------
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199 estimator : estimator object after setting new attributes
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200 X : numpy array
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201 y : numpy array
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202 """
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203 estimator_params = estimator.get_params()
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204
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205 input_type = params["input_options"]["selected_input"]
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206 # tabular input
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207 if input_type == "tabular":
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208 header = "infer" if params["input_options"]["header1"] else None
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209 column_option = params["input_options"]["column_selector_options_1"]["selected_column_selector_option"]
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210 if column_option in [
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211 "by_index_number",
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212 "all_but_by_index_number",
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213 "by_header_name",
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214 "all_but_by_header_name",
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215 ]:
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216 c = params["input_options"]["column_selector_options_1"]["col1"]
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217 else:
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218 c = None
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219
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220 df_key = infile1 + repr(header)
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221
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222 if df_key in loaded_df:
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223 infile1 = loaded_df[df_key]
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224
35
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225 df = pd.read_csv(infile1, sep="\t", header=header, parse_dates=True)
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226 loaded_df[df_key] = df
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227
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228 X = read_columns(df, c=c, c_option=column_option).astype(float)
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229 # sparse input
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230 elif input_type == "sparse":
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231 X = mmread(open(infile1, "r"))
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232
26
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233 # fasta_file input
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234 elif input_type == "seq_fasta":
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235 pyfaidx = get_module("pyfaidx")
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236 sequences = pyfaidx.Fasta(fasta_path)
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237 n_seqs = len(sequences.keys())
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238 X = np.arange(n_seqs)[:, np.newaxis]
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239 for param in estimator_params.keys():
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240 if param.endswith("fasta_path"):
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241 estimator.set_params(**{param: fasta_path})
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242 break
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243 else:
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244 raise ValueError(
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245 "The selected estimator doesn't support "
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246 "fasta file input! Please consider using "
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247 "KerasGBatchClassifier with "
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248 "FastaDNABatchGenerator/FastaProteinBatchGenerator "
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249 "or having GenomeOneHotEncoder/ProteinOneHotEncoder "
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250 "in pipeline!"
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251 )
26
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252
35
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253 elif input_type == "refseq_and_interval":
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254 path_params = {
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255 "data_batch_generator__ref_genome_path": ref_seq,
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256 "data_batch_generator__intervals_path": intervals,
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257 "data_batch_generator__target_path": targets,
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258 }
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259 estimator.set_params(**path_params)
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260 n_intervals = sum(1 for line in open(intervals))
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261 X = np.arange(n_intervals)[:, np.newaxis]
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262
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263 # Get target y
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264 header = "infer" if params["input_options"]["header2"] else None
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265 column_option = params["input_options"]["column_selector_options_2"]["selected_column_selector_option2"]
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266 if column_option in [
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267 "by_index_number",
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268 "all_but_by_index_number",
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269 "by_header_name",
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270 "all_but_by_header_name",
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271 ]:
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272 c = params["input_options"]["column_selector_options_2"]["col2"]
23
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273 else:
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274 c = None
26
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275
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276 df_key = infile2 + repr(header)
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277 if df_key in loaded_df:
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278 infile2 = loaded_df[df_key]
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279 else:
35
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280 infile2 = pd.read_csv(infile2, sep="\t", header=header, parse_dates=True)
26
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281 loaded_df[df_key] = infile2
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282
35
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283 y = read_columns(infile2, c=c, c_option=column_option, sep="\t", header=header, parse_dates=True)
26
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284 if len(y.shape) == 2 and y.shape[1] == 1:
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285 y = y.ravel()
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286 if input_type == "refseq_and_interval":
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287 estimator.set_params(data_batch_generator__features=y.ravel().tolist())
26
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288 y = None
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289 # end y
23
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290
31
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291 return estimator, X, y
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292
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293
35
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294 def _do_outer_cv(searcher, X, y, outer_cv, scoring, error_score="raise", outfile=None):
31
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295 """Do outer cross-validation for nested CV
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296
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297 Parameters
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298 ----------
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299 searcher : object
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300 SearchCV object
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301 X : numpy array
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302 Containing features
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303 y : numpy array
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304 Target values or labels
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305 outer_cv : int or CV splitter
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306 Control the cv splitting
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307 scoring : object
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308 Scorer
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309 error_score: str, float or numpy float
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310 Whether to raise fit error or return an value
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311 outfile : str
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312 File path to store the restuls
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313 """
35
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314 if error_score == "raise":
31
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315 rval = cross_validate(
35
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316 searcher,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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317 X,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
318 y,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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319 scoring=scoring,
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320 cv=outer_cv,
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321 n_jobs=N_JOBS,
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322 verbose=0,
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323 error_score=error_score,
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324 )
31
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325 else:
35
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326 warnings.simplefilter("always", FitFailedWarning)
31
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327 with warnings.catch_warnings(record=True) as w:
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328 try:
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329 rval = cross_validate(
35
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330 searcher,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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331 X,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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332 y,
31
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333 scoring=scoring,
35
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334 cv=outer_cv,
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335 n_jobs=N_JOBS,
31
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336 verbose=0,
35
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337 error_score=error_score,
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338 )
31
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339 except ValueError:
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340 pass
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341 for warning in w:
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342 print(repr(warning.message))
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343
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344 keys = list(rval.keys())
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345 for k in keys:
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346 if k.startswith("test"):
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347 rval["mean_" + k] = np.mean(rval[k])
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diff changeset
348 rval["std_" + k] = np.std(rval[k])
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
349 if k.endswith("time"):
31
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diff changeset
350 rval.pop(k)
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diff changeset
351 rval = pd.DataFrame(rval)
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diff changeset
352 rval = rval[sorted(rval.columns)]
35
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diff changeset
353 rval.to_csv(path_or_buf=outfile, sep="\t", header=True, index=False)
31
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diff changeset
354
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diff changeset
355
35
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diff changeset
356 def _do_train_test_split_val(
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
357 searcher,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
358 X,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
359 y,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
360 params,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
361 error_score="raise",
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
362 primary_scoring=None,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
363 groups=None,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
364 outfile=None,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
365 ):
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
366 """do train test split, searchCV validates on the train and then use
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
367 the best_estimator_ to evaluate on the test
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
368
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
369 Returns
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
370 --------
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
371 Fitted SearchCV object
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
372 """
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
373 train_test_split = try_get_attr("galaxy_ml.model_validations", "train_test_split")
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
374 split_options = params["outer_split"]
31
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diff changeset
375
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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376 # splits
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
377 if split_options["shuffle"] == "stratified":
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
378 split_options["labels"] = y
31
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diff changeset
379 X, X_test, y, y_test = train_test_split(X, y, **split_options)
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
380 elif split_options["shuffle"] == "group":
31
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381 if groups is None:
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
382 raise ValueError("No group based CV option was choosen for " "group shuffle!")
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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383 split_options["labels"] = groups
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
384 if y is None:
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
385 X, X_test, groups, _ = train_test_split(X, groups, **split_options)
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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386 else:
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
387 X, X_test, y, y_test, groups, _ = train_test_split(X, y, groups, **split_options)
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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388 else:
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
389 if split_options["shuffle"] == "None":
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
390 split_options["shuffle"] = None
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
391 X, X_test, y, y_test = train_test_split(X, y, **split_options)
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
392
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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393 if error_score == "raise":
31
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394 searcher.fit(X, y, groups=groups)
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diff changeset
395 else:
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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396 warnings.simplefilter("always", FitFailedWarning)
31
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397 with warnings.catch_warnings(record=True) as w:
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
398 try:
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
399 searcher.fit(X, y, groups=groups)
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
400 except ValueError:
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
401 pass
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
402 for warning in w:
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
403 print(repr(warning.message))
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
404
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
405 scorer_ = searcher.scorer_
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
406 if isinstance(scorer_, collections.Mapping):
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
407 is_multimetric = True
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
408 else:
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
409 is_multimetric = False
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
410
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
411 best_estimator_ = getattr(searcher, "best_estimator_")
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
412
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
413 # TODO Solve deep learning models in pipeline
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
414 if best_estimator_.__class__.__name__ == "KerasGBatchClassifier":
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
415 test_score = best_estimator_.evaluate(X_test, scorer=scorer_, is_multimetric=is_multimetric)
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
416 else:
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
417 test_score = _score(best_estimator_, X_test, y_test, scorer_, is_multimetric=is_multimetric)
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
418
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
419 if not is_multimetric:
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
420 test_score = {primary_scoring: test_score}
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
421 for key, value in test_score.items():
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
422 test_score[key] = [value]
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
423 result_df = pd.DataFrame(test_score)
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
424 result_df.to_csv(path_or_buf=outfile, sep="\t", header=True, index=False)
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
425
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
426 return searcher
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
427
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
428
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
429 def main(
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
430 inputs,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
431 infile_estimator,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
432 infile1,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
433 infile2,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
434 outfile_result,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
435 outfile_object=None,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
436 outfile_weights=None,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
437 groups=None,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
438 ref_seq=None,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
439 intervals=None,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
440 targets=None,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
441 fasta_path=None,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
442 ):
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
443 """
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
444 Parameter
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
445 ---------
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
446 inputs : str
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
447 File path to galaxy tool parameter
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
448
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
449 infile_estimator : str
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
450 File path to estimator
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
451
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
452 infile1 : str
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
453 File path to dataset containing features
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
454
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
455 infile2 : str
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
456 File path to dataset containing target values
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
457
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
458 outfile_result : str
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
459 File path to save the results, either cv_results or test result
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
460
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
461 outfile_object : str, optional
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
462 File path to save searchCV object
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
463
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
464 outfile_weights : str, optional
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
465 File path to save model weights
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
466
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
467 groups : str
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
468 File path to dataset containing groups labels
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
469
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
470 ref_seq : str
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
471 File path to dataset containing genome sequence file
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
472
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
473 intervals : str
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
474 File path to dataset containing interval file
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
475
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
476 targets : str
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
477 File path to dataset compressed target bed file
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
478
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
479 fasta_path : str
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
480 File path to dataset containing fasta file
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
481 """
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
482 warnings.simplefilter("ignore")
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
483
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
484 # store read dataframe object
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
485 loaded_df = {}
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
486
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
487 with open(inputs, "r") as param_handler:
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
488 params = json.load(param_handler)
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
489
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
490 # Override the refit parameter
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
491 params["search_schemes"]["options"]["refit"] = True if params["save"] != "nope" else False
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
492
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
493 with open(infile_estimator, "rb") as estimator_handler:
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
494 estimator = load_model(estimator_handler)
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
495
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
496 optimizer = params["search_schemes"]["selected_search_scheme"]
23
e3bc646e63b2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
diff changeset
497 optimizer = getattr(model_selection, optimizer)
e3bc646e63b2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
diff changeset
498
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
499 # handle gridsearchcv options
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
500 options = params["search_schemes"]["options"]
24
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents: 23
diff changeset
501
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
502 if groups:
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
503 header = "infer" if (options["cv_selector"]["groups_selector"]["header_g"]) else None
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
504 column_option = options["cv_selector"]["groups_selector"]["column_selector_options_g"][
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
505 "selected_column_selector_option_g"
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
506 ]
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
507 if column_option in [
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
508 "by_index_number",
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
509 "all_but_by_index_number",
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
510 "by_header_name",
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
511 "all_but_by_header_name",
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
512 ]:
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
513 c = options["cv_selector"]["groups_selector"]["column_selector_options_g"]["col_g"]
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
514 else:
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
515 c = None
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
516
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
517 df_key = groups + repr(header)
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
518
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
519 groups = pd.read_csv(groups, sep="\t", header=header, parse_dates=True)
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
520 loaded_df[df_key] = groups
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
521
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
522 groups = read_columns(
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
523 groups,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
524 c=c,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
525 c_option=column_option,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
526 sep="\t",
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
527 header=header,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
528 parse_dates=True,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
529 )
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
530 groups = groups.ravel()
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
531 options["cv_selector"]["groups_selector"] = groups
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
532
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
533 splitter, groups = get_cv(options.pop("cv_selector"))
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
534 options["cv"] = splitter
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
535 primary_scoring = options["scoring"]["primary_scoring"]
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
536 # get_scoring() expects secondary_scoring to be a comma separated string (not a list)
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
537 # Check if secondary_scoring is specified
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
538 secondary_scoring = options["scoring"].get("secondary_scoring", None)
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
539 if secondary_scoring is not None:
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
540 # If secondary_scoring is specified, convert the list into comman separated string
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
541 options["scoring"]["secondary_scoring"] = ",".join(options["scoring"]["secondary_scoring"])
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
542 options["scoring"] = get_scoring(options["scoring"])
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
543 if options["error_score"]:
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
544 options["error_score"] = "raise"
23
e3bc646e63b2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
diff changeset
545 else:
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
546 options["error_score"] = np.NaN
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
547 if options["refit"] and isinstance(options["scoring"], dict):
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
548 options["refit"] = primary_scoring
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
549 if "pre_dispatch" in options and options["pre_dispatch"] == "":
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
550 options["pre_dispatch"] = None
23
e3bc646e63b2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
diff changeset
551
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
552 params_builder = params["search_schemes"]["search_params_builder"]
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
553 param_grid = _eval_search_params(params_builder)
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
554
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
555 estimator = clean_params(estimator)
24
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents: 23
diff changeset
556
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
557 # save the SearchCV object without fit
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
558 if params["save"] == "save_no_fit":
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
559 searcher = optimizer(estimator, param_grid, **options)
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
560 print(searcher)
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
561 with open(outfile_object, "wb") as output_handler:
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
562 pickle.dump(searcher, output_handler, pickle.HIGHEST_PROTOCOL)
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
563 return 0
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
564
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
565 # read inputs and loads new attributes, like paths
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
566 estimator, X, y = _handle_X_y(
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
567 estimator,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
568 params,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
569 infile1,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
570 infile2,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
571 loaded_df=loaded_df,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
572 ref_seq=ref_seq,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
573 intervals=intervals,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
574 targets=targets,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
575 fasta_path=fasta_path,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
576 )
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
577
24
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents: 23
diff changeset
578 # cache iraps_core fits could increase search speed significantly
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
579 memory = joblib.Memory(location=CACHE_DIR, verbose=0)
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
580 main_est = get_main_estimator(estimator)
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
581 if main_est.__class__.__name__ == "IRAPSClassifier":
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
582 main_est.set_params(memory=memory)
24
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents: 23
diff changeset
583
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents: 23
diff changeset
584 searcher = optimizer(estimator, param_grid, **options)
23
e3bc646e63b2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
diff changeset
585
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
586 split_mode = params["outer_split"].pop("split_mode")
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
587
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
588 if split_mode == "nested_cv":
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
589 # make sure refit is choosen
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
590 # this could be True for sklearn models, but not the case for
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
591 # deep learning models
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
592 if not options["refit"] and not all(hasattr(estimator, attr) for attr in ("config", "model_type")):
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
593 warnings.warn("Refit is change to `True` for nested validation!")
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
594 setattr(searcher, "refit", True)
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
595
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
596 outer_cv, _ = get_cv(params["outer_split"]["cv_selector"])
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
597 # nested CV, outer cv using cross_validate
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
598 if options["error_score"] == "raise":
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
599 rval = cross_validate(
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
600 searcher,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
601 X,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
602 y,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
603 scoring=options["scoring"],
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
604 cv=outer_cv,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
605 n_jobs=N_JOBS,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
606 verbose=options["verbose"],
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
607 return_estimator=(params["save"] == "save_estimator"),
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
608 error_score=options["error_score"],
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
609 return_train_score=True,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
610 )
24
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents: 23
diff changeset
611 else:
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
612 warnings.simplefilter("always", FitFailedWarning)
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
613 with warnings.catch_warnings(record=True) as w:
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
614 try:
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
615 rval = cross_validate(
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
616 searcher,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
617 X,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
618 y,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
619 scoring=options["scoring"],
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
620 cv=outer_cv,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
621 n_jobs=N_JOBS,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
622 verbose=options["verbose"],
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
623 return_estimator=(params["save"] == "save_estimator"),
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
624 error_score=options["error_score"],
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
625 return_train_score=True,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
626 )
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
627 except ValueError:
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
628 pass
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
629 for warning in w:
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
630 print(repr(warning.message))
23
e3bc646e63b2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
diff changeset
631
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
632 fitted_searchers = rval.pop("estimator", [])
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
633 if fitted_searchers:
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
634 import os
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
635
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
636 pwd = os.getcwd()
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
637 save_dir = os.path.join(pwd, "cv_results_in_folds")
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
638 try:
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
639 os.mkdir(save_dir)
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
640 for idx, obj in enumerate(fitted_searchers):
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
641 target_name = "cv_results_" + "_" + "split%d" % idx
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
642 target_path = os.path.join(pwd, save_dir, target_name)
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
643 cv_results_ = getattr(obj, "cv_results_", None)
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
644 if not cv_results_:
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
645 print("%s is not available" % target_name)
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
646 continue
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
647 cv_results_ = pd.DataFrame(cv_results_)
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
648 cv_results_ = cv_results_[sorted(cv_results_.columns)]
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
649 cv_results_.to_csv(target_path, sep="\t", header=True, index=False)
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
650 except Exception as e:
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
651 print(e)
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
652 finally:
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
653 del os
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
654
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
655 keys = list(rval.keys())
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
656 for k in keys:
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
657 if k.startswith("test"):
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
658 rval["mean_" + k] = np.mean(rval[k])
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
659 rval["std_" + k] = np.std(rval[k])
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
660 if k.endswith("time"):
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
661 rval.pop(k)
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
662 rval = pd.DataFrame(rval)
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
663 rval = rval[sorted(rval.columns)]
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
664 rval.to_csv(path_or_buf=outfile_result, sep="\t", header=True, index=False)
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
665 # deprecate train test split mode
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
666 """searcher = _do_train_test_split_val(
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
667 searcher, X, y, params,
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
668 primary_scoring=primary_scoring,
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
669 error_score=options['error_score'],
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
670 groups=groups,
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
671 outfile=outfile_result)"""
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
672 return 0
24
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents: 23
diff changeset
673
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
674 # no outer split
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
675 else:
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
676 searcher.set_params(n_jobs=N_JOBS)
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
677 if options["error_score"] == "raise":
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
678 searcher.fit(X, y, groups=groups)
24
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents: 23
diff changeset
679 else:
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
680 warnings.simplefilter("always", FitFailedWarning)
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
681 with warnings.catch_warnings(record=True) as w:
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
682 try:
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
683 searcher.fit(X, y, groups=groups)
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
684 except ValueError:
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
685 pass
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
686 for warning in w:
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
687 print(repr(warning.message))
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
688
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
689 cv_results = pd.DataFrame(searcher.cv_results_)
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
690 cv_results = cv_results[sorted(cv_results.columns)]
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
691 cv_results.to_csv(path_or_buf=outfile_result, sep="\t", header=True, index=False)
24
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents: 23
diff changeset
692
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents: 23
diff changeset
693 memory.clear(warn=False)
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents: 23
diff changeset
694
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
695 # output best estimator, and weights if applicable
24
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents: 23
diff changeset
696 if outfile_object:
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
697 best_estimator_ = getattr(searcher, "best_estimator_", None)
26
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698 if not best_estimator_:
35
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699 warnings.warn(
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
700 "GridSearchCV object has no attribute "
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
701 "'best_estimator_', because either it's "
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
702 "nested gridsearch or `refit` is False!"
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
703 )
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
704 return
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff changeset
705
31
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diff changeset
706 # clean prams
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
707 best_estimator_ = clean_params(best_estimator_)
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
708
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 27
diff changeset
709 main_est = get_main_estimator(best_estimator_)
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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parents: 24
diff changeset
710
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
711 if hasattr(main_est, "model_") and hasattr(main_est, "save_weights"):
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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parents: 24
diff changeset
712 if outfile_weights:
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
713 main_est.save_weights(outfile_weights)
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
714 del main_est.model_
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
715 del main_est.fit_params
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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parents: 24
diff changeset
716 del main_est.model_class_
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
717 del main_est.validation_data
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
718 if getattr(main_est, "data_generator_", None):
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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parents: 24
diff changeset
719 del main_est.data_generator_
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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parents: 24
diff changeset
720
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
721 with open(outfile_object, "wb") as output_handler:
31
a8c7b9fa426c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
722 print("Best estimator is saved: %s " % repr(best_estimator_))
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
723 pickle.dump(best_estimator_, output_handler, pickle.HIGHEST_PROTOCOL)
24
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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parents: 23
diff changeset
724
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents: 23
diff changeset
725
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
726 if __name__ == "__main__":
24
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
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diff changeset
727 aparser = argparse.ArgumentParser()
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
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diff changeset
728 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents: 23
diff changeset
729 aparser.add_argument("-e", "--estimator", dest="infile_estimator")
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
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diff changeset
730 aparser.add_argument("-X", "--infile1", dest="infile1")
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
parents: 23
diff changeset
731 aparser.add_argument("-y", "--infile2", dest="infile2")
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
732 aparser.add_argument("-O", "--outfile_result", dest="outfile_result")
24
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
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diff changeset
733 aparser.add_argument("-o", "--outfile_object", dest="outfile_object")
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
734 aparser.add_argument("-w", "--outfile_weights", dest="outfile_weights")
24
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
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diff changeset
735 aparser.add_argument("-g", "--groups", dest="groups")
26
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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parents: 24
diff changeset
736 aparser.add_argument("-r", "--ref_seq", dest="ref_seq")
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
737 aparser.add_argument("-b", "--intervals", dest="intervals")
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
738 aparser.add_argument("-t", "--targets", dest="targets")
9d3a024cf2da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 24
diff changeset
739 aparser.add_argument("-f", "--fasta_path", dest="fasta_path")
24
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
bgruening
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diff changeset
740 args = aparser.parse_args()
b628de0d101f planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ab963ec9498bd05d2fb2f24f75adb2fccae7958c
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diff changeset
741
35
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
742 main(
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
743 args.inputs,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
744 args.infile_estimator,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
745 args.infile1,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
746 args.infile2,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
747 args.outfile_result,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
748 outfile_object=args.outfile_object,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
749 outfile_weights=args.outfile_weights,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
750 groups=args.groups,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
751 ref_seq=args.ref_seq,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
752 intervals=args.intervals,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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753 targets=args.targets,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
754 fasta_path=args.fasta_path,
602edec75e1d "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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755 )