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annotate simple_model_fit.py @ 7:65820fb7257b draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9e28f4466084464d38d3f8db2aff07974be4ba69"
author bgruening
date Wed, 11 Mar 2020 13:29:33 -0400
parents 919198d656dd
children 4aa701f5a393
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fb1fa391189e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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1 import argparse
fb1fa391189e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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2 import json
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3 import pandas as pd
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4 import pickle
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fb1fa391189e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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6 from galaxy_ml.utils import load_model, read_columns
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7 from sklearn.pipeline import Pipeline
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fb1fa391189e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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10 N_JOBS = int(__import__('os').environ.get('GALAXY_SLOTS', 1))
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13 # TODO import from galaxy_ml.utils in future versions
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14 def clean_params(estimator, n_jobs=None):
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15 """clean unwanted hyperparameter settings
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919198d656dd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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17 If n_jobs is not None, set it into the estimator, if applicable
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19 Return
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20 ------
919198d656dd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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21 Cleaned estimator object
919198d656dd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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22 """
919198d656dd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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23 ALLOWED_CALLBACKS = ('EarlyStopping', 'TerminateOnNaN',
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24 'ReduceLROnPlateau', 'CSVLogger', 'None')
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26 estimator_params = estimator.get_params()
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28 for name, p in estimator_params.items():
919198d656dd "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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29 # all potential unauthorized file write
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30 if name == 'memory' or name.endswith('__memory') \
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31 or name.endswith('_path'):
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32 new_p = {name: None}
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33 estimator.set_params(**new_p)
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34 elif n_jobs is not None and (name == 'n_jobs' or
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35 name.endswith('__n_jobs')):
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36 new_p = {name: n_jobs}
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37 estimator.set_params(**new_p)
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38 elif name.endswith('callbacks'):
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39 for cb in p:
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40 cb_type = cb['callback_selection']['callback_type']
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41 if cb_type not in ALLOWED_CALLBACKS:
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42 raise ValueError(
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43 "Prohibited callback type: %s!" % cb_type)
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45 return estimator
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47
3
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48 def _get_X_y(params, infile1, infile2):
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49 """ read from inputs and output X and y
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50
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51 Parameters
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52 ----------
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53 params : dict
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54 Tool inputs parameter
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55 infile1 : str
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56 File path to dataset containing features
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57 infile2 : str
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58 File path to dataset containing target values
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59
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60 """
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61 # store read dataframe object
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62 loaded_df = {}
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63
fb1fa391189e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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64 input_type = params['input_options']['selected_input']
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65 # tabular input
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66 if input_type == 'tabular':
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67 header = 'infer' if params['input_options']['header1'] else None
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68 column_option = (params['input_options']['column_selector_options_1']
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69 ['selected_column_selector_option'])
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70 if column_option in ['by_index_number', 'all_but_by_index_number',
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71 'by_header_name', 'all_but_by_header_name']:
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72 c = params['input_options']['column_selector_options_1']['col1']
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73 else:
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74 c = None
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75
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76 df_key = infile1 + repr(header)
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77 df = pd.read_csv(infile1, sep='\t', header=header,
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78 parse_dates=True)
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79 loaded_df[df_key] = df
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80
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81 X = read_columns(df, c=c, c_option=column_option).astype(float)
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82 # sparse input
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83 elif input_type == 'sparse':
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84 X = mmread(open(infile1, 'r'))
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85
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86 # Get target y
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87 header = 'infer' if params['input_options']['header2'] else None
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88 column_option = (params['input_options']['column_selector_options_2']
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89 ['selected_column_selector_option2'])
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90 if column_option in ['by_index_number', 'all_but_by_index_number',
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91 'by_header_name', 'all_but_by_header_name']:
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92 c = params['input_options']['column_selector_options_2']['col2']
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93 else:
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94 c = None
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95
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96 df_key = infile2 + repr(header)
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97 if df_key in loaded_df:
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98 infile2 = loaded_df[df_key]
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99 else:
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bgruening
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100 infile2 = pd.read_csv(infile2, sep='\t',
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101 header=header, parse_dates=True)
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102 loaded_df[df_key] = infile2
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103
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104 y = read_columns(
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105 infile2,
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106 c=c,
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107 c_option=column_option,
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108 sep='\t',
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109 header=header,
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110 parse_dates=True)
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111 if len(y.shape) == 2 and y.shape[1] == 1:
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112 y = y.ravel()
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113
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114 return X, y
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115
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116
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117 def main(inputs, infile_estimator, infile1, infile2, out_object,
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118 out_weights=None):
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119 """ main
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120
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121 Parameters
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122 ----------
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123 inputs : str
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124 File path to galaxy tool parameter
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125
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126 infile_estimator : str
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127 File paths of input estimator
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128
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129 infile1 : str
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130 File path to dataset containing features
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131
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132 infile2 : str
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133 File path to dataset containing target labels
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134
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135 out_object : str
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136 File path for output of fitted model or skeleton
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137
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138 out_weights : str
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139 File path for output of weights
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140
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141 """
fb1fa391189e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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142 with open(inputs, 'r') as param_handler:
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143 params = json.load(param_handler)
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144
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145 # load model
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146 with open(infile_estimator, 'rb') as est_handler:
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147 estimator = load_model(est_handler)
4
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148 estimator = clean_params(estimator, n_jobs=N_JOBS)
3
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149
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150 X_train, y_train = _get_X_y(params, infile1, infile2)
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151
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152 estimator.fit(X_train, y_train)
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153
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154 main_est = estimator
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155 if isinstance(main_est, Pipeline):
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156 main_est = main_est.steps[-1][-1]
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157 if hasattr(main_est, 'model_') \
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158 and hasattr(main_est, 'save_weights'):
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159 if out_weights:
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diff changeset
160 main_est.save_weights(out_weights)
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161 del main_est.model_
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162 del main_est.fit_params
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163 del main_est.model_class_
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164 del main_est.validation_data
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165 if getattr(main_est, 'data_generator_', None):
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166 del main_est.data_generator_
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167
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168 with open(out_object, 'wb') as output_handler:
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169 pickle.dump(estimator, output_handler,
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170 pickle.HIGHEST_PROTOCOL)
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171
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172
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173 if __name__ == '__main__':
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174 aparser = argparse.ArgumentParser()
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175 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
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176 aparser.add_argument("-X", "--infile_estimator", dest="infile_estimator")
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177 aparser.add_argument("-y", "--infile1", dest="infile1")
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178 aparser.add_argument("-g", "--infile2", dest="infile2")
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179 aparser.add_argument("-o", "--out_object", dest="out_object")
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180 aparser.add_argument("-t", "--out_weights", dest="out_weights")
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181 args = aparser.parse_args()
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182
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183 main(args.inputs, args.infile_estimator, args.infile1,
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184 args.infile2, args.out_object, args.out_weights)