annotate pycaret_predict.py @ 8:1aed7d47c5ec draft default tip

planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
author goeckslab
date Fri, 25 Jul 2025 19:02:32 +0000
parents ccd798db5abb
children
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1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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1 import argparse
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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2 import logging
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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3 import tempfile
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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5 import h5py
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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6 import joblib
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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7 import pandas as pd
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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8 from pycaret.classification import ClassificationExperiment
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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9 from pycaret.regression import RegressionExperiment
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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10 from sklearn.metrics import average_precision_score
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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11 from utils import encode_image_to_base64, get_html_closing, get_html_template
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12
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13
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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14 LOG = logging.getLogger(__name__)
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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17 class PyCaretModelEvaluator:
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18 def __init__(self, model_path, task, target):
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19 self.model_path = model_path
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20 self.task = task.lower()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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21 self.model = self.load_h5_model()
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22 self.target = target if target != "None" else None
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24 def load_h5_model(self):
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25 """Load a PyCaret model from an HDF5 file."""
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26 with h5py.File(self.model_path, 'r') as f:
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27 model_bytes = bytes(f['model'][()])
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28 with tempfile.NamedTemporaryFile(delete=False) as temp_file:
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29 temp_file.write(model_bytes)
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30 temp_file.seek(0)
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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31 loaded_model = joblib.load(temp_file.name)
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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32 return loaded_model
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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33
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34 def evaluate(self, data_path):
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35 """Evaluate the model using the specified data."""
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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36 raise NotImplementedError("Subclasses must implement this method")
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37
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38
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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39 class ClassificationEvaluator(PyCaretModelEvaluator):
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40 def evaluate(self, data_path):
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41 metrics = None
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42 plot_paths = {}
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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43 data = pd.read_csv(data_path, engine='python', sep=None)
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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44 if self.target:
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45 exp = ClassificationExperiment()
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46 names = data.columns.to_list()
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47 LOG.error(f"Column names: {names}")
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48 target_index = int(self.target) - 1
0
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49 target_name = names[target_index]
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50 exp.setup(data, target=target_name, test_data=data, index=False)
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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51 exp.add_metric(id='PR-AUC-Weighted',
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52 name='PR-AUC-Weighted',
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53 target='pred_proba',
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54 score_func=average_precision_score,
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55 average='weighted')
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56 predictions = exp.predict_model(self.model)
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57 metrics = exp.pull()
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58 plots = ['confusion_matrix', 'auc', 'threshold', 'pr',
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59 'error', 'class_report', 'learning', 'calibration',
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60 'vc', 'dimension', 'manifold', 'rfe', 'feature',
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61 'feature_all']
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62 for plot_name in plots:
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63 try:
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64 if plot_name == 'auc' and not exp.is_multiclass:
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65 plot_path = exp.plot_model(self.model,
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66 plot=plot_name,
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67 save=True,
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68 plot_kwargs={
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69 'micro': False,
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70 'macro': False,
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71 'per_class': False,
3
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72 'binary': True})
0
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73 plot_paths[plot_name] = plot_path
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74 continue
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75
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76 plot_path = exp.plot_model(self.model,
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77 plot=plot_name, save=True)
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78 plot_paths[plot_name] = plot_path
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79 except Exception as e:
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80 LOG.error(f"Error generating plot {plot_name}: {e}")
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81 continue
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82 generate_html_report(plot_paths, metrics)
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83
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84 else:
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85 exp = ClassificationExperiment()
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86 exp.setup(data, target=None, test_data=data, index=False)
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87 predictions = exp.predict_model(self.model, data=data)
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88
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89 return predictions, metrics, plot_paths
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90
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91
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92 class RegressionEvaluator(PyCaretModelEvaluator):
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93 def evaluate(self, data_path):
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94 metrics = None
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95 plot_paths = {}
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96 data = pd.read_csv(data_path, engine='python', sep=None)
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diff changeset
97 if self.target:
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98 names = data.columns.to_list()
3
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diff changeset
99 target_index = int(self.target) - 1
0
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100 target_name = names[target_index]
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101 exp = RegressionExperiment()
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102 exp.setup(data, target=target_name, test_data=data, index=False)
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103 predictions = exp.predict_model(self.model)
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104 metrics = exp.pull()
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105 plots = ['residuals', 'error', 'cooks',
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106 'learning', 'vc', 'manifold',
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107 'rfe', 'feature', 'feature_all']
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108 for plot_name in plots:
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109 try:
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110 plot_path = exp.plot_model(self.model,
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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111 plot=plot_name, save=True)
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112 plot_paths[plot_name] = plot_path
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113 except Exception as e:
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114 LOG.error(f"Error generating plot {plot_name}: {e}")
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diff changeset
115 continue
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116 generate_html_report(plot_paths, metrics)
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117 else:
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118 exp = RegressionExperiment()
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119 exp.setup(data, target=None, test_data=data, index=False)
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120 predictions = exp.predict_model(self.model, data=data)
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121
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122 return predictions, metrics, plot_paths
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123
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124
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125 def generate_html_report(plots, metrics):
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126 """Generate an HTML evaluation report."""
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127 plots_html = ""
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128 for plot_name, plot_path in plots.items():
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129 encoded_image = encode_image_to_base64(plot_path)
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130 plots_html += f"""
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131 <div class="plot">
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132 <h3>{plot_name.capitalize()}</h3>
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133 <img src="data:image/png;base64,{encoded_image}" alt="{plot_name}">
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134 </div>
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135 <hr>
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136 """
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137
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138 metrics_html = metrics.to_html(index=False, classes="table")
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139
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140 html_content = f"""
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141 {get_html_template()}
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142 <h1>Model Evaluation Report</h1>
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143 <div class="tabs">
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144 <div class="tab" onclick="openTab(event, 'metrics')">Metrics</div>
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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145 <div class="tab" onclick="openTab(event, 'plots')">Plots</div>
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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146 </div>
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147 <div id="metrics" class="tab-content">
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148 <h2>Metrics</h2>
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149 <table>
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150 {metrics_html}
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151 </table>
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152 </div>
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153 <div id="plots" class="tab-content">
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154 <h2>Plots</h2>
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155 {plots_html}
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156 </div>
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157 {get_html_closing()}
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diff changeset
158 """
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159
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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160 # Save HTML report
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161 with open("evaluation_report.html", "w") as html_file:
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162 html_file.write(html_content)
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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163
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164
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165 if __name__ == "__main__":
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diff changeset
166 parser = argparse.ArgumentParser(
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167 description="Evaluate a PyCaret model stored in HDF5 format.")
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diff changeset
168 parser.add_argument("--model_path",
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169 type=str,
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170 help="Path to the HDF5 model file.")
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171 parser.add_argument("--data_path",
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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172 type=str,
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173 help="Path to the evaluation data CSV file.")
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174 parser.add_argument("--task",
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175 type=str,
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176 choices=["classification", "regression"],
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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177 help="Specify the task: classification or regression.")
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178 parser.add_argument("--target",
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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179 default=None,
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180 help="Column number of the target")
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181 args = parser.parse_args()
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182
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183 if args.task == "classification":
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184 evaluator = ClassificationEvaluator(
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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185 args.model_path, args.task, args.target)
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186 elif args.task == "regression":
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187 evaluator = RegressionEvaluator(
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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188 args.model_path, args.task, args.target)
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189 else:
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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190 raise ValueError(
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191 "Unsupported task type. Use 'classification' or 'regression'.")
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
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192
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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193 predictions, metrics, plots = evaluator.evaluate(args.data_path)
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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194
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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195 predictions.to_csv("predictions.csv", index=False)