Mercurial > repos > bgruening > sklearn_train_test_eval
annotate simple_model_fit.py @ 4:bf2bcf7bd617 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
author | bgruening |
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date | Thu, 07 Nov 2019 05:22:04 -0500 |
parents | 20bb2a45f922 |
children | ead7adad8d0e |
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20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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1 import argparse |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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2 import json |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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3 import pandas as pd |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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4 import pickle |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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5 |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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6 from galaxy_ml.utils import load_model, read_columns |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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7 from sklearn.pipeline import Pipeline |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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8 |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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9 |
4
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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10 N_JOBS = int(__import__('os').environ.get('GALAXY_SLOTS', 1)) |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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11 |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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12 |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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13 # TODO import from galaxy_ml.utils in future versions |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
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14 def clean_params(estimator, n_jobs=None): |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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15 """clean unwanted hyperparameter settings |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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16 |
bf2bcf7bd617
"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 |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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18 |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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19 Return |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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20 ------ |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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21 Cleaned estimator object |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
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22 """ |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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23 ALLOWED_CALLBACKS = ('EarlyStopping', 'TerminateOnNaN', |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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24 'ReduceLROnPlateau', 'CSVLogger', 'None') |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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25 |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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26 estimator_params = estimator.get_params() |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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27 |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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28 for name, p in estimator_params.items(): |
bf2bcf7bd617
"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 |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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30 if name == 'memory' or name.endswith('__memory') \ |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
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31 or name.endswith('_path'): |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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32 new_p = {name: None} |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
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33 estimator.set_params(**new_p) |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
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34 elif n_jobs is not None and (name == 'n_jobs' or |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
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35 name.endswith('__n_jobs')): |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
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36 new_p = {name: n_jobs} |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
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37 estimator.set_params(**new_p) |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
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38 elif name.endswith('callbacks'): |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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39 for cb in p: |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
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40 cb_type = cb['callback_selection']['callback_type'] |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
bgruening
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41 if cb_type not in ALLOWED_CALLBACKS: |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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42 raise ValueError( |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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43 "Prohibited callback type: %s!" % cb_type) |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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44 |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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45 return estimator |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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46 |
bf2bcf7bd617
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d6333e7294e67be5968a41f404b66699cad4ae53"
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47 |
3
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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48 def _get_X_y(params, infile1, infile2): |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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49 """ read from inputs and output X and y |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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50 |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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51 Parameters |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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52 ---------- |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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53 params : dict |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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54 Tool inputs parameter |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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55 infile1 : str |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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56 File path to dataset containing features |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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57 infile2 : str |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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58 File path to dataset containing target values |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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59 |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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60 """ |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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61 # store read dataframe object |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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62 loaded_df = {} |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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63 |
20bb2a45f922
"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'] |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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65 # tabular input |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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66 if input_type == 'tabular': |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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67 header = 'infer' if params['input_options']['header1'] else None |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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68 column_option = (params['input_options']['column_selector_options_1'] |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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69 ['selected_column_selector_option']) |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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70 if column_option in ['by_index_number', 'all_but_by_index_number', |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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71 'by_header_name', 'all_but_by_header_name']: |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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72 c = params['input_options']['column_selector_options_1']['col1'] |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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73 else: |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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74 c = None |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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75 |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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76 df_key = infile1 + repr(header) |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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77 df = pd.read_csv(infile1, sep='\t', header=header, |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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78 parse_dates=True) |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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79 loaded_df[df_key] = df |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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80 |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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81 X = read_columns(df, c=c, c_option=column_option).astype(float) |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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82 # sparse input |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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83 elif input_type == 'sparse': |
20bb2a45f922
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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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', |
20bb2a45f922
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91 'by_header_name', 'all_but_by_header_name']: |
20bb2a45f922
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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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100 infile2 = pd.read_csv(infile2, sep='\t', |
20bb2a45f922
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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: |
20bb2a45f922
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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, |
20bb2a45f922
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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 ---------- |
20bb2a45f922
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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 |
20bb2a45f922
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141 """ |
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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) |
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148 estimator = clean_params(estimator, n_jobs=N_JOBS) |
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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 |
20bb2a45f922
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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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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) |