Mercurial > repos > bgruening > sklearn_svm_classifier

annotate keras_train_and_eval.py @ 15:2df8f5c30edc draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
author bgruening
date Mon, 16 Dec 2019 05:21:05 -0500
parents
children d67dcd63f6cb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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15
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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1 import argparse
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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2 import joblib
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3 import json
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4 import numpy as np
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5 import os
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6 import pandas as pd
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7 import pickle
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8 import warnings
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9 from itertools import chain
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10 from scipy.io import mmread
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11 from sklearn.pipeline import Pipeline
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12 from sklearn.metrics.scorer import _check_multimetric_scoring
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13 from sklearn import model_selection
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14 from sklearn.model_selection._validation import _score
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15 from sklearn.model_selection import _search, _validation
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16 from sklearn.utils import indexable, safe_indexing
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17
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18 from galaxy_ml.externals.selene_sdk.utils import compute_score
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19 from galaxy_ml.model_validations import train_test_split
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20 from galaxy_ml.keras_galaxy_models import _predict_generator
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21 from galaxy_ml.utils import (SafeEval, get_scoring, load_model,
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22 read_columns, try_get_attr, get_module,
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23 clean_params, get_main_estimator)
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24
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25
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26 _fit_and_score = try_get_attr('galaxy_ml.model_validations', '_fit_and_score')
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27 setattr(_search, '_fit_and_score', _fit_and_score)
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28 setattr(_validation, '_fit_and_score', _fit_and_score)
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29
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30 N_JOBS = int(os.environ.get('GALAXY_SLOTS', 1))
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31 CACHE_DIR = os.path.join(os.getcwd(), 'cached')
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32 del os
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33 NON_SEARCHABLE = ('n_jobs', 'pre_dispatch', 'memory', '_path',
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34 'nthread', 'callbacks')
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35 ALLOWED_CALLBACKS = ('EarlyStopping', 'TerminateOnNaN', 'ReduceLROnPlateau',
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36 'CSVLogger', 'None')
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37
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38
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39 def _eval_swap_params(params_builder):
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40 swap_params = {}
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41
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42 for p in params_builder['param_set']:
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43 swap_value = p['sp_value'].strip()
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44 if swap_value == '':
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45 continue
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46
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47 param_name = p['sp_name']
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48 if param_name.lower().endswith(NON_SEARCHABLE):
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49 warnings.warn("Warning: `%s` is not eligible for search and was "
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50 "omitted!" % param_name)
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51 continue
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52
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53 if not swap_value.startswith(':'):
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54 safe_eval = SafeEval(load_scipy=True, load_numpy=True)
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55 ev = safe_eval(swap_value)
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56 else:
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57 # Have `:` before search list, asks for estimator evaluatio
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58 safe_eval_es = SafeEval(load_estimators=True)
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59 swap_value = swap_value[1:].strip()
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60 # TODO maybe add regular express check
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61 ev = safe_eval_es(swap_value)
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62
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63 swap_params[param_name] = ev
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64
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65 return swap_params
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66
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67
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68 def train_test_split_none(*arrays, **kwargs):
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69 """extend train_test_split to take None arrays
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70 and support split by group names.
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71 """
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72 nones = []
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73 new_arrays = []
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74 for idx, arr in enumerate(arrays):
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75 if arr is None:
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76 nones.append(idx)
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77 else:
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78 new_arrays.append(arr)
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79
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80 if kwargs['shuffle'] == 'None':
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81 kwargs['shuffle'] = None
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82
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83 group_names = kwargs.pop('group_names', None)
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84
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85 if group_names is not None and group_names.strip():
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86 group_names = [name.strip() for name in
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87 group_names.split(',')]
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88 new_arrays = indexable(*new_arrays)
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89 groups = kwargs['labels']
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
90 n_samples = new_arrays[0].shape[0]
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
91 index_arr = np.arange(n_samples)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
92 test = index_arr[np.isin(groups, group_names)]
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
93 train = index_arr[~np.isin(groups, group_names)]
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
94 rval = list(chain.from_iterable(
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
95 (safe_indexing(a, train),
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
96 safe_indexing(a, test)) for a in new_arrays))
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
97 else:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
98 rval = train_test_split(*new_arrays, **kwargs)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
99
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
100 for pos in nones:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
101 rval[pos * 2: 2] = [None, None]
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
102
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
103 return rval
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
104
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
105
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
106 def _evaluate(y_true, pred_probas, scorer, is_multimetric=True):
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
107 """ output scores based on input scorer
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
108
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
109 Parameters
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
110 ----------
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
111 y_true : array
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
112 True label or target values
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
113 pred_probas : array
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
114 Prediction values, probability for classification problem
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
115 scorer : dict
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
116 dict of `sklearn.metrics.scorer.SCORER`
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
117 is_multimetric : bool, default is True
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
118 """
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
119 if y_true.ndim == 1 or y_true.shape[-1] == 1:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
120 pred_probas = pred_probas.ravel()
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
121 pred_labels = (pred_probas > 0.5).astype('int32')
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
122 targets = y_true.ravel().astype('int32')
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
123 if not is_multimetric:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
124 preds = pred_labels if scorer.__class__.__name__ == \
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
125 '_PredictScorer' else pred_probas
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
126 score = scorer._score_func(targets, preds, **scorer._kwargs)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
127
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
128 return score
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
129 else:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
130 scores = {}
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
131 for name, one_scorer in scorer.items():
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
132 preds = pred_labels if one_scorer.__class__.__name__\
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
133 == '_PredictScorer' else pred_probas
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
134 score = one_scorer._score_func(targets, preds,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
135 **one_scorer._kwargs)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
136 scores[name] = score
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
137
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
138 # TODO: multi-class metrics
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
139 # multi-label
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
140 else:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
141 pred_labels = (pred_probas > 0.5).astype('int32')
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
142 targets = y_true.astype('int32')
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
143 if not is_multimetric:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
144 preds = pred_labels if scorer.__class__.__name__ == \
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
145 '_PredictScorer' else pred_probas
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
146 score, _ = compute_score(preds, targets,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
147 scorer._score_func)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
148 return score
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
149 else:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
150 scores = {}
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
151 for name, one_scorer in scorer.items():
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
152 preds = pred_labels if one_scorer.__class__.__name__\
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
153 == '_PredictScorer' else pred_probas
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
154 score, _ = compute_score(preds, targets,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
155 one_scorer._score_func)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
156 scores[name] = score
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
157
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
158 return scores
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
159
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
160
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
161 def main(inputs, infile_estimator, infile1, infile2,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
162 outfile_result, outfile_object=None,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
163 outfile_weights=None, outfile_y_true=None,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
164 outfile_y_preds=None, groups=None,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
165 ref_seq=None, intervals=None, targets=None,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
166 fasta_path=None):
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
167 """
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
168 Parameter
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
169 ---------
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
170 inputs : str
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
171 File path to galaxy tool parameter
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
172
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
173 infile_estimator : str
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
174 File path to estimator
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
175
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
176 infile1 : str
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
177 File path to dataset containing features
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
178
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
179 infile2 : str
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
180 File path to dataset containing target values
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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181
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182 outfile_result : str
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183 File path to save the results, either cv_results or test result
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184
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185 outfile_object : str, optional
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186 File path to save searchCV object
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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187
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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188 outfile_weights : str, optional
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189 File path to save deep learning model weights
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190
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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191 outfile_y_true : str, optional
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192 File path to target values for prediction
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193
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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194 outfile_y_preds : str, optional
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195 File path to save deep learning model weights
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196
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197 groups : str
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198 File path to dataset containing groups labels
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199
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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200 ref_seq : str
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201 File path to dataset containing genome sequence file
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202
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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203 intervals : str
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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204 File path to dataset containing interval file
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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205
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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206 targets : str
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207 File path to dataset compressed target bed file
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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208
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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209 fasta_path : str
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210 File path to dataset containing fasta file
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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211 """
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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212 warnings.simplefilter('ignore')
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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213
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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214 with open(inputs, 'r') as param_handler:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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215 params = json.load(param_handler)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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216
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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217 # load estimator
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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218 with open(infile_estimator, 'rb') as estimator_handler:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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219 estimator = load_model(estimator_handler)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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220
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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221 estimator = clean_params(estimator)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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222
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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223 # swap hyperparameter
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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224 swapping = params['experiment_schemes']['hyperparams_swapping']
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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225 swap_params = _eval_swap_params(swapping)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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226 estimator.set_params(**swap_params)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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227
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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228 estimator_params = estimator.get_params()
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229
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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230 # store read dataframe object
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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231 loaded_df = {}
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232
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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233 input_type = params['input_options']['selected_input']
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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234 # tabular input
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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235 if input_type == 'tabular':
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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236 header = 'infer' if params['input_options']['header1'] else None
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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237 column_option = (params['input_options']['column_selector_options_1']
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
238 ['selected_column_selector_option'])
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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239 if column_option in ['by_index_number', 'all_but_by_index_number',
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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240 'by_header_name', 'all_but_by_header_name']:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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241 c = params['input_options']['column_selector_options_1']['col1']
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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diff changeset
242 else:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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243 c = None
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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244
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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245 df_key = infile1 + repr(header)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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246 df = pd.read_csv(infile1, sep='\t', header=header,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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parents:
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247 parse_dates=True)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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248 loaded_df[df_key] = df
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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249
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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250 X = read_columns(df, c=c, c_option=column_option).astype(float)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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251 # sparse input
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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252 elif input_type == 'sparse':
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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253 X = mmread(open(infile1, 'r'))
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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254
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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255 # fasta_file input
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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256 elif input_type == 'seq_fasta':
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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parents:
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257 pyfaidx = get_module('pyfaidx')
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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258 sequences = pyfaidx.Fasta(fasta_path)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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259 n_seqs = len(sequences.keys())
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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260 X = np.arange(n_seqs)[:, np.newaxis]
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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261 for param in estimator_params.keys():
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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262 if param.endswith('fasta_path'):
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
263 estimator.set_params(
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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264 **{param: fasta_path})
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
265 break
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
266 else:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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267 raise ValueError(
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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268 "The selected estimator doesn't support "
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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269 "fasta file input! Please consider using "
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
270 "KerasGBatchClassifier with "
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
271 "FastaDNABatchGenerator/FastaProteinBatchGenerator "
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
272 "or having GenomeOneHotEncoder/ProteinOneHotEncoder "
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
273 "in pipeline!")
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
274
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
275 elif input_type == 'refseq_and_interval':
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
276 path_params = {
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
277 'data_batch_generator__ref_genome_path': ref_seq,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
278 'data_batch_generator__intervals_path': intervals,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
279 'data_batch_generator__target_path': targets
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
280 }
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
281 estimator.set_params(**path_params)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
282 n_intervals = sum(1 for line in open(intervals))
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
283 X = np.arange(n_intervals)[:, np.newaxis]
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
284
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
285 # Get target y
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
286 header = 'infer' if params['input_options']['header2'] else None
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
287 column_option = (params['input_options']['column_selector_options_2']
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
288 ['selected_column_selector_option2'])
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
289 if column_option in ['by_index_number', 'all_but_by_index_number',
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
290 'by_header_name', 'all_but_by_header_name']:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
291 c = params['input_options']['column_selector_options_2']['col2']
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
292 else:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
293 c = None
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
294
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
295 df_key = infile2 + repr(header)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
296 if df_key in loaded_df:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
297 infile2 = loaded_df[df_key]
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
298 else:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
299 infile2 = pd.read_csv(infile2, sep='\t',
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
300 header=header, parse_dates=True)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
301 loaded_df[df_key] = infile2
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
302
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
303 y = read_columns(
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
304 infile2,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
305 c=c,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
306 c_option=column_option,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
307 sep='\t',
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
308 header=header,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
309 parse_dates=True)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
310 if len(y.shape) == 2 and y.shape[1] == 1:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
311 y = y.ravel()
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
312 if input_type == 'refseq_and_interval':
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
313 estimator.set_params(
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
314 data_batch_generator__features=y.ravel().tolist())
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
315 y = None
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
316 # end y
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
317
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
318 # load groups
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
319 if groups:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
320 groups_selector = (params['experiment_schemes']['test_split']
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
321 ['split_algos']).pop('groups_selector')
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
322
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
323 header = 'infer' if groups_selector['header_g'] else None
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
324 column_option = \
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
325 (groups_selector['column_selector_options_g']
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
326 ['selected_column_selector_option_g'])
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
327 if column_option in ['by_index_number', 'all_but_by_index_number',
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
328 'by_header_name', 'all_but_by_header_name']:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
329 c = groups_selector['column_selector_options_g']['col_g']
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
330 else:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
331 c = None
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
332
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
333 df_key = groups + repr(header)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
334 if df_key in loaded_df:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
335 groups = loaded_df[df_key]
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
336
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
337 groups = read_columns(
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
338 groups,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
339 c=c,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
340 c_option=column_option,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
341 sep='\t',
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
342 header=header,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
343 parse_dates=True)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
344 groups = groups.ravel()
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
345
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
346 # del loaded_df
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
347 del loaded_df
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
348
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
349 # cache iraps_core fits could increase search speed significantly
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
350 memory = joblib.Memory(location=CACHE_DIR, verbose=0)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
351 main_est = get_main_estimator(estimator)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
352 if main_est.__class__.__name__ == 'IRAPSClassifier':
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
353 main_est.set_params(memory=memory)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
354
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
355 # handle scorer, convert to scorer dict
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
356 scoring = params['experiment_schemes']['metrics']['scoring']
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
357 scorer = get_scoring(scoring)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
358 scorer, _ = _check_multimetric_scoring(estimator, scoring=scorer)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
359
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
360 # handle test (first) split
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
361 test_split_options = (params['experiment_schemes']
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
362 ['test_split']['split_algos'])
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
363
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
364 if test_split_options['shuffle'] == 'group':
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
365 test_split_options['labels'] = groups
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
366 if test_split_options['shuffle'] == 'stratified':
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
367 if y is not None:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
368 test_split_options['labels'] = y
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
369 else:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
370 raise ValueError("Stratified shuffle split is not "
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
371 "applicable on empty target values!")
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
372
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
373 X_train, X_test, y_train, y_test, groups_train, groups_test = \
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
374 train_test_split_none(X, y, groups, **test_split_options)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
375
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
376 exp_scheme = params['experiment_schemes']['selected_exp_scheme']
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
377
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
378 # handle validation (second) split
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
379 if exp_scheme == 'train_val_test':
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
380 val_split_options = (params['experiment_schemes']
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
381 ['val_split']['split_algos'])
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
382
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
383 if val_split_options['shuffle'] == 'group':
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
384 val_split_options['labels'] = groups_train
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
385 if val_split_options['shuffle'] == 'stratified':
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
386 if y_train is not None:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
387 val_split_options['labels'] = y_train
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
388 else:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
389 raise ValueError("Stratified shuffle split is not "
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
390 "applicable on empty target values!")
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
391
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
392 X_train, X_val, y_train, y_val, groups_train, groups_val = \
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
393 train_test_split_none(X_train, y_train, groups_train,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
394 **val_split_options)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
395
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
396 # train and eval
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
397 if hasattr(estimator, 'validation_data'):
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
398 if exp_scheme == 'train_val_test':
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
399 estimator.fit(X_train, y_train,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
400 validation_data=(X_val, y_val))
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
401 else:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
402 estimator.fit(X_train, y_train,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
403 validation_data=(X_test, y_test))
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
404 else:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
405 estimator.fit(X_train, y_train)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
406
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
407 if hasattr(estimator, 'evaluate'):
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
408 steps = estimator.prediction_steps
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
409 batch_size = estimator.batch_size
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
410 generator = estimator.data_generator_.flow(X_test, y=y_test,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
411 batch_size=batch_size)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
412 predictions, y_true = _predict_generator(estimator.model_, generator,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
413 steps=steps)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
414 scores = _evaluate(y_true, predictions, scorer, is_multimetric=True)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
415
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
416 else:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
417 if hasattr(estimator, 'predict_proba'):
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
418 predictions = estimator.predict_proba(X_test)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
419 else:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
420 predictions = estimator.predict(X_test)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
421
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
422 y_true = y_test
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
423 scores = _score(estimator, X_test, y_test, scorer,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
424 is_multimetric=True)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
425 if outfile_y_true:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
426 try:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
427 pd.DataFrame(y_true).to_csv(outfile_y_true, sep='\t',
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
428 index=False)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
429 pd.DataFrame(predictions).astype(np.float32).to_csv(
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
430 outfile_y_preds, sep='\t', index=False,
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
431 float_format='%g', chunksize=10000)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
432 except Exception as e:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
433 print("Error in saving predictions: %s" % e)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
434
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
435 # handle output
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
436 for name, score in scores.items():
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
437 scores[name] = [score]
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
438 df = pd.DataFrame(scores)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
439 df = df[sorted(df.columns)]
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
440 df.to_csv(path_or_buf=outfile_result, sep='\t',
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
441 header=True, index=False)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
442
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
443 memory.clear(warn=False)
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
444
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
445 if outfile_object:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
446 main_est = estimator
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
447 if isinstance(estimator, Pipeline):
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
448 main_est = estimator.steps[-1][-1]
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
449
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
450 if hasattr(main_est, 'model_') \
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
451 and hasattr(main_est, 'save_weights'):
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
452 if outfile_weights:
2df8f5c30edc "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
diff changeset
453 main_est.save_weights(outfile_weights)
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454 del main_est.model_
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455 del main_est.fit_params
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456 del main_est.model_class_
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457 del main_est.validation_data
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458 if getattr(main_est, 'data_generator_', None):
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459 del main_est.data_generator_
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460
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461 with open(outfile_object, 'wb') as output_handler:
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462 pickle.dump(estimator, output_handler,
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463 pickle.HIGHEST_PROTOCOL)
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464
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465
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466 if __name__ == '__main__':
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467 aparser = argparse.ArgumentParser()
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468 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
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469 aparser.add_argument("-e", "--estimator", dest="infile_estimator")
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470 aparser.add_argument("-X", "--infile1", dest="infile1")
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471 aparser.add_argument("-y", "--infile2", dest="infile2")
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472 aparser.add_argument("-O", "--outfile_result", dest="outfile_result")
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473 aparser.add_argument("-o", "--outfile_object", dest="outfile_object")
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474 aparser.add_argument("-w", "--outfile_weights", dest="outfile_weights")
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475 aparser.add_argument("-l", "--outfile_y_true", dest="outfile_y_true")
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476 aparser.add_argument("-p", "--outfile_y_preds", dest="outfile_y_preds")
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477 aparser.add_argument("-g", "--groups", dest="groups")
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478 aparser.add_argument("-r", "--ref_seq", dest="ref_seq")
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479 aparser.add_argument("-b", "--intervals", dest="intervals")
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480 aparser.add_argument("-t", "--targets", dest="targets")
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481 aparser.add_argument("-f", "--fasta_path", dest="fasta_path")
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482 args = aparser.parse_args()
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483
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484 main(args.inputs, args.infile_estimator, args.infile1, args.infile2,
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485 args.outfile_result, outfile_object=args.outfile_object,
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486 outfile_weights=args.outfile_weights,
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487 outfile_y_true=args.outfile_y_true,
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488 outfile_y_preds=args.outfile_y_preds,
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489 groups=args.groups,
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490 ref_seq=args.ref_seq, intervals=args.intervals,
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491 targets=args.targets, fasta_path=args.fasta_path)