Mercurial > repos > bgruening > sklearn_feature_selection
diff feature_selection.xml @ 3:3a1acc39b39b draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 4ed8c4f6ef9ece81797a398b17a99bbaf49a6978
author | bgruening |
---|---|
date | Wed, 30 May 2018 08:25:49 -0400 |
parents | 2eb90e73f0d5 |
children | 44e26f8a82c6 |
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--- a/feature_selection.xml Tue May 22 19:31:59 2018 -0400 +++ b/feature_selection.xml Wed May 30 08:25:49 2018 -0400 @@ -25,6 +25,8 @@ @COLUMNS_FUNCTION@ +@FEATURE_SELECTOR_FUNCTION@ + input_json_path = sys.argv[1] params = json.load(open(input_json_path, "r")) @@ -57,42 +59,10 @@ y=y.ravel() ## Create feature selector -selector = params["feature_selection_algorithms"]["selected_algorithm"] -selector = getattr(sklearn.feature_selection, selector) -options = params["feature_selection_algorithms"]["options"] - -if params['feature_selection_algorithms']['selected_algorithm'] == 'SelectFromModel': - if not options['threshold'] or options['threshold'] == 'None': - options['threshold'] = None - if 'extra_estimator' in params['feature_selection_algorithms'] and params['feature_selection_algorithms']['extra_estimator']['has_estimator'] == 'no_load': - fitted_estimator = pickle.load(open("params['feature_selection_algorithms']['extra_estimator']['fitted_estimator']", 'r')) - new_selector = selector(fitted_estimator, prefit=True, **options) - else: - estimator=params["feature_selection_algorithms"]["estimator"] - if params["feature_selection_algorithms"]["extra_estimator"]["has_estimator"]=='no': - estimator=params["feature_selection_algorithms"]["extra_estimator"]["new_estimator"] - estimator=eval(estimator.replace('__dq__', '"').replace("__sq__","'")) - new_selector = selector(estimator, **options) - new_selector.fit(X, y) - -elif params['feature_selection_algorithms']['selected_algorithm'] in ['RFE', 'RFECV']: - if 'scoring' in options and (not options['scoring'] or options['scoring'] == 'None'): - options['scoring'] = None - estimator=params["feature_selection_algorithms"]["estimator"] - if params["feature_selection_algorithms"]["extra_estimator"]["has_estimator"]=='no': - estimator=params["feature_selection_algorithms"]["extra_estimator"]["new_estimator"] - estimator=eval(estimator.replace('__dq__', '"').replace("__sq__","'")) - new_selector = selector(estimator, **options) - new_selector.fit(X, y) - -elif params['feature_selection_algorithms']['selected_algorithm'] == "VarianceThreshold": - new_selector = selector(**options) - new_selector.fit(X, y) - -else: - score_func = params["feature_selection_algorithms"]["score_func"] - score_func = getattr(sklearn.feature_selection, score_func) - new_selector = selector(score_func, **options) +new_selector = feature_selector(params['feature_selection_algorithms']) +if params['feature_selection_algorithms']['selected_algorithm'] != 'SelectFromModel' or \ + 'extra_estimator' not in params['feature_selection_algorithms'] or \ + params['feature_selection_algorithms']['extra_estimator']['has_estimator'] != 'no_load' : new_selector.fit(X, y) ## Transform to select features