Mercurial > repos > bgruening > sklearn_ensemble

annotate stacking_ensembles.py @ 36:a98fdfcd9f5f draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
author bgruening
date Tue, 13 Apr 2021 22:18:06 +0000
parents 19d6c2745d34
children 4ecc0ce9d0a2
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1 import argparse
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2 import ast
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3 import json
e94395c672bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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4 import pickle
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5 import sys
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6 import warnings
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8 import mlxtend.classifier
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9 import mlxtend.regressor
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10 import pandas as pd
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11 from galaxy_ml.utils import get_cv, get_estimator, get_search_params, load_model
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14 warnings.filterwarnings("ignore")
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16 N_JOBS = int(__import__("os").environ.get("GALAXY_SLOTS", 1))
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19 def main(inputs_path, output_obj, base_paths=None, meta_path=None, outfile_params=None):
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20 """
e94395c672bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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21 Parameter
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22 ---------
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23 inputs_path : str
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24 File path for Galaxy parameters
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26 output_obj : str
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27 File path for ensemble estimator ouput
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29 base_paths : str
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30 File path or paths concatenated by comma.
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32 meta_path : str
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33 File path
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35 outfile_params : str
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36 File path for params output
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37 """
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38 with open(inputs_path, "r") as param_handler:
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39 params = json.load(param_handler)
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41 estimator_type = params["algo_selection"]["estimator_type"]
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42 # get base estimators
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43 base_estimators = []
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44 for idx, base_file in enumerate(base_paths.split(",")):
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45 if base_file and base_file != "None":
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46 with open(base_file, "rb") as handler:
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47 model = load_model(handler)
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48 else:
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49 estimator_json = params["base_est_builder"][idx]["estimator_selector"]
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50 model = get_estimator(estimator_json)
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52 if estimator_type.startswith("sklearn"):
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53 named = model.__class__.__name__.lower()
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54 named = "base_%d_%s" % (idx, named)
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55 base_estimators.append((named, model))
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56 else:
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57 base_estimators.append(model)
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58
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59 # get meta estimator, if applicable
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60 if estimator_type.startswith("mlxtend"):
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61 if meta_path:
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62 with open(meta_path, "rb") as f:
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63 meta_estimator = load_model(f)
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64 else:
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65 estimator_json = params["algo_selection"]["meta_estimator"]["estimator_selector"]
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66 meta_estimator = get_estimator(estimator_json)
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68 options = params["algo_selection"]["options"]
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70 cv_selector = options.pop("cv_selector", None)
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71 if cv_selector:
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72 splitter, _groups = get_cv(cv_selector)
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73 options["cv"] = splitter
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74 # set n_jobs
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75 options["n_jobs"] = N_JOBS
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77 weights = options.pop("weights", None)
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78 if weights:
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79 weights = ast.literal_eval(weights)
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80 if weights:
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81 options["weights"] = weights
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82
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83 mod_and_name = estimator_type.split("_")
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84 mod = sys.modules[mod_and_name[0]]
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85 klass = getattr(mod, mod_and_name[1])
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87 if estimator_type.startswith("sklearn"):
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88 options["n_jobs"] = N_JOBS
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89 ensemble_estimator = klass(base_estimators, **options)
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90
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91 elif mod == mlxtend.classifier:
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92 ensemble_estimator = klass(classifiers=base_estimators, meta_classifier=meta_estimator, **options)
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93
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94 else:
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95 ensemble_estimator = klass(regressors=base_estimators, meta_regressor=meta_estimator, **options)
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96
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97 print(ensemble_estimator)
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98 for base_est in base_estimators:
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99 print(base_est)
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100
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101 with open(output_obj, "wb") as out_handler:
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102 pickle.dump(ensemble_estimator, out_handler, pickle.HIGHEST_PROTOCOL)
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103
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104 if params["get_params"] and outfile_params:
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105 results = get_search_params(ensemble_estimator)
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106 df = pd.DataFrame(results, columns=["", "Parameter", "Value"])
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107 df.to_csv(outfile_params, sep="\t", index=False)
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108
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109
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110 if __name__ == "__main__":
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111 aparser = argparse.ArgumentParser()
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112 aparser.add_argument("-b", "--bases", dest="bases")
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113 aparser.add_argument("-m", "--meta", dest="meta")
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114 aparser.add_argument("-i", "--inputs", dest="inputs")
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115 aparser.add_argument("-o", "--outfile", dest="outfile")
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116 aparser.add_argument("-p", "--outfile_params", dest="outfile_params")
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117 args = aparser.parse_args()
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118
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119 main(
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120 args.inputs,
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121 args.outfile,
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122 base_paths=args.bases,
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123 meta_path=args.meta,
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124 outfile_params=args.outfile_params,
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125 )