Mercurial > repos > bgruening > stacking_ensemble_models

annotate train_test_split.py @ 3:0a1812986bc3 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
author bgruening
date Wed, 09 Aug 2023 11:10:37 +0000 (20 months ago)
parents 38c4f8a98038
children
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38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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1 import argparse
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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2 import json
3
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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3 import warnings
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4 from distutils.version import LooseVersion as Version
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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5
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6 import pandas as pd
3
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7 from galaxy_ml import __version__ as galaxy_ml_version
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8 from galaxy_ml.model_validations import train_test_split
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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9 from galaxy_ml.utils import get_cv, read_columns
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3
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12 def _get_single_cv_split(params, array, infile_labels=None, infile_groups=None):
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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13 """output (train, test) subset from a cv splitter
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14
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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15 Parameters
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16 ----------
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17 params : dict
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18 Galaxy tool inputs
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19 array : pandas DataFrame object
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20 The target dataset to split
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21 infile_labels : str
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22 File path to dataset containing target values
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23 infile_groups : str
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24 File path to dataset containing group values
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25 """
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26 y = None
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27 groups = None
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28
3
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29 nth_split = params["mode_selection"]["nth_split"]
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30
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31 # read groups
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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32 if infile_groups:
3
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33 header = (
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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34 "infer"
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35 if (params["mode_selection"]["cv_selector"]["groups_selector"]["header_g"])
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36 else None
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37 )
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38 column_option = params["mode_selection"]["cv_selector"]["groups_selector"][
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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39 "column_selector_options_g"
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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40 ]["selected_column_selector_option_g"]
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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41 if column_option in [
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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42 "by_index_number",
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43 "all_but_by_index_number",
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44 "by_header_name",
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45 "all_but_by_header_name",
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46 ]:
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47 c = params["mode_selection"]["cv_selector"]["groups_selector"][
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48 "column_selector_options_g"
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49 ]["col_g"]
2
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50 else:
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51 c = None
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52
3
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53 groups = read_columns(
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54 infile_groups,
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55 c=c,
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56 c_option=column_option,
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57 sep="\t",
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58 header=header,
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59 parse_dates=True,
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60 )
2
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61 groups = groups.ravel()
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62
3
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63 params["mode_selection"]["cv_selector"]["groups_selector"] = groups
2
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64
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65 # read labels
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66 if infile_labels:
3
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67 target_input = params["mode_selection"]["cv_selector"].pop("target_input")
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68 header = "infer" if target_input["header1"] else None
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69 col_index = target_input["col"][0] - 1
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70 df = pd.read_csv(infile_labels, sep="\t", header=header, parse_dates=True)
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71 y = df.iloc[:, col_index].values
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72
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73 # construct the cv splitter object
3
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74 cv_selector = params["mode_selection"]["cv_selector"]
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75 if Version(galaxy_ml_version) < Version("0.8.3"):
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76 cv_selector.pop("n_stratification_bins", None)
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77 splitter, groups = get_cv(cv_selector)
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78
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79 total_n_splits = splitter.get_n_splits(array.values, y=y, groups=groups)
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80 if nth_split > total_n_splits:
3
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81 raise ValueError(
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82 "Total number of splits is {}, but got `nth_split` "
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83 "= {}".format(total_n_splits, nth_split)
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84 )
2
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85
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86 i = 1
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87 for train_index, test_index in splitter.split(array.values, y=y, groups=groups):
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88 # suppose nth_split >= 1
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89 if i == nth_split:
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90 break
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91 else:
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92 i += 1
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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93
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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94 train = array.iloc[train_index, :]
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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95 test = array.iloc[test_index, :]
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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diff changeset
96
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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97 return train, test
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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98
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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99
3
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100 def main(
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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101 inputs,
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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102 infile_array,
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103 outfile_train,
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104 outfile_test,
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105 infile_labels=None,
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106 infile_groups=None,
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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107 ):
2
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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108 """
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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109 Parameter
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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110 ---------
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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111 inputs : str
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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112 File path to galaxy tool parameter
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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113
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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114 infile_array : str
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115 File paths of input arrays separated by comma
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116
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117 infile_labels : str
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118 File path to dataset containing labels
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119
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120 infile_groups : str
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121 File path to dataset containing groups
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122
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123 outfile_train : str
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124 File path to dataset containing train split
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125
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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126 outfile_test : str
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127 File path to dataset containing test split
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128 """
3
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129 warnings.simplefilter("ignore")
2
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130
3
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131 with open(inputs, "r") as param_handler:
2
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132 params = json.load(param_handler)
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133
3
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134 input_header = params["header0"]
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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135 header = "infer" if input_header else None
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136 array = pd.read_csv(infile_array, sep="\t", header=header, parse_dates=True)
2
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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137
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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138 # train test split
3
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139 if params["mode_selection"]["selected_mode"] == "train_test_split":
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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140 options = params["mode_selection"]["options"]
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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141 shuffle_selection = options.pop("shuffle_selection")
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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142 options["shuffle"] = shuffle_selection["shuffle"]
2
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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143 if infile_labels:
3
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144 header = "infer" if shuffle_selection["header1"] else None
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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145 col_index = shuffle_selection["col"][0] - 1
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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146 df = pd.read_csv(infile_labels, sep="\t", header=header, parse_dates=True)
2
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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147 labels = df.iloc[:, col_index].values
3
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148 options["labels"] = labels
2
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149
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150 train, test = train_test_split(array, **options)
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151
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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152 # cv splitter
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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153 else:
3
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154 train, test = _get_single_cv_split(
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155 params, array, infile_labels=infile_labels, infile_groups=infile_groups
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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156 )
2
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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157
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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158 print("Input shape: %s" % repr(array.shape))
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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159 print("Train shape: %s" % repr(train.shape))
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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160 print("Test shape: %s" % repr(test.shape))
3
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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161 train.to_csv(outfile_train, sep="\t", header=input_header, index=False)
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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162 test.to_csv(outfile_test, sep="\t", header=input_header, index=False)
2
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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163
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164
3
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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165 if __name__ == "__main__":
2
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166 aparser = argparse.ArgumentParser()
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167 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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168 aparser.add_argument("-X", "--infile_array", dest="infile_array")
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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169 aparser.add_argument("-y", "--infile_labels", dest="infile_labels")
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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170 aparser.add_argument("-g", "--infile_groups", dest="infile_groups")
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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171 aparser.add_argument("-o", "--outfile_train", dest="outfile_train")
38c4f8a98038 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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172 aparser.add_argument("-t", "--outfile_test", dest="outfile_test")
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173 args = aparser.parse_args()
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174
3
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parents: 2
diff changeset
175 main(
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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176 args.inputs,
0a1812986bc3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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177 args.infile_array,
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178 args.outfile_train,
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179 args.outfile_test,
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180 args.infile_labels,
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181 args.infile_groups,
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182 )