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annotate label_encoder.py @ 44:fce065687d98 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 11:26:43 +0000
parents 3f0d5b7d2556
children
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3f0d5b7d2556 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
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1 import argparse
3f0d5b7d2556 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
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2 import json
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3 import warnings
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5 import numpy as np
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6 import pandas as pd
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7 from sklearn.preprocessing import LabelEncoder
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10 def main(inputs, infile, outfile):
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11 """
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12 Parameter
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13 ---------
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14 input : str
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15 File path to galaxy tool parameter
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17 infile : str
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18 File paths of input vector
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20 outfile : str
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21 File path to output vector
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23 """
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fce065687d98 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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24 warnings.simplefilter("ignore")
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fce065687d98 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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26 with open(inputs, "r") as param_handler:
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27 params = json.load(param_handler)
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fce065687d98 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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29 input_header = params["header0"]
fce065687d98 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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30 header = "infer" if input_header else None
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fce065687d98 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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32 input_vector = pd.read_csv(infile, sep="\t", header=header)
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34 le = LabelEncoder()
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36 output_vector = le.fit_transform(input_vector)
3f0d5b7d2556 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
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fce065687d98 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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38 np.savetxt(outfile, output_vector, fmt="%d", delimiter="\t")
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fce065687d98 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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41 if __name__ == "__main__":
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42 aparser = argparse.ArgumentParser()
3f0d5b7d2556 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
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43 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
3f0d5b7d2556 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
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44 aparser.add_argument("-y", "--infile", dest="infile")
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45 aparser.add_argument("-o", "--outfile", dest="outfile")
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46 args = aparser.parse_args()
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48 main(args.inputs, args.infile, args.outfile)