Mercurial > repos > bgruening > sklearn_feature_selection

annotate label_encoder.py @ 35:d3ab5b9028b9 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
author bgruening
date Mon, 02 Oct 2023 09:15:54 +0000
parents b9d86fc6359d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
29
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
1 import argparse
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
2 import json
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
3 import warnings
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
4
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
5 import numpy as np
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
6 import pandas as pd
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
7 from sklearn.preprocessing import LabelEncoder
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
8
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
9
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
10 def main(inputs, infile, outfile):
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
11 """
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
12 Parameter
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
13 ---------
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
14 input : str
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
15 File path to galaxy tool parameter
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
16
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
17 infile : str
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
18 File paths of input vector
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
19
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
20 outfile : str
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
21 File path to output vector
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
22
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
23 """
34
b9d86fc6359d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 29
diff changeset
24 warnings.simplefilter("ignore")
29
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
25
34
b9d86fc6359d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 29
diff changeset
26 with open(inputs, "r") as param_handler:
29
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
27 params = json.load(param_handler)
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
28
34
b9d86fc6359d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 29
diff changeset
29 input_header = params["header0"]
b9d86fc6359d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 29
diff changeset
30 header = "infer" if input_header else None
29
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
31
34
b9d86fc6359d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 29
diff changeset
32 input_vector = pd.read_csv(infile, sep="\t", header=header)
29
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
33
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
34 le = LabelEncoder()
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
35
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
36 output_vector = le.fit_transform(input_vector)
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
37
34
b9d86fc6359d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 29
diff changeset
38 np.savetxt(outfile, output_vector, fmt="%d", delimiter="\t")
29
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
39
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
40
34
b9d86fc6359d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 29
diff changeset
41 if __name__ == "__main__":
29
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
42 aparser = argparse.ArgumentParser()
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
43 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
44 aparser.add_argument("-y", "--infile", dest="infile")
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
45 aparser.add_argument("-o", "--outfile", dest="outfile")
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
46 args = aparser.parse_args()
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
47
75e9f6fb6536 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ca87db9c038a6fcf96aa39da50f384865fd932ff"
bgruening
parents:
diff changeset
48 main(args.inputs, args.infile, args.outfile)