Mercurial > repos > bgruening > sklearn_model_fit
annotate fitted_model_eval.py @ 12:f903c8cf1455 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
author | bgruening |
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date | Wed, 09 Aug 2023 13:06:45 +0000 |
parents | 17999807dc1b |
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734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
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1 import argparse |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
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2 import json |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
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3 import warnings |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
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4 |
7
5dc03d8e137e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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5 import pandas as pd |
12
f903c8cf1455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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6 from galaxy_ml.model_persist import load_model_from_h5 |
f903c8cf1455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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7 from galaxy_ml.utils import clean_params, get_scoring, read_columns |
0
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
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8 from scipy.io import mmread |
12
f903c8cf1455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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9 from sklearn.metrics._scorer import _check_multimetric_scoring |
0
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
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10 from sklearn.model_selection._validation import _score |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
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11 |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
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12 |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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13 def _get_X_y(params, infile1, infile2): |
6
26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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14 """read from inputs and output X and y |
0
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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15 |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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16 Parameters |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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17 ---------- |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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18 params : dict |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
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19 Tool inputs parameter |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
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20 infile1 : str |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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21 File path to dataset containing features |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
parents:
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22 infile2 : str |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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23 File path to dataset containing target values |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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24 |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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25 """ |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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26 # store read dataframe object |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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27 loaded_df = {} |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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28 |
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26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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29 input_type = params["input_options"]["selected_input"] |
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734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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30 # tabular input |
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26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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31 if input_type == "tabular": |
26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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32 header = "infer" if params["input_options"]["header1"] else None |
8
17999807dc1b
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
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33 column_option = params["input_options"]["column_selector_options_1"][ |
17999807dc1b
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
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34 "selected_column_selector_option" |
17999807dc1b
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
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35 ] |
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26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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36 if column_option in [ |
26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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37 "by_index_number", |
26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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38 "all_but_by_index_number", |
26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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39 "by_header_name", |
26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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40 "all_but_by_header_name", |
26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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41 ]: |
26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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42 c = params["input_options"]["column_selector_options_1"]["col1"] |
0
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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43 else: |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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44 c = None |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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45 |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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46 df_key = infile1 + repr(header) |
6
26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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47 df = pd.read_csv(infile1, sep="\t", header=header, parse_dates=True) |
0
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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48 loaded_df[df_key] = df |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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49 |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
bgruening
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50 X = read_columns(df, c=c, c_option=column_option).astype(float) |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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51 # sparse input |
6
26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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52 elif input_type == "sparse": |
26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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53 X = mmread(open(infile1, "r")) |
0
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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54 |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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55 # Get target y |
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26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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56 header = "infer" if params["input_options"]["header2"] else None |
8
17999807dc1b
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
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57 column_option = params["input_options"]["column_selector_options_2"][ |
17999807dc1b
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
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58 "selected_column_selector_option2" |
17999807dc1b
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
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59 ] |
6
26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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60 if column_option in [ |
26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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61 "by_index_number", |
26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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62 "all_but_by_index_number", |
26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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63 "by_header_name", |
26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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64 "all_but_by_header_name", |
26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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65 ]: |
26decbf4bdb8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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66 c = params["input_options"]["column_selector_options_2"]["col2"] |
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734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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67 else: |
734c66aa945a
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68 c = None |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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69 |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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70 df_key = infile2 + repr(header) |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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71 if df_key in loaded_df: |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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72 infile2 = loaded_df[df_key] |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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73 else: |
6
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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74 infile2 = pd.read_csv(infile2, sep="\t", header=header, parse_dates=True) |
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734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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75 loaded_df[df_key] = infile2 |
734c66aa945a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
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76 |
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77 y = read_columns( |
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f903c8cf1455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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78 infile2, |
f903c8cf1455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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79 c=c, |
f903c8cf1455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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80 c_option=column_option, |
f903c8cf1455
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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81 sep="\t", |
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82 header=header, |
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83 parse_dates=True, |
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84 ) |
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85 if len(y.shape) == 2 and y.shape[1] == 1: |
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86 y = y.ravel() |
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87 |
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88 return X, y |
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89 |
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90 |
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91 def main(inputs, infile_estimator, outfile_eval, infile1=None, infile2=None): |
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92 """ |
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93 Parameter |
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94 --------- |
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95 inputs : str |
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96 File path to galaxy tool parameter |
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97 |
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98 infile_estimator : strgit |
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99 File path to trained estimator input |
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100 |
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101 outfile_eval : str |
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102 File path to save the evalulation results, tabular |
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103 |
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104 infile1 : str |
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105 File path to dataset containing features |
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106 |
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107 infile2 : str |
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108 File path to dataset containing target values |
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109 """ |
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110 warnings.filterwarnings("ignore") |
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111 |
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112 with open(inputs, "r") as param_handler: |
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113 params = json.load(param_handler) |
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114 |
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115 X_test, y_test = _get_X_y(params, infile1, infile2) |
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116 |
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117 # load model |
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118 estimator = load_model_from_h5(infile_estimator) |
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119 estimator = clean_params(estimator) |
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120 |
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121 # handle scorer, convert to scorer dict |
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122 scoring = params["scoring"] |
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123 scorer = get_scoring(scoring) |
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124 if not isinstance(scorer, (dict, list)): |
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125 scorer = [scoring["primary_scoring"]] |
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126 scorer = _check_multimetric_scoring(estimator, scoring=scorer) |
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127 |
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128 if hasattr(estimator, "evaluate"): |
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129 scores = estimator.evaluate(X_test, y_test=y_test, scorer=scorer) |
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130 else: |
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131 scores = _score(estimator, X_test, y_test, scorer) |
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132 |
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133 # handle output |
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134 for name, score in scores.items(): |
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135 scores[name] = [score] |
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136 df = pd.DataFrame(scores) |
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137 df = df[sorted(df.columns)] |
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138 df.to_csv(path_or_buf=outfile_eval, sep="\t", header=True, index=False) |
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139 |
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140 |
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141 if __name__ == "__main__": |
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142 aparser = argparse.ArgumentParser() |
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143 aparser.add_argument("-i", "--inputs", dest="inputs", required=True) |
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144 aparser.add_argument("-e", "--infile_estimator", dest="infile_estimator") |
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145 aparser.add_argument("-X", "--infile1", dest="infile1") |
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146 aparser.add_argument("-y", "--infile2", dest="infile2") |
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147 aparser.add_argument("-O", "--outfile_eval", dest="outfile_eval") |
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148 args = aparser.parse_args() |
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149 |
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150 main( |
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151 args.inputs, |
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152 args.infile_estimator, |
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153 args.outfile_eval, |
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154 infile1=args.infile1, |
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155 infile2=args.infile2, |
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156 ) |