Mercurial > repos > bgruening > sklearn_build_pipeline
annotate search_model_validation.py @ 27:7442b94d6a1e draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
author | bgruening |
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date | Mon, 02 Oct 2023 09:28:19 +0000 |
parents | 118e230e85ce |
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rev | line source |
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913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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1 import argparse |
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664666bd14ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents:
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2 import json |
664666bd14ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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3 import os |
664666bd14ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents:
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4 import sys |
664666bd14ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents:
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5 import warnings |
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118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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6 from distutils.version import LooseVersion as Version |
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664666bd14ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
parents:
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7 |
7
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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8 import imblearn |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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parents:
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9 import joblib |
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99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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changeset
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10 import numpy as np |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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11 import pandas as pd |
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99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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12 import skrebate |
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118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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13 from galaxy_ml import __version__ as galaxy_ml_version |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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14 from galaxy_ml.binarize_target import IRAPSClassifier |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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15 from galaxy_ml.model_persist import dump_model_to_h5, load_model_from_h5 |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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16 from galaxy_ml.utils import ( |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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17 clean_params, |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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18 get_cv, |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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19 get_main_estimator, |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
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changeset
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20 get_module, |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
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changeset
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21 get_scoring, |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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22 read_columns, |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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changeset
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23 SafeEval, |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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24 try_get_attr |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
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changeset
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25 ) |
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913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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26 from scipy.io import mmread |
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118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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27 from sklearn import ( |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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28 cluster, |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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changeset
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29 decomposition, |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
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changeset
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30 feature_selection, |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
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changeset
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31 kernel_approximation, |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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32 model_selection, |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
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changeset
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33 preprocessing, |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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34 ) |
7
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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35 from sklearn.exceptions import FitFailedWarning |
20
664666bd14ec
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"
bgruening
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36 from sklearn.model_selection import _search, _validation |
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775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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37 from sklearn.model_selection._validation import _score, cross_validate |
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118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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38 from sklearn.preprocessing import LabelEncoder |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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39 from skopt import BayesSearchCV |
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99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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40 |
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4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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41 N_JOBS = int(os.environ.get("GALAXY_SLOTS", 1)) |
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3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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42 # handle disk cache |
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4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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43 CACHE_DIR = os.path.join(os.getcwd(), "cached") |
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118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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44 NON_SEARCHABLE = ( |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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45 "n_jobs", |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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46 "pre_dispatch", |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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47 "memory", |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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48 "_path", |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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49 "_dir", |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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50 "nthread", |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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51 "callbacks", |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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52 ) |
7
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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53 |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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54 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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55 def _eval_search_params(params_builder): |
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99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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56 search_params = {} |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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57 |
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4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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58 for p in params_builder["param_set"]: |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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59 search_list = p["sp_list"].strip() |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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60 if search_list == "": |
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99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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61 continue |
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913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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62 |
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4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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63 param_name = p["sp_name"] |
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913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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64 if param_name.lower().endswith(NON_SEARCHABLE): |
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0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
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65 print( |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
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66 "Warning: `%s` is not eligible for search and was " |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
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67 "omitted!" % param_name |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
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68 ) |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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69 continue |
7
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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70 |
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4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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71 if not search_list.startswith(":"): |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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72 safe_eval = SafeEval(load_scipy=True, load_numpy=True) |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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73 ev = safe_eval(search_list) |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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74 search_params[param_name] = ev |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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75 else: |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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76 # Have `:` before search list, asks for estimator evaluatio |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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77 safe_eval_es = SafeEval(load_estimators=True) |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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78 search_list = search_list[1:].strip() |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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79 # TODO maybe add regular express check |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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80 ev = safe_eval_es(search_list) |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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81 preprocessings = ( |
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4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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82 preprocessing.StandardScaler(), |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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83 preprocessing.Binarizer(), |
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84 preprocessing.MaxAbsScaler(), |
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85 preprocessing.Normalizer(), |
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86 preprocessing.MinMaxScaler(), |
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87 preprocessing.PolynomialFeatures(), |
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88 preprocessing.RobustScaler(), |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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89 feature_selection.SelectKBest(), |
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90 feature_selection.GenericUnivariateSelect(), |
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91 feature_selection.SelectPercentile(), |
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92 feature_selection.SelectFpr(), |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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93 feature_selection.SelectFdr(), |
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94 feature_selection.SelectFwe(), |
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95 feature_selection.VarianceThreshold(), |
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96 decomposition.FactorAnalysis(random_state=0), |
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97 decomposition.FastICA(random_state=0), |
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98 decomposition.IncrementalPCA(), |
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99 decomposition.KernelPCA(random_state=0, n_jobs=N_JOBS), |
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100 decomposition.LatentDirichletAllocation(random_state=0, n_jobs=N_JOBS), |
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101 decomposition.MiniBatchDictionaryLearning( |
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102 random_state=0, n_jobs=N_JOBS |
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103 ), |
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104 decomposition.MiniBatchSparsePCA(random_state=0, n_jobs=N_JOBS), |
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105 decomposition.NMF(random_state=0), |
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106 decomposition.PCA(random_state=0), |
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107 decomposition.SparsePCA(random_state=0, n_jobs=N_JOBS), |
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108 decomposition.TruncatedSVD(random_state=0), |
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109 kernel_approximation.Nystroem(random_state=0), |
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110 kernel_approximation.RBFSampler(random_state=0), |
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111 kernel_approximation.AdditiveChi2Sampler(), |
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112 kernel_approximation.SkewedChi2Sampler(random_state=0), |
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113 cluster.FeatureAgglomeration(), |
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114 skrebate.ReliefF(n_jobs=N_JOBS), |
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115 skrebate.SURF(n_jobs=N_JOBS), |
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116 skrebate.SURFstar(n_jobs=N_JOBS), |
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117 skrebate.MultiSURF(n_jobs=N_JOBS), |
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118 skrebate.MultiSURFstar(n_jobs=N_JOBS), |
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119 imblearn.under_sampling.ClusterCentroids(random_state=0, n_jobs=N_JOBS), |
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120 imblearn.under_sampling.CondensedNearestNeighbour( |
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121 random_state=0, n_jobs=N_JOBS |
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122 ), |
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123 imblearn.under_sampling.EditedNearestNeighbours(n_jobs=N_JOBS), |
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124 imblearn.under_sampling.RepeatedEditedNearestNeighbours(n_jobs=N_JOBS), |
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125 imblearn.under_sampling.AllKNN(n_jobs=N_JOBS), |
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126 imblearn.under_sampling.InstanceHardnessThreshold( |
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127 random_state=0, n_jobs=N_JOBS |
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128 ), |
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129 imblearn.under_sampling.NearMiss(n_jobs=N_JOBS), |
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130 imblearn.under_sampling.NeighbourhoodCleaningRule(n_jobs=N_JOBS), |
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131 imblearn.under_sampling.OneSidedSelection( |
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132 random_state=0, n_jobs=N_JOBS |
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133 ), |
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134 imblearn.under_sampling.RandomUnderSampler(random_state=0), |
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135 imblearn.under_sampling.TomekLinks(n_jobs=N_JOBS), |
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136 imblearn.over_sampling.ADASYN(random_state=0, n_jobs=N_JOBS), |
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137 imblearn.over_sampling.BorderlineSMOTE(random_state=0, n_jobs=N_JOBS), |
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138 imblearn.over_sampling.KMeansSMOTE(random_state=0, n_jobs=N_JOBS), |
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139 imblearn.over_sampling.RandomOverSampler(random_state=0), |
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140 imblearn.over_sampling.SMOTE(random_state=0, n_jobs=N_JOBS), |
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141 imblearn.over_sampling.SMOTEN(random_state=0, n_jobs=N_JOBS), |
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142 imblearn.over_sampling.SMOTENC( |
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143 categorical_features=[], random_state=0, n_jobs=N_JOBS |
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144 ), |
25
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145 imblearn.over_sampling.SVMSMOTE(random_state=0, n_jobs=N_JOBS), |
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146 imblearn.combine.SMOTEENN(random_state=0), |
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147 imblearn.combine.SMOTETomek(random_state=0), |
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148 ) |
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149 newlist = [] |
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150 for obj in ev: |
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151 if obj is None: |
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152 newlist.append(None) |
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153 elif obj == "all_0": |
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154 newlist.extend(preprocessings[0:35]) |
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155 elif obj == "sk_prep_all": # no KernalCenter() |
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156 newlist.extend(preprocessings[0:7]) |
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157 elif obj == "fs_all": |
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158 newlist.extend(preprocessings[7:14]) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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159 elif obj == "decomp_all": |
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160 newlist.extend(preprocessings[14:25]) |
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161 elif obj == "k_appr_all": |
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162 newlist.extend(preprocessings[25:29]) |
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163 elif obj == "reb_all": |
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164 newlist.extend(preprocessings[30:35]) |
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165 elif obj == "imb_all": |
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166 newlist.extend(preprocessings[35:54]) |
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167 elif type(obj) is int and -1 < obj < len(preprocessings): |
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168 newlist.append(preprocessings[obj]) |
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169 elif hasattr(obj, "get_params"): # user uploaded object |
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170 if "n_jobs" in obj.get_params(): |
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171 newlist.append(obj.set_params(n_jobs=N_JOBS)) |
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172 else: |
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173 newlist.append(obj) |
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174 else: |
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175 sys.exit("Unsupported estimator type: %r" % (obj)) |
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176 |
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177 search_params[param_name] = newlist |
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178 |
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179 return search_params |
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180 |
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181 |
19
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182 def _handle_X_y( |
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183 estimator, |
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184 params, |
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185 infile1, |
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186 infile2, |
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187 loaded_df={}, |
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188 ref_seq=None, |
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189 intervals=None, |
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190 targets=None, |
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191 fasta_path=None, |
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192 ): |
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193 """read inputs |
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194 |
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195 Params |
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196 ------- |
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197 estimator : estimator object |
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198 params : dict |
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199 Galaxy tool parameter inputs |
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200 infile1 : str |
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201 File path to dataset containing features |
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202 infile2 : str |
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203 File path to dataset containing target values |
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204 loaded_df : dict |
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205 Contains loaded DataFrame objects with file path as keys |
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206 ref_seq : str |
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207 File path to dataset containing genome sequence file |
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208 interval : str |
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209 File path to dataset containing interval file |
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210 targets : str |
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211 File path to dataset compressed target bed file |
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212 fasta_path : str |
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213 File path to dataset containing fasta file |
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214 |
11
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215 |
15
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216 Returns |
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217 ------- |
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218 estimator : estimator object after setting new attributes |
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219 X : numpy array |
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220 y : numpy array |
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221 """ |
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222 estimator_params = estimator.get_params() |
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223 |
19
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224 input_type = params["input_options"]["selected_input"] |
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225 # tabular input |
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226 if input_type == "tabular": |
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227 header = "infer" if params["input_options"]["header1"] else None |
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228 column_option = params["input_options"]["column_selector_options_1"][ |
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229 "selected_column_selector_option" |
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230 ] |
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231 if column_option in [ |
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232 "by_index_number", |
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233 "all_but_by_index_number", |
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234 "by_header_name", |
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235 "all_but_by_header_name", |
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236 ]: |
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237 c = params["input_options"]["column_selector_options_1"]["col1"] |
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238 else: |
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239 c = None |
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240 |
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241 df_key = infile1 + repr(header) |
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242 |
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243 if df_key in loaded_df: |
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244 infile1 = loaded_df[df_key] |
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245 |
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246 df = pd.read_csv(infile1, sep="\t", header=header, parse_dates=True) |
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247 loaded_df[df_key] = df |
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248 |
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249 X = read_columns(df, c=c, c_option=column_option).astype(float) |
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250 # sparse input |
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251 elif input_type == "sparse": |
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252 X = mmread(open(infile1, "r")) |
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253 |
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254 # fasta_file input |
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255 elif input_type == "seq_fasta": |
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256 pyfaidx = get_module("pyfaidx") |
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257 sequences = pyfaidx.Fasta(fasta_path) |
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258 n_seqs = len(sequences.keys()) |
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259 X = np.arange(n_seqs)[:, np.newaxis] |
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260 for param in estimator_params.keys(): |
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261 if param.endswith("fasta_path"): |
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262 estimator.set_params(**{param: fasta_path}) |
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263 break |
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264 else: |
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265 raise ValueError( |
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266 "The selected estimator doesn't support " |
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267 "fasta file input! Please consider using " |
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268 "KerasGBatchClassifier with " |
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269 "FastaDNABatchGenerator/FastaProteinBatchGenerator " |
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270 "or having GenomeOneHotEncoder/ProteinOneHotEncoder " |
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271 "in pipeline!" |
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272 ) |
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273 |
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274 elif input_type == "refseq_and_interval": |
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275 path_params = { |
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276 "data_batch_generator__ref_genome_path": ref_seq, |
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277 "data_batch_generator__intervals_path": intervals, |
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278 "data_batch_generator__target_path": targets, |
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279 } |
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280 estimator.set_params(**path_params) |
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281 n_intervals = sum(1 for line in open(intervals)) |
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282 X = np.arange(n_intervals)[:, np.newaxis] |
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283 |
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284 # Get target y |
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285 header = "infer" if params["input_options"]["header2"] else None |
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286 column_option = params["input_options"]["column_selector_options_2"][ |
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287 "selected_column_selector_option2" |
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288 ] |
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289 if column_option in [ |
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290 "by_index_number", |
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291 "all_but_by_index_number", |
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292 "by_header_name", |
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293 "all_but_by_header_name", |
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294 ]: |
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295 c = params["input_options"]["column_selector_options_2"]["col2"] |
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296 else: |
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297 c = None |
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298 |
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299 df_key = infile2 + repr(header) |
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300 if df_key in loaded_df: |
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301 infile2 = loaded_df[df_key] |
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302 else: |
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303 infile2 = pd.read_csv(infile2, sep="\t", header=header, parse_dates=True) |
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304 loaded_df[df_key] = infile2 |
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305 |
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306 y = read_columns( |
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307 infile2, |
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308 c=c, |
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309 c_option=column_option, |
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310 sep="\t", |
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311 header=header, |
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312 parse_dates=True, |
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313 ) |
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314 if len(y.shape) == 2 and y.shape[1] == 1: |
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315 y = y.ravel() |
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316 if input_type == "refseq_and_interval": |
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317 estimator.set_params(data_batch_generator__features=y.ravel().tolist()) |
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318 y = None |
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319 # end y |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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320 |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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321 return estimator, X, y |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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322 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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323 |
19
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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324 def _do_outer_cv(searcher, X, y, outer_cv, scoring, error_score="raise", outfile=None): |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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325 """Do outer cross-validation for nested CV |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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326 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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327 Parameters |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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328 ---------- |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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329 searcher : object |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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330 SearchCV object |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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331 X : numpy array |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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332 Containing features |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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333 y : numpy array |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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334 Target values or labels |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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335 outer_cv : int or CV splitter |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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336 Control the cv splitting |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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337 scoring : object |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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338 Scorer |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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339 error_score: str, float or numpy float |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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340 Whether to raise fit error or return an value |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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341 outfile : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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342 File path to store the restuls |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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343 """ |
19
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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344 if error_score == "raise": |
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3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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345 rval = cross_validate( |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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346 searcher, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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347 X, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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348 y, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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349 scoring=scoring, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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350 cv=outer_cv, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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351 n_jobs=N_JOBS, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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352 verbose=0, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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353 error_score=error_score, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
354 ) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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355 else: |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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356 warnings.simplefilter("always", FitFailedWarning) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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357 with warnings.catch_warnings(record=True) as w: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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358 try: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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359 rval = cross_validate( |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
360 searcher, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
361 X, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
362 y, |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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363 scoring=scoring, |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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364 cv=outer_cv, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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365 n_jobs=N_JOBS, |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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366 verbose=0, |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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367 error_score=error_score, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
368 ) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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369 except ValueError: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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370 pass |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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371 for warning in w: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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372 print(repr(warning.message)) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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373 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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374 keys = list(rval.keys()) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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375 for k in keys: |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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376 if k.startswith("test"): |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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377 rval["mean_" + k] = np.mean(rval[k]) |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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378 rval["std_" + k] = np.std(rval[k]) |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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379 if k.endswith("time"): |
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3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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380 rval.pop(k) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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381 rval = pd.DataFrame(rval) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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382 rval = rval[sorted(rval.columns)] |
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4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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383 rval.to_csv(path_or_buf=outfile, sep="\t", header=True, index=False) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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|
384 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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|
385 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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386 def _do_train_test_split_val( |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
387 searcher, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
388 X, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
389 y, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
390 params, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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391 error_score="raise", |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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392 primary_scoring=None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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393 groups=None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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394 outfile=None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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395 ): |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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396 """do train test split, searchCV validates on the train and then use |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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397 the best_estimator_ to evaluate on the test |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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|
398 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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|
399 Returns |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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400 -------- |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
401 Fitted SearchCV object |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
402 """ |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
403 train_test_split = try_get_attr("galaxy_ml.model_validations", "train_test_split") |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
404 split_options = params["outer_split"] |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
405 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
406 # splits |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
407 if split_options["shuffle"] == "stratified": |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
408 split_options["labels"] = y |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
409 X, X_test, y, y_test = train_test_split(X, y, **split_options) |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
410 elif split_options["shuffle"] == "group": |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
411 if groups is None: |
21
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
412 raise ValueError( |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
413 "No group based CV option was choosen for " "group shuffle!" |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
414 ) |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
415 split_options["labels"] = groups |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
416 if y is None: |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
417 X, X_test, groups, _ = train_test_split(X, groups, **split_options) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
418 else: |
21
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
419 X, X_test, y, y_test, groups, _ = train_test_split( |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
420 X, y, groups, **split_options |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
421 ) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
422 else: |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
423 if split_options["shuffle"] == "None": |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
424 split_options["shuffle"] = None |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
425 X, X_test, y, y_test = train_test_split(X, y, **split_options) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
426 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
427 if error_score == "raise": |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
428 searcher.fit(X, y, groups=groups) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
429 else: |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
430 warnings.simplefilter("always", FitFailedWarning) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
431 with warnings.catch_warnings(record=True) as w: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
432 try: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
433 searcher.fit(X, y, groups=groups) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
434 except ValueError: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
435 pass |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
436 for warning in w: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
437 print(repr(warning.message)) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
438 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
439 scorer_ = searcher.scorer_ |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
440 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
441 best_estimator_ = getattr(searcher, "best_estimator_") |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
442 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
443 # TODO Solve deep learning models in pipeline |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
444 if best_estimator_.__class__.__name__ == "KerasGBatchClassifier": |
21
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
445 test_score = best_estimator_.evaluate( |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
446 X_test, |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
447 scorer=scorer_, |
21
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
448 ) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
449 else: |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
450 test_score = _score(best_estimator_, X_test, y_test, scorer_) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
451 |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
452 if not isinstance(scorer_, dict): |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
453 test_score = {primary_scoring: test_score} |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
454 for key, value in test_score.items(): |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
455 test_score[key] = [value] |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
456 result_df = pd.DataFrame(test_score) |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
457 result_df.to_csv(path_or_buf=outfile, sep="\t", header=True, index=False) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
458 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
459 return searcher |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
460 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
461 |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
462 def _set_memory(estimator, memory): |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
463 """set memeory cache |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
464 |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
465 Parameters |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
466 ---------- |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
467 estimator : python object |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
468 memory : joblib.Memory object |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
469 |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
470 Returns |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
471 ------- |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
472 estimator : estimator object after setting new attributes |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
473 """ |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
474 if isinstance(estimator, IRAPSClassifier): |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
475 estimator.set_params(memory=memory) |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
476 return estimator |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
477 |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
478 estimator_params = estimator.get_params() |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
479 |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
480 new_params = {} |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
481 for k in estimator_params.keys(): |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
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diff
changeset
|
482 if k.endswith("irapsclassifier__memory"): |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
483 new_params[k] = memory |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
484 |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
485 estimator.set_params(**new_params) |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
486 |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
487 return estimator |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
488 |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
489 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
490 def main( |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
491 inputs, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
492 infile_estimator, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
493 infile1, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
494 infile2, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
495 outfile_result, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
496 outfile_object=None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
497 groups=None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
498 ref_seq=None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
499 intervals=None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
500 targets=None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
501 fasta_path=None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
502 ): |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
503 """ |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
504 Parameter |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
505 --------- |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
506 inputs : str |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
507 File path to galaxy tool parameter. |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
508 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
509 infile_estimator : str |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
510 File path to estimator. |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
511 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
512 infile1 : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
513 File path to dataset containing features |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
514 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
515 infile2 : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
516 File path to dataset containing target values |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
517 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
518 outfile_result : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
519 File path to save the results, either cv_results or test result |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
520 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
521 outfile_object : str, optional |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
522 File path to save searchCV object |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
523 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
524 groups : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
525 File path to dataset containing groups labels |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
526 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
527 ref_seq : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
528 File path to dataset containing genome sequence file |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
529 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
530 intervals : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
531 File path to dataset containing interval file |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
532 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
533 targets : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
534 File path to dataset compressed target bed file |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
535 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
536 fasta_path : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
537 File path to dataset containing fasta file |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
538 """ |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
539 warnings.simplefilter("ignore") |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
540 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
541 # store read dataframe object |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
542 loaded_df = {} |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
543 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
544 with open(inputs, "r") as param_handler: |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
545 params = json.load(param_handler) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
546 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
547 # Override the refit parameter |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
548 params["options"]["refit"] = ( |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
549 True |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
550 if ( |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
551 params["save"] != "nope" |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
552 or params["outer_split"]["split_mode"] == "nested_cv" |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
553 ) |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
554 else False |
21
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
555 ) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
556 |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
557 estimator = load_model_from_h5(infile_estimator) |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
558 |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
559 estimator = clean_params(estimator) |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
560 |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
561 if estimator.__class__.__name__ == "KerasGBatchClassifier": |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
562 _fit_and_score = try_get_attr( |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
563 "galaxy_ml.model_validations", |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
564 "_fit_and_score", |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
565 ) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
566 |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
567 setattr(_search, "_fit_and_score", _fit_and_score) |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
568 setattr(_validation, "_fit_and_score", _fit_and_score) |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
569 |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
570 search_algos_and_options = params["search_algos"] |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
571 optimizer = search_algos_and_options.pop("selected_search_algo") |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
572 if optimizer == "skopt.BayesSearchCV": |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
573 optimizer = BayesSearchCV |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
574 else: |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
575 optimizer = getattr(model_selection, optimizer) |
7
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
diff
changeset
|
576 |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
577 # handle gridsearchcv options |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
578 options = params["options"] |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
579 options.update(search_algos_and_options) |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
580 |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
581 if groups: |
21
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
582 header = ( |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
583 "infer" if (options["cv_selector"]["groups_selector"]["header_g"]) else None |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
584 ) |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
585 column_option = options["cv_selector"]["groups_selector"][ |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
586 "column_selector_options_g" |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
587 ]["selected_column_selector_option_g"] |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
588 if column_option in [ |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
589 "by_index_number", |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
590 "all_but_by_index_number", |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
591 "by_header_name", |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
592 "all_but_by_header_name", |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
593 ]: |
21
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
594 c = options["cv_selector"]["groups_selector"]["column_selector_options_g"][ |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
595 "col_g" |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
596 ] |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
597 else: |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
598 c = None |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
599 |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
600 df_key = groups + repr(header) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
601 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
602 groups = pd.read_csv(groups, sep="\t", header=header, parse_dates=True) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
603 loaded_df[df_key] = groups |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
604 |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
605 groups = read_columns( |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
606 groups, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
607 c=c, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
608 c_option=column_option, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
609 sep="\t", |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
610 header=header, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
611 parse_dates=True, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
612 ) |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
613 groups = groups.ravel() |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
614 options["cv_selector"]["groups_selector"] = groups |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
615 |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
616 cv_selector = options.pop("cv_selector") |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
617 if Version(galaxy_ml_version) < Version("0.8.3"): |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
618 cv_selector.pop("n_stratification_bins", None) |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
619 splitter, groups = get_cv(cv_selector) |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
620 options["cv"] = splitter |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
621 primary_scoring = options["scoring"]["primary_scoring"] |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
622 options["scoring"] = get_scoring(options["scoring"]) |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
623 # TODO make BayesSearchCV support multiple scoring |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
624 if optimizer == "skopt.BayesSearchCV" and isinstance(options["scoring"], dict): |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
625 options["scoring"] = options["scoring"][primary_scoring] |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
626 warnings.warn( |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
627 "BayesSearchCV doesn't support multiple " |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
628 "scorings! Primary scoring is used." |
21
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
629 ) |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
630 if options["error_score"]: |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
631 options["error_score"] = "raise" |
7
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
diff
changeset
|
632 else: |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
633 options["error_score"] = np.NaN |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
634 if options["refit"] and isinstance(options["scoring"], dict): |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
635 options["refit"] = primary_scoring |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
636 if "pre_dispatch" in options and options["pre_dispatch"] == "": |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
637 options["pre_dispatch"] = None |
7
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
diff
changeset
|
638 |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
639 params_builder = params["search_params_builder"] |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
640 param_grid = _eval_search_params(params_builder) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
641 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
642 # save the SearchCV object without fit |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
643 if params["save"] == "save_no_fit": |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
644 searcher = optimizer(estimator, param_grid, **options) |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
645 dump_model_to_h5(searcher, outfile_object) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
646 return 0 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
647 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
648 # read inputs and loads new attributes, like paths |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
649 estimator, X, y = _handle_X_y( |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
650 estimator, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
651 params, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
652 infile1, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
653 infile2, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
654 loaded_df=loaded_df, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
655 ref_seq=ref_seq, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
656 intervals=intervals, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
657 targets=targets, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
658 fasta_path=fasta_path, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
659 ) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
660 |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
661 label_encoder = LabelEncoder() |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
662 if get_main_estimator(estimator).__class__.__name__ == "XGBClassifier": |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
663 y = label_encoder.fit_transform(y) |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
664 |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
665 # cache iraps_core fits could increase search speed significantly |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
666 memory = joblib.Memory(location=CACHE_DIR, verbose=0) |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
667 estimator = _set_memory(estimator, memory) |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
668 |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
669 searcher = optimizer(estimator, param_grid, **options) |
7
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
diff
changeset
|
670 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
671 split_mode = params["outer_split"].pop("split_mode") |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
672 |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
673 # Nested CV |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
674 if split_mode == "nested_cv": |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
675 cv_selector = params["outer_split"]["cv_selector"] |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
676 if Version(galaxy_ml_version) < Version("0.8.3"): |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
677 cv_selector.pop("n_stratification_bins", None) |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
678 outer_cv, _ = get_cv(cv_selector) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
679 # nested CV, outer cv using cross_validate |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
680 if options["error_score"] == "raise": |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
681 rval = cross_validate( |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
682 searcher, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
683 X, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
684 y, |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
685 groups=groups, |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
686 scoring=options["scoring"], |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
687 cv=outer_cv, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
688 n_jobs=N_JOBS, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
689 verbose=options["verbose"], |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
690 fit_params={"groups": groups}, |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
691 return_estimator=(params["save"] == "save_estimator"), |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
692 error_score=options["error_score"], |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
693 return_train_score=True, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
694 ) |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
695 else: |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
696 warnings.simplefilter("always", FitFailedWarning) |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
697 with warnings.catch_warnings(record=True) as w: |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
698 try: |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
699 rval = cross_validate( |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
700 searcher, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
701 X, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
702 y, |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
703 groups=groups, |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
704 scoring=options["scoring"], |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
705 cv=outer_cv, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
706 n_jobs=N_JOBS, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
707 verbose=options["verbose"], |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
708 fit_params={"groups": groups}, |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
709 return_estimator=(params["save"] == "save_estimator"), |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
710 error_score=options["error_score"], |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
711 return_train_score=True, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
712 ) |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
713 except ValueError: |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
714 pass |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
715 for warning in w: |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
716 print(repr(warning.message)) |
7
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
diff
changeset
|
717 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
718 fitted_searchers = rval.pop("estimator", []) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
719 if fitted_searchers: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
720 import os |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
721 |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
722 pwd = os.getcwd() |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
723 save_dir = os.path.join(pwd, "cv_results_in_folds") |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
724 try: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
725 os.mkdir(save_dir) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
726 for idx, obj in enumerate(fitted_searchers): |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
727 target_name = "cv_results_" + "_" + "split%d" % idx |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
728 target_path = os.path.join(pwd, save_dir, target_name) |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
729 cv_results_ = getattr(obj, "cv_results_", None) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
730 if not cv_results_: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
731 print("%s is not available" % target_name) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
732 continue |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
733 cv_results_ = pd.DataFrame(cv_results_) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
734 cv_results_ = cv_results_[sorted(cv_results_.columns)] |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
735 cv_results_.to_csv(target_path, sep="\t", header=True, index=False) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
736 except Exception as e: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
737 print(e) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
738 |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
739 keys = list(rval.keys()) |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
740 for k in keys: |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
741 if k.startswith("test"): |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
742 rval["mean_" + k] = np.mean(rval[k]) |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
743 rval["std_" + k] = np.std(rval[k]) |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
744 if k.endswith("time"): |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
745 rval.pop(k) |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
746 rval = pd.DataFrame(rval) |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
747 rval = rval[sorted(rval.columns)] |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
748 rval.to_csv(path_or_buf=outfile_result, sep="\t", header=True, index=False) |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
749 |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
750 return 0 |
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
751 |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
752 # deprecate train test split mode |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
753 """searcher = _do_train_test_split_val( |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
754 searcher, X, y, params, |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
755 primary_scoring=primary_scoring, |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
756 error_score=options['error_score'], |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
757 groups=groups, |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
758 outfile=outfile_result)""" |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
759 |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
760 # no outer split |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
761 else: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
762 searcher.set_params(n_jobs=N_JOBS) |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
763 if options["error_score"] == "raise": |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
764 searcher.fit(X, y, groups=groups) |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
765 else: |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
766 warnings.simplefilter("always", FitFailedWarning) |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
767 with warnings.catch_warnings(record=True) as w: |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
768 try: |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
769 searcher.fit(X, y, groups=groups) |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
770 except ValueError: |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
771 pass |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
772 for warning in w: |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
773 print(repr(warning.message)) |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
774 |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
775 cv_results = pd.DataFrame(searcher.cv_results_) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
776 cv_results = cv_results[sorted(cv_results.columns)] |
21
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
777 cv_results.to_csv( |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
778 path_or_buf=outfile_result, sep="\t", header=True, index=False |
0c74d3164ac8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
parents:
20
diff
changeset
|
779 ) |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
780 |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
781 memory.clear(warn=False) |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
782 |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
783 # output best estimator, and weights if applicable |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
784 if outfile_object: |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
785 best_estimator_ = getattr(searcher, "best_estimator_", None) |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
786 if not best_estimator_: |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
787 warnings.warn( |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
788 "GridSearchCV object has no attribute " |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
789 "'best_estimator_', because either it's " |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
790 "nested gridsearch or `refit` is False!" |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
791 ) |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
792 return |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
793 |
25
118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents:
21
diff
changeset
|
794 dump_model_to_h5(best_estimator_, outfile_object) |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
795 |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
796 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
797 if __name__ == "__main__": |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
798 aparser = argparse.ArgumentParser() |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
799 aparser.add_argument("-i", "--inputs", dest="inputs", required=True) |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
800 aparser.add_argument("-e", "--estimator", dest="infile_estimator") |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
801 aparser.add_argument("-X", "--infile1", dest="infile1") |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
802 aparser.add_argument("-y", "--infile2", dest="infile2") |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
803 aparser.add_argument("-O", "--outfile_result", dest="outfile_result") |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
804 aparser.add_argument("-o", "--outfile_object", dest="outfile_object") |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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805 aparser.add_argument("-g", "--groups", dest="groups") |
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775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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806 aparser.add_argument("-r", "--ref_seq", dest="ref_seq") |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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807 aparser.add_argument("-b", "--intervals", dest="intervals") |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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808 aparser.add_argument("-t", "--targets", dest="targets") |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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809 aparser.add_argument("-f", "--fasta_path", dest="fasta_path") |
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913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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diff
changeset
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810 args = aparser.parse_args() |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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changeset
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811 |
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118e230e85ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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812 main(**vars(args)) |