Mercurial > repos > bgruening > sklearn_build_pipeline
annotate search_model_validation.py @ 19:4de3d598c116 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
author | bgruening |
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date | Tue, 13 Apr 2021 18:57:31 +0000 |
parents | 3f3c6dc38f3e |
children | 664666bd14ec |
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 |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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2 import collections |
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99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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3 import imblearn |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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4 import joblib |
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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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5 import json |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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6 import numpy as np |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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7 import os |
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775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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8 import pandas as pd |
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99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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9 import pickle |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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10 import skrebate |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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11 import sys |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
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12 import warnings |
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913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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13 from scipy.io import mmread |
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4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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14 from sklearn import ( |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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15 cluster, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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16 decomposition, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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17 feature_selection, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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18 kernel_approximation, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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19 model_selection, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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20 preprocessing, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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21 ) |
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99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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22 from sklearn.exceptions import FitFailedWarning |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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23 from sklearn.model_selection._validation import _score, cross_validate |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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24 from sklearn.model_selection import _search, _validation |
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3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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25 from sklearn.pipeline import Pipeline |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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26 |
19
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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27 from galaxy_ml.utils import ( |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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28 SafeEval, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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29 get_cv, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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30 get_scoring, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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31 load_model, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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32 read_columns, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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33 try_get_attr, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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34 get_module, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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35 clean_params, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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36 get_main_estimator, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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37 ) |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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38 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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39 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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40 _fit_and_score = try_get_attr("galaxy_ml.model_validations", "_fit_and_score") |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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41 setattr(_search, "_fit_and_score", _fit_and_score) |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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42 setattr(_validation, "_fit_and_score", _fit_and_score) |
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99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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43 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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44 N_JOBS = int(os.environ.get("GALAXY_SLOTS", 1)) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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45 # handle disk cache |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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46 CACHE_DIR = os.path.join(os.getcwd(), "cached") |
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3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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47 del os |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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48 NON_SEARCHABLE = ("n_jobs", "pre_dispatch", "memory", "_path", "nthread", "callbacks") |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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49 |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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50 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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51 def _eval_search_params(params_builder): |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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52 search_params = {} |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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53 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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54 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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55 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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56 if search_list == "": |
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99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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57 continue |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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58 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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59 param_name = p["sp_name"] |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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60 if param_name.lower().endswith(NON_SEARCHABLE): |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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61 print("Warning: `%s` is not eligible for search and was " "omitted!" % param_name) |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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62 continue |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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63 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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64 if not search_list.startswith(":"): |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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65 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
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66 ev = safe_eval(search_list) |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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67 search_params[param_name] = ev |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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68 else: |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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69 # Have `:` before search list, asks for estimator evaluatio |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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70 safe_eval_es = SafeEval(load_estimators=True) |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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71 search_list = search_list[1:].strip() |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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72 # TODO maybe add regular express check |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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73 ev = safe_eval_es(search_list) |
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74 preprocessings = ( |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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75 preprocessing.StandardScaler(), |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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76 preprocessing.Binarizer(), |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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77 preprocessing.MaxAbsScaler(), |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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78 preprocessing.Normalizer(), |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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79 preprocessing.MinMaxScaler(), |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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80 preprocessing.PolynomialFeatures(), |
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81 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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82 feature_selection.SelectKBest(), |
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83 feature_selection.GenericUnivariateSelect(), |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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84 feature_selection.SelectPercentile(), |
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85 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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86 feature_selection.SelectFdr(), |
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87 feature_selection.SelectFwe(), |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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88 feature_selection.VarianceThreshold(), |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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89 decomposition.FactorAnalysis(random_state=0), |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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90 decomposition.FastICA(random_state=0), |
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91 decomposition.IncrementalPCA(), |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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92 decomposition.KernelPCA(random_state=0, n_jobs=N_JOBS), |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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93 decomposition.LatentDirichletAllocation(random_state=0, n_jobs=N_JOBS), |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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94 decomposition.MiniBatchDictionaryLearning(random_state=0, n_jobs=N_JOBS), |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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95 decomposition.MiniBatchSparsePCA(random_state=0, n_jobs=N_JOBS), |
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96 decomposition.NMF(random_state=0), |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
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97 decomposition.PCA(random_state=0), |
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98 decomposition.SparsePCA(random_state=0, n_jobs=N_JOBS), |
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99 decomposition.TruncatedSVD(random_state=0), |
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100 kernel_approximation.Nystroem(random_state=0), |
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101 kernel_approximation.RBFSampler(random_state=0), |
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102 kernel_approximation.AdditiveChi2Sampler(), |
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103 kernel_approximation.SkewedChi2Sampler(random_state=0), |
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104 cluster.FeatureAgglomeration(), |
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105 skrebate.ReliefF(n_jobs=N_JOBS), |
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106 skrebate.SURF(n_jobs=N_JOBS), |
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107 skrebate.SURFstar(n_jobs=N_JOBS), |
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108 skrebate.MultiSURF(n_jobs=N_JOBS), |
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109 skrebate.MultiSURFstar(n_jobs=N_JOBS), |
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110 imblearn.under_sampling.ClusterCentroids(random_state=0, n_jobs=N_JOBS), |
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111 imblearn.under_sampling.CondensedNearestNeighbour(random_state=0, n_jobs=N_JOBS), |
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112 imblearn.under_sampling.EditedNearestNeighbours(random_state=0, n_jobs=N_JOBS), |
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113 imblearn.under_sampling.RepeatedEditedNearestNeighbours(random_state=0, n_jobs=N_JOBS), |
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114 imblearn.under_sampling.AllKNN(random_state=0, n_jobs=N_JOBS), |
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115 imblearn.under_sampling.InstanceHardnessThreshold(random_state=0, n_jobs=N_JOBS), |
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116 imblearn.under_sampling.NearMiss(random_state=0, n_jobs=N_JOBS), |
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117 imblearn.under_sampling.NeighbourhoodCleaningRule(random_state=0, n_jobs=N_JOBS), |
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118 imblearn.under_sampling.OneSidedSelection(random_state=0, n_jobs=N_JOBS), |
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119 imblearn.under_sampling.RandomUnderSampler(random_state=0), |
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120 imblearn.under_sampling.TomekLinks(random_state=0, n_jobs=N_JOBS), |
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121 imblearn.over_sampling.ADASYN(random_state=0, n_jobs=N_JOBS), |
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122 imblearn.over_sampling.RandomOverSampler(random_state=0), |
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123 imblearn.over_sampling.SMOTE(random_state=0, n_jobs=N_JOBS), |
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124 imblearn.over_sampling.SVMSMOTE(random_state=0, n_jobs=N_JOBS), |
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125 imblearn.over_sampling.BorderlineSMOTE(random_state=0, n_jobs=N_JOBS), |
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126 imblearn.over_sampling.SMOTENC(categorical_features=[], random_state=0, n_jobs=N_JOBS), |
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127 imblearn.combine.SMOTEENN(random_state=0), |
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128 imblearn.combine.SMOTETomek(random_state=0), |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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129 ) |
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130 newlist = [] |
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131 for obj in ev: |
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132 if obj is None: |
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133 newlist.append(None) |
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134 elif obj == "all_0": |
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135 newlist.extend(preprocessings[0:35]) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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136 elif obj == "sk_prep_all": # no KernalCenter() |
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137 newlist.extend(preprocessings[0:7]) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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138 elif obj == "fs_all": |
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139 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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140 elif obj == "decomp_all": |
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141 newlist.extend(preprocessings[14:25]) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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142 elif obj == "k_appr_all": |
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143 newlist.extend(preprocessings[25:29]) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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144 elif obj == "reb_all": |
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145 newlist.extend(preprocessings[30:35]) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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146 elif obj == "imb_all": |
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147 newlist.extend(preprocessings[35:54]) |
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148 elif type(obj) is int and -1 < obj < len(preprocessings): |
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149 newlist.append(preprocessings[obj]) |
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150 elif hasattr(obj, "get_params"): # user uploaded object |
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151 if "n_jobs" in obj.get_params(): |
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152 newlist.append(obj.set_params(n_jobs=N_JOBS)) |
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153 else: |
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154 newlist.append(obj) |
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155 else: |
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156 sys.exit("Unsupported estimator type: %r" % (obj)) |
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157 |
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158 search_params[param_name] = newlist |
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159 |
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160 return search_params |
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161 |
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162 |
19
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163 def _handle_X_y( |
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164 estimator, |
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165 params, |
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166 infile1, |
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167 infile2, |
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168 loaded_df={}, |
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169 ref_seq=None, |
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170 intervals=None, |
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171 targets=None, |
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172 fasta_path=None, |
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173 ): |
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174 """read inputs |
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175 |
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176 Params |
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177 ------- |
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178 estimator : estimator object |
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179 params : dict |
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180 Galaxy tool parameter inputs |
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181 infile1 : str |
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182 File path to dataset containing features |
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183 infile2 : str |
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184 File path to dataset containing target values |
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185 loaded_df : dict |
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186 Contains loaded DataFrame objects with file path as keys |
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187 ref_seq : str |
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188 File path to dataset containing genome sequence file |
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189 interval : str |
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190 File path to dataset containing interval file |
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191 targets : str |
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192 File path to dataset compressed target bed file |
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193 fasta_path : str |
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194 File path to dataset containing fasta file |
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195 |
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196 |
15
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197 Returns |
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198 ------- |
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199 estimator : estimator object after setting new attributes |
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200 X : numpy array |
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201 y : numpy array |
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202 """ |
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203 estimator_params = estimator.get_params() |
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204 |
19
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205 input_type = params["input_options"]["selected_input"] |
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206 # tabular input |
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207 if input_type == "tabular": |
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208 header = "infer" if params["input_options"]["header1"] else None |
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209 column_option = params["input_options"]["column_selector_options_1"]["selected_column_selector_option"] |
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210 if column_option in [ |
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211 "by_index_number", |
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212 "all_but_by_index_number", |
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213 "by_header_name", |
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214 "all_but_by_header_name", |
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215 ]: |
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216 c = params["input_options"]["column_selector_options_1"]["col1"] |
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217 else: |
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218 c = None |
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219 |
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220 df_key = infile1 + repr(header) |
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221 |
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222 if df_key in loaded_df: |
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223 infile1 = loaded_df[df_key] |
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224 |
19
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225 df = pd.read_csv(infile1, sep="\t", header=header, parse_dates=True) |
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226 loaded_df[df_key] = df |
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227 |
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228 X = read_columns(df, c=c, c_option=column_option).astype(float) |
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229 # sparse input |
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230 elif input_type == "sparse": |
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231 X = mmread(open(infile1, "r")) |
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232 |
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233 # fasta_file input |
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234 elif input_type == "seq_fasta": |
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235 pyfaidx = get_module("pyfaidx") |
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236 sequences = pyfaidx.Fasta(fasta_path) |
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237 n_seqs = len(sequences.keys()) |
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238 X = np.arange(n_seqs)[:, np.newaxis] |
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239 for param in estimator_params.keys(): |
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240 if param.endswith("fasta_path"): |
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241 estimator.set_params(**{param: fasta_path}) |
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242 break |
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243 else: |
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244 raise ValueError( |
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245 "The selected estimator doesn't support " |
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246 "fasta file input! Please consider using " |
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247 "KerasGBatchClassifier with " |
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248 "FastaDNABatchGenerator/FastaProteinBatchGenerator " |
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249 "or having GenomeOneHotEncoder/ProteinOneHotEncoder " |
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250 "in pipeline!" |
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251 ) |
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252 |
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253 elif input_type == "refseq_and_interval": |
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254 path_params = { |
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255 "data_batch_generator__ref_genome_path": ref_seq, |
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256 "data_batch_generator__intervals_path": intervals, |
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257 "data_batch_generator__target_path": targets, |
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258 } |
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259 estimator.set_params(**path_params) |
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260 n_intervals = sum(1 for line in open(intervals)) |
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261 X = np.arange(n_intervals)[:, np.newaxis] |
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262 |
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263 # Get target y |
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264 header = "infer" if params["input_options"]["header2"] else None |
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265 column_option = params["input_options"]["column_selector_options_2"]["selected_column_selector_option2"] |
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266 if column_option in [ |
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267 "by_index_number", |
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268 "all_but_by_index_number", |
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269 "by_header_name", |
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270 "all_but_by_header_name", |
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271 ]: |
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272 c = params["input_options"]["column_selector_options_2"]["col2"] |
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273 else: |
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274 c = None |
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275 |
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276 df_key = infile2 + repr(header) |
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277 if df_key in loaded_df: |
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278 infile2 = loaded_df[df_key] |
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279 else: |
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280 infile2 = pd.read_csv(infile2, sep="\t", header=header, parse_dates=True) |
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281 loaded_df[df_key] = infile2 |
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282 |
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283 y = read_columns(infile2, c=c, c_option=column_option, sep="\t", header=header, parse_dates=True) |
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284 if len(y.shape) == 2 and y.shape[1] == 1: |
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285 y = y.ravel() |
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286 if input_type == "refseq_and_interval": |
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287 estimator.set_params(data_batch_generator__features=y.ravel().tolist()) |
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288 y = None |
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289 # end y |
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290 |
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291 return estimator, X, y |
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292 |
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293 |
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294 def _do_outer_cv(searcher, X, y, outer_cv, scoring, error_score="raise", outfile=None): |
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295 """Do outer cross-validation for nested CV |
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296 |
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297 Parameters |
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298 ---------- |
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299 searcher : object |
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300 SearchCV object |
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301 X : numpy array |
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302 Containing features |
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303 y : numpy array |
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304 Target values or labels |
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305 outer_cv : int or CV splitter |
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306 Control the cv splitting |
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307 scoring : object |
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308 Scorer |
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309 error_score: str, float or numpy float |
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310 Whether to raise fit error or return an value |
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311 outfile : str |
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312 File path to store the restuls |
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313 """ |
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314 if error_score == "raise": |
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315 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
|
316 searcher, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
317 X, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
318 y, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
319 scoring=scoring, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
320 cv=outer_cv, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
321 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
|
322 verbose=0, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
323 error_score=error_score, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
324 ) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
325 else: |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
326 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
|
327 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
|
328 try: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
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|
329 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
|
330 searcher, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
331 X, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
332 y, |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
333 scoring=scoring, |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
334 cv=outer_cv, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
335 n_jobs=N_JOBS, |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
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|
336 verbose=0, |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
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|
337 error_score=error_score, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
338 ) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
339 except ValueError: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
340 pass |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
341 for warning in w: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
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|
342 print(repr(warning.message)) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
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changeset
|
343 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
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|
344 keys = list(rval.keys()) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
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|
345 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
|
346 if k.startswith("test"): |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
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|
347 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
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changeset
|
348 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
|
349 if k.endswith("time"): |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
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|
350 rval.pop(k) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
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|
351 rval = pd.DataFrame(rval) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
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|
352 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
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changeset
|
353 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
parents:
11
diff
changeset
|
354 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
355 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
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changeset
|
356 def _do_train_test_split_val( |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
357 searcher, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
358 X, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
359 y, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
360 params, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
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changeset
|
361 error_score="raise", |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
362 primary_scoring=None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
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changeset
|
363 groups=None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
364 outfile=None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
365 ): |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
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|
366 """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
parents:
11
diff
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|
367 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
parents:
11
diff
changeset
|
368 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
369 Returns |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
370 -------- |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
371 Fitted SearchCV object |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
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|
372 """ |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
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|
373 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:
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|
374 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
|
375 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
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|
376 # splits |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
377 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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|
378 split_options["labels"] = y |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
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|
379 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
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changeset
|
380 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
|
381 if groups is None: |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
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changeset
|
382 raise ValueError("No group based CV option was choosen for " "group shuffle!") |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
383 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
|
384 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
|
385 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
|
386 else: |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
387 X, X_test, y, y_test, groups, _ = train_test_split(X, y, 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
|
388 else: |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
389 if split_options["shuffle"] == "None": |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
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changeset
|
390 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
|
391 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
|
392 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
393 if error_score == "raise": |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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changeset
|
394 searcher.fit(X, y, groups=groups) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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diff
changeset
|
395 else: |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
396 warnings.simplefilter("always", FitFailedWarning) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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397 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:
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changeset
|
398 try: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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changeset
|
399 searcher.fit(X, y, groups=groups) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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changeset
|
400 except ValueError: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
401 pass |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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diff
changeset
|
402 for warning in w: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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changeset
|
403 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
|
404 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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changeset
|
405 scorer_ = searcher.scorer_ |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
406 if isinstance(scorer_, collections.Mapping): |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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changeset
|
407 is_multimetric = True |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
408 else: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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changeset
|
409 is_multimetric = False |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
410 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
411 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
|
412 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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changeset
|
413 # 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
|
414 if best_estimator_.__class__.__name__ == "KerasGBatchClassifier": |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
415 test_score = best_estimator_.evaluate(X_test, scorer=scorer_, is_multimetric=is_multimetric) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
416 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
|
417 test_score = _score(best_estimator_, X_test, y_test, scorer_, is_multimetric=is_multimetric) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
418 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
419 if not is_multimetric: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
420 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
|
421 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
|
422 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
|
423 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:
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diff
changeset
|
424 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
|
425 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
426 return searcher |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
427 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
428 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
429 def main( |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
430 inputs, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
431 infile_estimator, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
432 infile1, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
433 infile2, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
434 outfile_result, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
435 outfile_object=None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
436 outfile_weights=None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
437 groups=None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
438 ref_seq=None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
439 intervals=None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
440 targets=None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
441 fasta_path=None, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
442 ): |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
443 """ |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
444 Parameter |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
445 --------- |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
446 inputs : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
447 File path to galaxy tool parameter |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
448 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
449 infile_estimator : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
450 File path to estimator |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
451 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
452 infile1 : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
453 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
|
454 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
455 infile2 : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
456 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
|
457 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
458 outfile_result : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
459 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
|
460 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
461 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
|
462 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
|
463 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
464 outfile_weights : str, optional |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
465 File path to save model weights |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
466 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
467 groups : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
468 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
|
469 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
470 ref_seq : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
471 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
|
472 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
473 intervals : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
474 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
|
475 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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diff
changeset
|
476 targets : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
477 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:
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changeset
|
478 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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changeset
|
479 fasta_path : str |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
480 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:
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changeset
|
481 """ |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
482 warnings.simplefilter("ignore") |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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diff
changeset
|
483 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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diff
changeset
|
484 # store read dataframe object |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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diff
changeset
|
485 loaded_df = {} |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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changeset
|
486 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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changeset
|
487 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:
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diff
changeset
|
488 params = json.load(param_handler) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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diff
changeset
|
489 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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diff
changeset
|
490 # Override the refit parameter |
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
|
491 params["search_schemes"]["options"]["refit"] = True if params["save"] != "nope" else False |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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changeset
|
492 |
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
|
493 with open(infile_estimator, "rb") as estimator_handler: |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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changeset
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494 estimator = load_model(estimator_handler) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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changeset
|
495 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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496 optimizer = params["search_schemes"]["selected_search_scheme"] |
7
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
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changeset
|
497 optimizer = getattr(model_selection, optimizer) |
99038af8deda
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents:
diff
changeset
|
498 |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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diff
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|
499 # handle gridsearchcv options |
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
|
500 options = params["search_schemes"]["options"] |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
501 |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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diff
changeset
|
502 if groups: |
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
|
503 header = "infer" if (options["cv_selector"]["groups_selector"]["header_g"]) else None |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
504 column_option = options["cv_selector"]["groups_selector"]["column_selector_options_g"][ |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
505 "selected_column_selector_option_g" |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
506 ] |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
507 if column_option in [ |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
508 "by_index_number", |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
509 "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
|
510 "by_header_name", |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
511 "all_but_by_header_name", |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
512 ]: |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
513 c = options["cv_selector"]["groups_selector"]["column_selector_options_g"]["col_g"] |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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diff
changeset
|
514 else: |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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diff
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|
515 c = None |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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diff
changeset
|
516 |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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diff
changeset
|
517 df_key = groups + repr(header) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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diff
changeset
|
518 |
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
|
519 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:
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diff
changeset
|
520 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:
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diff
changeset
|
521 |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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diff
changeset
|
522 groups = read_columns( |
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
|
523 groups, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
524 c=c, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
525 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
|
526 sep="\t", |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
527 header=header, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
528 parse_dates=True, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
529 ) |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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diff
changeset
|
530 groups = groups.ravel() |
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
|
531 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:
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diff
changeset
|
532 |
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
|
533 splitter, groups = get_cv(options.pop("cv_selector")) |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
534 options["cv"] = splitter |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
535 primary_scoring = options["scoring"]["primary_scoring"] |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
536 # get_scoring() expects secondary_scoring to be a comma separated string (not a list) |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
537 # Check if secondary_scoring is specified |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
538 secondary_scoring = options["scoring"].get("secondary_scoring", None) |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
539 if secondary_scoring is not None: |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
540 # If secondary_scoring is specified, convert the list into comman separated string |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
541 options["scoring"]["secondary_scoring"] = ",".join(options["scoring"]["secondary_scoring"]) |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
542 options["scoring"] = get_scoring(options["scoring"]) |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
543 if options["error_score"]: |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
544 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
|
545 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
|
546 options["error_score"] = np.NaN |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
547 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:
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diff
changeset
|
548 options["refit"] = primary_scoring |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
549 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:
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diff
changeset
|
550 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
|
551 |
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
|
552 params_builder = params["search_schemes"]["search_params_builder"] |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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diff
changeset
|
553 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:
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diff
changeset
|
554 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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diff
changeset
|
555 estimator = clean_params(estimator) |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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diff
changeset
|
556 |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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changeset
|
557 # 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:
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diff
changeset
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558 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:
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diff
changeset
|
559 searcher = optimizer(estimator, param_grid, **options) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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changeset
|
560 print(searcher) |
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
|
561 with open(outfile_object, "wb") as output_handler: |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
562 pickle.dump(searcher, output_handler, pickle.HIGHEST_PROTOCOL) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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diff
changeset
|
563 return 0 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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diff
changeset
|
564 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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diff
changeset
|
565 # 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:
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diff
changeset
|
566 estimator, X, y = _handle_X_y( |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
567 estimator, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
568 params, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
569 infile1, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
570 infile2, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
571 loaded_df=loaded_df, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
572 ref_seq=ref_seq, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
573 intervals=intervals, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
574 targets=targets, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
575 fasta_path=fasta_path, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
576 ) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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diff
changeset
|
577 |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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diff
changeset
|
578 # 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:
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diff
changeset
|
579 memory = joblib.Memory(location=CACHE_DIR, verbose=0) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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diff
changeset
|
580 main_est = get_main_estimator(estimator) |
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
|
581 if main_est.__class__.__name__ == "IRAPSClassifier": |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
582 main_est.set_params(memory=memory) |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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diff
changeset
|
583 |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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diff
changeset
|
584 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
|
585 |
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
|
586 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
|
587 |
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
|
588 if split_mode == "nested_cv": |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
589 # make sure refit is choosen |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
590 # this could be True for sklearn models, but not the case for |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
591 # deep learning models |
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
|
592 if not options["refit"] and not all(hasattr(estimator, attr) for attr in ("config", "model_type")): |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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diff
changeset
|
593 warnings.warn("Refit is change to `True` for nested validation!") |
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
|
594 setattr(searcher, "refit", True) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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diff
changeset
|
595 |
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
|
596 outer_cv, _ = get_cv(params["outer_split"]["cv_selector"]) |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
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diff
changeset
|
597 # 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:
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diff
changeset
|
598 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:
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diff
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|
599 rval = cross_validate( |
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
|
600 searcher, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
601 X, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
602 y, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
603 scoring=options["scoring"], |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
604 cv=outer_cv, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
605 n_jobs=N_JOBS, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
606 verbose=options["verbose"], |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
607 return_estimator=(params["save"] == "save_estimator"), |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
608 error_score=options["error_score"], |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
609 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
|
610 ) |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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diff
changeset
|
611 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
|
612 warnings.simplefilter("always", FitFailedWarning) |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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diff
changeset
|
613 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
|
614 try: |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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diff
changeset
|
615 rval = cross_validate( |
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
|
616 searcher, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
617 X, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
618 y, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
619 scoring=options["scoring"], |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
620 cv=outer_cv, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
621 n_jobs=N_JOBS, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
622 verbose=options["verbose"], |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
623 return_estimator=(params["save"] == "save_estimator"), |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
624 error_score=options["error_score"], |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
625 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
|
626 ) |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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diff
changeset
|
627 except ValueError: |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
628 pass |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
629 for warning in w: |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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diff
changeset
|
630 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
|
631 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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changeset
|
632 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
|
633 if fitted_searchers: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
634 import os |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
635 |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
636 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
|
637 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
|
638 try: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
639 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
|
640 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
|
641 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
|
642 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
|
643 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
|
644 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
|
645 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
|
646 continue |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
647 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
|
648 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
|
649 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
|
650 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
|
651 print(e) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
652 finally: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
653 del os |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
654 |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
655 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
|
656 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
|
657 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
|
658 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
|
659 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
|
660 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
|
661 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
|
662 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
|
663 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
|
664 rval.to_csv(path_or_buf=outfile_result, 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
|
665 # 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
|
666 """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
|
667 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
|
668 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
|
669 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
|
670 groups=groups, |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
671 outfile=outfile_result)""" |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
672 return 0 |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
673 |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
674 # no outer split |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
675 else: |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
676 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
|
677 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
|
678 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
|
679 else: |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
680 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
|
681 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
|
682 try: |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
683 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
|
684 except ValueError: |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
685 pass |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
686 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
|
687 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
|
688 |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
689 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
|
690 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
|
691 cv_results.to_csv(path_or_buf=outfile_result, sep="\t", header=True, index=False) |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
692 |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
7
diff
changeset
|
693 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
|
694 |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
695 # 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
|
696 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
|
697 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
|
698 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
|
699 warnings.warn( |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
diff
changeset
|
700 "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
|
701 "'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
|
702 "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
|
703 ) |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
704 return |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
705 |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
706 # clean prams |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
707 best_estimator_ = clean_params(best_estimator_) |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
708 |
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents:
11
diff
changeset
|
709 main_est = get_main_estimator(best_estimator_) |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
8
diff
changeset
|
710 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
15
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|
711 if hasattr(main_est, "model_") and hasattr(main_est, "save_weights"): |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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712 if outfile_weights: |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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diff
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713 main_est.save_weights(outfile_weights) |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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714 del main_est.model_ |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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715 del main_est.fit_params |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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716 del main_est.model_class_ |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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717 del main_est.validation_data |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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718 if getattr(main_est, "data_generator_", None): |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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719 del main_est.data_generator_ |
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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720 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
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|
721 with open(outfile_object, "wb") as output_handler: |
15
3f3c6dc38f3e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
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722 print("Best estimator is saved: %s " % repr(best_estimator_)) |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff
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|
723 pickle.dump(best_estimator_, output_handler, pickle.HIGHEST_PROTOCOL) |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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diff
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|
724 |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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725 |
19
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
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|
726 if __name__ == "__main__": |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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diff
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|
727 aparser = argparse.ArgumentParser() |
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
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|
728 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:
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diff
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|
729 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:
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diff
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|
730 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:
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diff
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|
731 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
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732 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
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diff
changeset
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733 aparser.add_argument("-o", "--outfile_object", dest="outfile_object") |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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diff
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|
734 aparser.add_argument("-w", "--outfile_weights", dest="outfile_weights") |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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diff
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|
735 aparser.add_argument("-g", "--groups", dest="groups") |
10
775b004b7920
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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diff
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|
736 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
parents:
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diff
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737 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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diff
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|
738 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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diff
changeset
|
739 aparser.add_argument("-f", "--fasta_path", dest="fasta_path") |
8
913ee94945f3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents:
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diff
changeset
|
740 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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diff
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|
741 |
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
|
742 main( |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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743 args.inputs, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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744 args.infile_estimator, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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745 args.infile1, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
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|
746 args.infile2, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff
changeset
|
747 args.outfile_result, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
748 outfile_object=args.outfile_object, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
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|
749 outfile_weights=args.outfile_weights, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
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|
750 groups=args.groups, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff
changeset
|
751 ref_seq=args.ref_seq, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
752 intervals=args.intervals, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
753 targets=args.targets, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
754 fasta_path=args.fasta_path, |
4de3d598c116
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
755 ) |