Mercurial > repos > bgruening > sklearn_train_test_eval
annotate train_test_eval.py @ 18:ddc4fe317a92 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 80417bf0158a9b596e485dd66408f738f405145a
author | bgruening |
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date | Mon, 02 Oct 2023 10:28:18 +0000 |
parents | 2eb5c017958d |
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68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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1 import argparse |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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2 import json |
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2b8406e74f9e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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3 import os |
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68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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4 import warnings |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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5 from itertools import chain |
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ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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6 |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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7 import joblib |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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8 import numpy as np |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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9 import pandas as pd |
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2eb5c017958d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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10 from galaxy_ml.model_persist import dump_model_to_h5, load_model_from_h5 |
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ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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11 from galaxy_ml.model_validations import train_test_split |
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2eb5c017958d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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12 from galaxy_ml.utils import ( |
2eb5c017958d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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13 clean_params, |
2eb5c017958d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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14 get_module, |
2eb5c017958d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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15 get_scoring, |
2eb5c017958d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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16 read_columns, |
2eb5c017958d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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17 SafeEval, |
2eb5c017958d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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18 try_get_attr |
2eb5c017958d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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19 ) |
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68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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20 from scipy.io import mmread |
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ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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21 from sklearn import pipeline |
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68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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22 from sklearn.model_selection import _search, _validation |
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ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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23 from sklearn.model_selection._validation import _score |
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2eb5c017958d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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24 from sklearn.utils import _safe_indexing, indexable |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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25 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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26 _fit_and_score = try_get_attr("galaxy_ml.model_validations", "_fit_and_score") |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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27 setattr(_search, "_fit_and_score", _fit_and_score) |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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28 setattr(_validation, "_fit_and_score", _fit_and_score) |
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68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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29 |
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ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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30 N_JOBS = int(os.environ.get("GALAXY_SLOTS", 1)) |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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31 CACHE_DIR = os.path.join(os.getcwd(), "cached") |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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32 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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33 NON_SEARCHABLE = ("n_jobs", "pre_dispatch", "memory", "_path", "nthread", "callbacks") |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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34 ALLOWED_CALLBACKS = ( |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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35 "EarlyStopping", |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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36 "TerminateOnNaN", |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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37 "ReduceLROnPlateau", |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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38 "CSVLogger", |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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39 "None", |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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40 ) |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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41 |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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42 |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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43 def _eval_swap_params(params_builder): |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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44 swap_params = {} |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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45 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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46 for p in params_builder["param_set"]: |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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47 swap_value = p["sp_value"].strip() |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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48 if swap_value == "": |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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49 continue |
68aaa903052a
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50 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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51 param_name = p["sp_name"] |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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52 if param_name.lower().endswith(NON_SEARCHABLE): |
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ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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53 warnings.warn( |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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54 "Warning: `%s` is not eligible for search and was " |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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55 "omitted!" % param_name |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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56 ) |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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57 continue |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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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 if not swap_value.startswith(":"): |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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60 safe_eval = SafeEval(load_scipy=True, load_numpy=True) |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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61 ev = safe_eval(swap_value) |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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62 else: |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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63 # Have `:` before search list, asks for estimator evaluatio |
68aaa903052a
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64 safe_eval_es = SafeEval(load_estimators=True) |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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65 swap_value = swap_value[1:].strip() |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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66 # TODO maybe add regular express check |
68aaa903052a
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67 ev = safe_eval_es(swap_value) |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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68 |
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69 swap_params[param_name] = ev |
68aaa903052a
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70 |
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71 return swap_params |
68aaa903052a
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72 |
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73 |
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74 def train_test_split_none(*arrays, **kwargs): |
68aaa903052a
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75 """extend train_test_split to take None arrays |
68aaa903052a
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76 and support split by group names. |
68aaa903052a
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77 """ |
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78 nones = [] |
68aaa903052a
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79 new_arrays = [] |
68aaa903052a
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80 for idx, arr in enumerate(arrays): |
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81 if arr is None: |
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82 nones.append(idx) |
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83 else: |
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84 new_arrays.append(arr) |
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85 |
9
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86 if kwargs["shuffle"] == "None": |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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87 kwargs["shuffle"] = None |
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88 |
9
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89 group_names = kwargs.pop("group_names", None) |
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90 |
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91 if group_names is not None and group_names.strip(): |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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92 group_names = [name.strip() for name in group_names.split(",")] |
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93 new_arrays = indexable(*new_arrays) |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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94 groups = kwargs["labels"] |
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95 n_samples = new_arrays[0].shape[0] |
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96 index_arr = np.arange(n_samples) |
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97 test = index_arr[np.isin(groups, group_names)] |
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98 train = index_arr[~np.isin(groups, group_names)] |
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99 rval = list( |
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100 chain.from_iterable( |
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101 (_safe_indexing(a, train), _safe_indexing(a, test)) for a in new_arrays |
9
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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102 ) |
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103 ) |
0
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104 else: |
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105 rval = train_test_split(*new_arrays, **kwargs) |
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106 |
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107 for pos in nones: |
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108 rval[pos * 2: 2] = [None, None] |
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109 |
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110 return rval |
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111 |
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112 |
9
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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113 def main( |
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114 inputs, |
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115 infile_estimator, |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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116 infile1, |
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117 infile2, |
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118 outfile_result, |
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119 outfile_object=None, |
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120 outfile_weights=None, |
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121 groups=None, |
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122 ref_seq=None, |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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123 intervals=None, |
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124 targets=None, |
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125 fasta_path=None, |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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126 ): |
0
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127 """ |
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128 Parameter |
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129 --------- |
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130 inputs : str |
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131 File path to galaxy tool parameter |
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132 |
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133 infile_estimator : str |
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134 File path to estimator |
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135 |
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136 infile1 : str |
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137 File path to dataset containing features |
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138 |
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139 infile2 : str |
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140 File path to dataset containing target values |
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141 |
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142 outfile_result : str |
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143 File path to save the results, either cv_results or test result |
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144 |
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145 outfile_object : str, optional |
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146 File path to save searchCV object |
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147 |
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148 outfile_weights : str, optional |
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149 File path to save deep learning model weights |
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150 |
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151 groups : str |
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152 File path to dataset containing groups labels |
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153 |
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154 ref_seq : str |
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155 File path to dataset containing genome sequence file |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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156 |
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157 intervals : str |
68aaa903052a
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158 File path to dataset containing interval file |
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159 |
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160 targets : str |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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161 File path to dataset compressed target bed file |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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162 |
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163 fasta_path : str |
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164 File path to dataset containing fasta file |
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165 """ |
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166 warnings.simplefilter("ignore") |
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167 |
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168 with open(inputs, "r") as param_handler: |
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169 params = json.load(param_handler) |
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170 |
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171 # load estimator |
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172 estimator = load_model_from_h5(infile_estimator) |
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173 estimator = clean_params(estimator) |
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174 |
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175 # swap hyperparameter |
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176 swapping = params["experiment_schemes"]["hyperparams_swapping"] |
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177 swap_params = _eval_swap_params(swapping) |
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178 estimator.set_params(**swap_params) |
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179 |
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180 estimator_params = estimator.get_params() |
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181 |
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182 # store read dataframe object |
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183 loaded_df = {} |
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184 |
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185 input_type = params["input_options"]["selected_input"] |
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186 # tabular input |
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187 if input_type == "tabular": |
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188 header = "infer" if params["input_options"]["header1"] else None |
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189 column_option = params["input_options"]["column_selector_options_1"][ |
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190 "selected_column_selector_option" |
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191 ] |
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192 if column_option in [ |
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193 "by_index_number", |
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194 "all_but_by_index_number", |
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195 "by_header_name", |
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196 "all_but_by_header_name", |
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197 ]: |
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198 c = params["input_options"]["column_selector_options_1"]["col1"] |
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199 else: |
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200 c = None |
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201 |
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202 df_key = infile1 + repr(header) |
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203 df = pd.read_csv(infile1, sep="\t", header=header, parse_dates=True) |
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204 loaded_df[df_key] = df |
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205 |
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206 X = read_columns(df, c=c, c_option=column_option).astype(float) |
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207 # sparse input |
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208 elif input_type == "sparse": |
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209 X = mmread(open(infile1, "r")) |
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210 |
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211 # fasta_file input |
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212 elif input_type == "seq_fasta": |
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213 pyfaidx = get_module("pyfaidx") |
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214 sequences = pyfaidx.Fasta(fasta_path) |
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215 n_seqs = len(sequences.keys()) |
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216 X = np.arange(n_seqs)[:, np.newaxis] |
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217 for param in estimator_params.keys(): |
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218 if param.endswith("fasta_path"): |
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219 estimator.set_params(**{param: fasta_path}) |
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220 break |
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221 else: |
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222 raise ValueError( |
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223 "The selected estimator doesn't support " |
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224 "fasta file input! Please consider using " |
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225 "KerasGBatchClassifier with " |
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226 "FastaDNABatchGenerator/FastaProteinBatchGenerator " |
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227 "or having GenomeOneHotEncoder/ProteinOneHotEncoder " |
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228 "in pipeline!" |
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229 ) |
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230 |
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231 elif input_type == "refseq_and_interval": |
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232 path_params = { |
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233 "data_batch_generator__ref_genome_path": ref_seq, |
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234 "data_batch_generator__intervals_path": intervals, |
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235 "data_batch_generator__target_path": targets, |
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236 } |
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237 estimator.set_params(**path_params) |
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238 n_intervals = sum(1 for line in open(intervals)) |
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239 X = np.arange(n_intervals)[:, np.newaxis] |
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240 |
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241 # Get target y |
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242 header = "infer" if params["input_options"]["header2"] else None |
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243 column_option = params["input_options"]["column_selector_options_2"][ |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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244 "selected_column_selector_option2" |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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245 ] |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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246 if column_option in [ |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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247 "by_index_number", |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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248 "all_but_by_index_number", |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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249 "by_header_name", |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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250 "all_but_by_header_name", |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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251 ]: |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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252 c = params["input_options"]["column_selector_options_2"]["col2"] |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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253 else: |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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254 c = None |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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255 |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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256 df_key = infile2 + repr(header) |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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257 if df_key in loaded_df: |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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258 infile2 = loaded_df[df_key] |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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259 else: |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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260 infile2 = pd.read_csv(infile2, sep="\t", header=header, parse_dates=True) |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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261 loaded_df[df_key] = infile2 |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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262 |
11
caf7d2b71a48
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
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263 y = read_columns( |
caf7d2b71a48
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
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264 infile2, c=c, c_option=column_option, sep="\t", header=header, parse_dates=True |
caf7d2b71a48
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
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265 ) |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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266 if len(y.shape) == 2 and y.shape[1] == 1: |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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267 y = y.ravel() |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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268 if input_type == "refseq_and_interval": |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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269 estimator.set_params(data_batch_generator__features=y.ravel().tolist()) |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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270 y = None |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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271 # end y |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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272 |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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273 # load groups |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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274 if groups: |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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275 groups_selector = ( |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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276 params["experiment_schemes"]["test_split"]["split_algos"] |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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277 ).pop("groups_selector") |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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278 |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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279 header = "infer" if groups_selector["header_g"] else None |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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280 column_option = groups_selector["column_selector_options_g"][ |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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281 "selected_column_selector_option_g" |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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282 ] |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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283 if column_option in [ |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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284 "by_index_number", |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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285 "all_but_by_index_number", |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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286 "by_header_name", |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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287 "all_but_by_header_name", |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
288 ]: |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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289 c = groups_selector["column_selector_options_g"]["col_g"] |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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290 else: |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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291 c = None |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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292 |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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293 df_key = groups + repr(header) |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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294 if df_key in loaded_df: |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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295 groups = loaded_df[df_key] |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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296 |
11
caf7d2b71a48
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
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297 groups = read_columns( |
caf7d2b71a48
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
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298 groups, |
caf7d2b71a48
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
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299 c=c, |
caf7d2b71a48
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
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300 c_option=column_option, |
caf7d2b71a48
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
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301 sep="\t", |
caf7d2b71a48
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
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302 header=header, |
caf7d2b71a48
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
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303 parse_dates=True, |
caf7d2b71a48
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
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|
304 ) |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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305 groups = groups.ravel() |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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306 |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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307 # del loaded_df |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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308 del loaded_df |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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309 |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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310 # handle memory |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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311 memory = joblib.Memory(location=CACHE_DIR, verbose=0) |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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312 # cache iraps_core fits could increase search speed significantly |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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313 if estimator.__class__.__name__ == "IRAPSClassifier": |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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314 estimator.set_params(memory=memory) |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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315 else: |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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316 # For iraps buried in pipeline |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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317 new_params = {} |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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318 for p, v in estimator_params.items(): |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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319 if p.endswith("memory"): |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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320 # for case of `__irapsclassifier__memory` |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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321 if len(p) > 8 and p[:-8].endswith("irapsclassifier"): |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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322 # cache iraps_core fits could increase search |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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323 # speed significantly |
68aaa903052a
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324 new_params[p] = memory |
68aaa903052a
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325 # security reason, we don't want memory being |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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326 # modified unexpectedly |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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327 elif v: |
68aaa903052a
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328 new_params[p] = None |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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329 # handle n_jobs |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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330 elif p.endswith("n_jobs"): |
0
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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331 # For now, 1 CPU is suggested for iprasclassifier |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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332 if len(p) > 8 and p[:-8].endswith("irapsclassifier"): |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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333 new_params[p] = 1 |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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334 else: |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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335 new_params[p] = N_JOBS |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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336 # for security reason, types of callback are limited |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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337 elif p.endswith("callbacks"): |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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338 for cb in v: |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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339 cb_type = cb["callback_selection"]["callback_type"] |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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340 if cb_type not in ALLOWED_CALLBACKS: |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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341 raise ValueError("Prohibited callback type: %s!" % cb_type) |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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342 |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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343 estimator.set_params(**new_params) |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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344 |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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345 # handle scorer, convert to scorer dict |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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346 # Check if scoring is specified |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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347 scoring = params["experiment_schemes"]["metrics"].get("scoring", None) |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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348 if scoring is not None: |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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349 # get_scoring() expects secondary_scoring to be a comma separated string (not a list) |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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350 # Check if secondary_scoring is specified |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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351 secondary_scoring = scoring.get("secondary_scoring", None) |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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352 if secondary_scoring is not None: |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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353 # If secondary_scoring is specified, convert the list into comman separated string |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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354 scoring["secondary_scoring"] = ",".join(scoring["secondary_scoring"]) |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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355 scorer = get_scoring(scoring) |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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356 |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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357 # handle test (first) split |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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358 test_split_options = params["experiment_schemes"]["test_split"]["split_algos"] |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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359 |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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360 if test_split_options["shuffle"] == "group": |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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361 test_split_options["labels"] = groups |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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362 if test_split_options["shuffle"] == "stratified": |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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363 if y is not None: |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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364 test_split_options["labels"] = y |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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|
365 else: |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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366 raise ValueError( |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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367 "Stratified shuffle split is not " "applicable on empty target values!" |
ead7adad8d0e
"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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|
368 ) |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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369 |
11
caf7d2b71a48
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
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|
370 ( |
caf7d2b71a48
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
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371 X_train, |
caf7d2b71a48
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
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372 X_test, |
caf7d2b71a48
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
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373 y_train, |
caf7d2b71a48
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
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374 y_test, |
caf7d2b71a48
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
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375 groups_train, |
caf7d2b71a48
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
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376 _groups_test, |
caf7d2b71a48
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ea12f973df4b97a2691d9e4ce6bf6fae59d57717"
bgruening
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377 ) = train_test_split_none(X, y, groups, **test_split_options) |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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378 |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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379 exp_scheme = params["experiment_schemes"]["selected_exp_scheme"] |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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380 |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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381 # handle validation (second) split |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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382 if exp_scheme == "train_val_test": |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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383 val_split_options = params["experiment_schemes"]["val_split"]["split_algos"] |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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|
384 |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
385 if val_split_options["shuffle"] == "group": |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
386 val_split_options["labels"] = groups_train |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
387 if val_split_options["shuffle"] == "stratified": |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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|
388 if y_train is not None: |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
389 val_split_options["labels"] = y_train |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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|
390 else: |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
391 raise ValueError( |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
392 "Stratified shuffle split is not " |
ead7adad8d0e
"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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|
393 "applicable on empty target values!" |
ead7adad8d0e
"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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|
394 ) |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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|
395 |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
396 ( |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
397 X_train, |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
398 X_val, |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
399 y_train, |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
400 y_val, |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
401 groups_train, |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
402 _groups_val, |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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403 ) = train_test_split_none(X_train, y_train, groups_train, **val_split_options) |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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404 |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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405 # train and eval |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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406 if hasattr(estimator, "validation_data"): |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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407 if exp_scheme == "train_val_test": |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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408 estimator.fit(X_train, y_train, validation_data=(X_val, y_val)) |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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409 else: |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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410 estimator.fit(X_train, y_train, validation_data=(X_test, y_test)) |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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411 else: |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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412 estimator.fit(X_train, y_train) |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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413 |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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414 if hasattr(estimator, "evaluate"): |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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415 scores = estimator.evaluate( |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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416 X_test, y_test=y_test, scorer=scorer, is_multimetric=True |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
417 ) |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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418 else: |
15
2eb5c017958d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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419 scores = _score(estimator, X_test, y_test, scorer) |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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420 # handle output |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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421 for name, score in scores.items(): |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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422 scores[name] = [score] |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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423 df = pd.DataFrame(scores) |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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424 df = df[sorted(df.columns)] |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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425 df.to_csv(path_or_buf=outfile_result, sep="\t", header=True, index=False) |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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426 |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
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427 memory.clear(warn=False) |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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|
428 |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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changeset
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429 if outfile_object: |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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|
430 main_est = estimator |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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431 if isinstance(estimator, pipeline.Pipeline): |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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432 main_est = estimator.steps[-1][-1] |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
diff
changeset
|
433 |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
5
diff
changeset
|
434 if hasattr(main_est, "model_") and hasattr(main_est, "save_weights"): |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
diff
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|
435 if outfile_weights: |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
diff
changeset
|
436 main_est.save_weights(outfile_weights) |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
437 if getattr(main_est, "model_", None): |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
438 del main_est.model_ |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
5
diff
changeset
|
439 if getattr(main_est, "fit_params", None): |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
5
diff
changeset
|
440 del main_est.fit_params |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
5
diff
changeset
|
441 if getattr(main_est, "model_class_", None): |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
442 del main_est.model_class_ |
ead7adad8d0e
"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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|
443 if getattr(main_est, "validation_data", None): |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
444 del main_est.validation_data |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
445 if getattr(main_est, "data_generator_", None): |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
diff
changeset
|
446 del main_est.data_generator_ |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
diff
changeset
|
447 |
15
2eb5c017958d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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|
448 dump_model_to_h5(estimator, outfile_object) |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
diff
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|
449 |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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changeset
|
450 |
9
ead7adad8d0e
"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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|
451 if __name__ == "__main__": |
0
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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|
452 aparser = argparse.ArgumentParser() |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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453 aparser.add_argument("-i", "--inputs", dest="inputs", required=True) |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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454 aparser.add_argument("-e", "--estimator", dest="infile_estimator") |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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changeset
|
455 aparser.add_argument("-X", "--infile1", dest="infile1") |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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|
456 aparser.add_argument("-y", "--infile2", dest="infile2") |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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457 aparser.add_argument("-O", "--outfile_result", dest="outfile_result") |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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458 aparser.add_argument("-o", "--outfile_object", dest="outfile_object") |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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459 aparser.add_argument("-w", "--outfile_weights", dest="outfile_weights") |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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changeset
|
460 aparser.add_argument("-g", "--groups", dest="groups") |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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461 aparser.add_argument("-r", "--ref_seq", dest="ref_seq") |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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462 aparser.add_argument("-b", "--intervals", dest="intervals") |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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463 aparser.add_argument("-t", "--targets", dest="targets") |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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464 aparser.add_argument("-f", "--fasta_path", dest="fasta_path") |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
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465 args = aparser.parse_args() |
68aaa903052a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents:
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|
466 |
9
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
467 main( |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
468 args.inputs, |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
469 args.infile_estimator, |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
470 args.infile1, |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
471 args.infile2, |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
472 args.outfile_result, |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
473 outfile_object=args.outfile_object, |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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|
474 outfile_weights=args.outfile_weights, |
ead7adad8d0e
"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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|
475 groups=args.groups, |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents:
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diff
changeset
|
476 ref_seq=args.ref_seq, |
ead7adad8d0e
"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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|
477 intervals=args.intervals, |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
478 targets=args.targets, |
ead7adad8d0e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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|
479 fasta_path=args.fasta_path, |
ead7adad8d0e
"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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|
480 ) |