Mercurial > repos > galaxy-australia > alphafold2
annotate gen_extra_outputs.py @ 7:eb085b3dbaf8 draft
"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"
author | galaxy-australia |
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date | Tue, 19 Apr 2022 00:39:29 +0000 |
parents | 7ae9d78b06f5 |
children | 3bd420ec162d |
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7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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1 |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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2 |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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3 import json |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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4 import pickle |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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5 import argparse |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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6 from typing import Any, Dict, List |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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7 |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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8 |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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9 class Settings: |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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10 """parses then keeps track of program settings""" |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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11 def __init__(self): |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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12 self.workdir = None |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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13 self.output_confidence_scores = True |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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14 self.output_residue_scores = False |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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15 |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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16 def parse_settings(self) -> None: |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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17 parser = argparse.ArgumentParser() |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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18 parser.add_argument( |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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19 "workdir", |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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20 help="alphafold output directory", |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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21 type=str |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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22 ) |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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23 parser.add_argument( |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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24 "-p", |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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25 "--plddts", |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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26 help="output per-residue confidence scores (pLDDTs)", |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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27 action="store_true" |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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28 ) |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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29 args = parser.parse_args() |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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30 self.workdir = args.workdir.rstrip('/') |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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31 self.output_residue_scores = args.plddts |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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32 |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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33 |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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34 class ExecutionContext: |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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35 """uses program settings to get paths to files etc""" |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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36 def __init__(self, settings: Settings): |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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37 self.settings = settings |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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38 |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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39 @property |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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40 def ranking_debug(self) -> str: |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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41 return f'{self.settings.workdir}/ranking_debug.json' |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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42 |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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43 @property |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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44 def model_pkls(self) -> List[str]: |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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45 return [f'{self.settings.workdir}/result_model_{i}.pkl' |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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46 for i in range(1, 6)] |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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47 |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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48 @property |
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49 def model_conf_score_output(self) -> str: |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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50 return f'{self.settings.workdir}/model_confidence_scores.tsv' |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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51 |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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52 @property |
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53 def plddt_output(self) -> str: |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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54 return f'{self.settings.workdir}/plddts.tsv' |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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55 |
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56 |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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57 class FileLoader: |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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58 """loads file data for use by other classes""" |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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59 def __init__(self, context: ExecutionContext): |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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60 self.context = context |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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61 |
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62 def get_model_mapping(self) -> Dict[str, int]: |
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63 data = self.load_ranking_debug() |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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64 return {name: int(rank) + 1 |
7ae9d78b06f5
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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65 for (rank, name) in enumerate(data['order'])} |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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66 |
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67 def get_conf_scores(self) -> Dict[str, float]: |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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68 data = self.load_ranking_debug() |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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69 return {name: float(f'{score:.2f}') |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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70 for name, score in data['plddts'].items()} |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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71 |
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72 def load_ranking_debug(self) -> Dict[str, Any]: |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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73 with open(self.context.ranking_debug, 'r') as fp: |
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74 return json.load(fp) |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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75 |
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76 def get_model_plddts(self) -> Dict[str, List[float]]: |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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77 plddts: Dict[str, List[float]] = {} |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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78 model_pkls = self.context.model_pkls |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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79 for i in range(5): |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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80 pklfile = model_pkls[i] |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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81 with open(pklfile, 'rb') as fp: |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
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82 data = pickle.load(fp) |
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83 plddts[f'model_{i+1}'] = [float(f'{x:.2f}') for x in data['plddt']] |
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84 return plddts |
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85 |
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86 |
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87 class OutputGenerator: |
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88 """generates the output data we are interested in creating""" |
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89 def __init__(self, loader: FileLoader): |
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90 self.loader = loader |
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91 |
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92 def gen_conf_scores(self): |
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93 mapping = self.loader.get_model_mapping() |
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94 scores = self.loader.get_conf_scores() |
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95 ranked = list(scores.items()) |
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96 ranked.sort(key=lambda x: x[1], reverse=True) |
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97 return {f'model_{mapping[name]}': score |
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98 for name, score in ranked} |
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99 |
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100 def gen_residue_scores(self) -> Dict[str, List[float]]: |
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101 mapping = self.loader.get_model_mapping() |
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102 model_plddts = self.loader.get_model_plddts() |
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103 return {f'model_{mapping[name]}': plddts |
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104 for name, plddts in model_plddts.items()} |
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105 |
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106 |
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107 class OutputWriter: |
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108 """writes generated data to files""" |
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109 def __init__(self, context: ExecutionContext): |
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110 self.context = context |
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111 |
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112 def write_conf_scores(self, data: Dict[str, float]) -> None: |
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113 outfile = self.context.model_conf_score_output |
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114 with open(outfile, 'w') as fp: |
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115 for model, score in data.items(): |
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116 fp.write(f'{model}\t{score}\n') |
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117 |
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118 def write_residue_scores(self, data: Dict[str, List[float]]) -> None: |
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119 outfile = self.context.plddt_output |
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120 model_plddts = list(data.items()) |
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121 model_plddts.sort() |
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122 |
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123 with open(outfile, 'w') as fp: |
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124 for model, plddts in model_plddts: |
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125 plddt_str_list = [str(x) for x in plddts] |
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126 plddt_str = ','.join(plddt_str_list) |
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127 fp.write(f'{model}\t{plddt_str}\n') |
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128 |
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129 |
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130 def main(): |
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131 # setup |
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132 settings = Settings() |
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133 settings.parse_settings() |
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134 context = ExecutionContext(settings) |
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135 loader = FileLoader(context) |
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136 |
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137 # generate & write outputs |
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138 generator = OutputGenerator(loader) |
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139 writer = OutputWriter(context) |
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140 |
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141 # confidence scores |
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142 conf_scores = generator.gen_conf_scores() |
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143 writer.write_conf_scores(conf_scores) |
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144 |
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145 # per-residue plddts |
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146 if settings.output_residue_scores: |
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147 residue_scores = generator.gen_residue_scores() |
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148 writer.write_residue_scores(residue_scores) |
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149 |
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150 |
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151 if __name__ == '__main__': |
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152 main() |
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153 |
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154 |
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155 |