annotate scripts/outputs.py @ 17:5b85006245f3 draft

planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2e1eba8094c506a99a844546e8343849d3cef694
author galaxy-australia
date Wed, 31 May 2023 01:30:22 +0000
parents f9eb041c518c
children 6ab1a261520a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
16
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
1 """Generate additional output files not produced by AlphaFold.
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
2
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
3 Currently this is includes:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
4 - model confidence scores
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
5 - per-residue confidence scores (pLDDTs - optional output)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
6 - model_*.pkl files renamed with rank order
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
7
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
8 N.B. There have been issues with this script breaking between AlphaFold
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
9 versions due to minor changes in the output directory structure across minor
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
10 versions. It will likely need updating with future releases of AlphaFold.
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
11
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
12 This code is more complex than you might expect due to the output files
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
13 'moving around' considerably, depending on run parameters. You will see that
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
14 several output paths are determined dynamically.
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
15 """
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
16
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
17 import argparse
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
18 import json
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
19 import os
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
20 import pickle as pk
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
21 import shutil
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
22 from pathlib import Path
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
23 from typing import List
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
24
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
25 from matplotlib import pyplot as plt
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
26
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
27 # Output file paths
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
28 OUTPUT_DIR = 'extra'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
29 OUTPUTS = {
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
30 'model_pkl': OUTPUT_DIR + '/ranked_{rank}.pkl',
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
31 'model_pae': OUTPUT_DIR + '/pae_ranked_{rank}.csv',
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
32 'model_plot': OUTPUT_DIR + '/ranked_{rank}.png',
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
33 'model_confidence_scores': OUTPUT_DIR + '/model_confidence_scores.tsv',
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
34 'plddts': OUTPUT_DIR + '/plddts.tsv',
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
35 'relax': OUTPUT_DIR + '/relax_metrics_ranked.json',
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
36 }
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
37
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
38 # Keys for accessing confidence data from JSON/pkl files
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
39 # They change depending on whether the run was monomer or multimer
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
40 PLDDT_KEY = {
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
41 'monomer': 'plddts',
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
42 'multimer': 'iptm+ptm',
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
43 }
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
44
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
45
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
46 class Settings:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
47 """Parse and store settings/config."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
48 def __init__(self):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
49 self.workdir = None
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
50 self.output_confidence_scores = True
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
51 self.output_residue_scores = False
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
52 self.is_multimer = False
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
53 self.parse()
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
54
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
55 def parse(self) -> None:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
56 parser = argparse.ArgumentParser()
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
57 parser.add_argument(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
58 "workdir",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
59 help="alphafold output directory",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
60 type=str
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
61 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
62 parser.add_argument(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
63 "-p",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
64 "--plddts",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
65 help="output per-residue confidence scores (pLDDTs)",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
66 action="store_true"
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
67 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
68 parser.add_argument(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
69 "-m",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
70 "--multimer",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
71 help="parse output from AlphaFold multimer",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
72 action="store_true"
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
73 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
74 parser.add_argument(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
75 "--pkl",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
76 help="rename model pkl outputs with rank order",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
77 action="store_true"
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
78 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
79 parser.add_argument(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
80 "--pae",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
81 help="extract PAE from pkl files to CSV format",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
82 action="store_true"
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
83 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
84 parser.add_argument(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
85 "--plot",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
86 help="Plot pLDDT and PAE for each model",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
87 action="store_true"
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
88 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
89 args = parser.parse_args()
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
90 self.workdir = Path(args.workdir.rstrip('/'))
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
91 self.output_residue_scores = args.plddts
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
92 self.output_model_pkls = args.pkl
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
93 self.output_model_plots = args.plot
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
94 self.output_pae = args.pae
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
95 self.is_multimer = args.multimer
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
96 self.output_dir = self.workdir / OUTPUT_DIR
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
97 os.makedirs(self.output_dir, exist_ok=True)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
98
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
99
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
100 class ExecutionContext:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
101 """Collect file paths etc."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
102 def __init__(self, settings: Settings):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
103 self.settings = settings
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
104 if settings.is_multimer:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
105 self.plddt_key = PLDDT_KEY['multimer']
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
106 else:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
107 self.plddt_key = PLDDT_KEY['monomer']
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
108
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
109 def get_model_key(self, ix: int) -> str:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
110 """Return json key for model index.
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
111
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
112 The key format changed between minor AlphaFold versions so this
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
113 function determines the correct key.
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
114 """
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
115 with open(self.ranking_debug) as f:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
116 data = json.load(f)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
117 model_keys = list(data[self.plddt_key].keys())
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
118 for k in model_keys:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
119 if k.startswith(f"model_{ix}_"):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
120 return k
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
121 return KeyError(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
122 f'Could not find key for index={ix} in'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
123 ' ranking_debug.json')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
124
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
125 @property
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
126 def ranking_debug(self) -> str:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
127 return self.settings.workdir / 'ranking_debug.json'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
128
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
129 @property
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
130 def relax_metrics(self) -> str:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
131 return self.settings.workdir / 'relax_metrics.json'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
132
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
133 @property
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
134 def relax_metrics_ranked(self) -> str:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
135 return self.settings.workdir / 'relax_metrics_ranked.json'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
136
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
137 @property
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
138 def model_pkl_paths(self) -> List[str]:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
139 return sorted([
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
140 self.settings.workdir / f
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
141 for f in os.listdir(self.settings.workdir)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
142 if f.startswith('result_model_') and f.endswith('.pkl')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
143 ])
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
144
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
145
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
146 class ResultModelPrediction:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
147 """Load and manipulate data from result_model_*.pkl files."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
148 def __init__(self, path: str, context: ExecutionContext):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
149 self.context = context
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
150 self.path = path
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
151 self.name = os.path.basename(path).replace('result_', '').split('.')[0]
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
152 with open(path, 'rb') as path:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
153 self.data = pk.load(path)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
154
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
155 @property
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
156 def plddts(self) -> List[float]:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
157 """Return pLDDT scores for each residue."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
158 return list(self.data['plddt'])
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
159
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
160
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
161 class ResultRanking:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
162 """Load and manipulate data from ranking_debug.json file."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
163
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
164 def __init__(self, context: ExecutionContext):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
165 self.path = context.ranking_debug
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
166 self.context = context
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
167 with open(self.path, 'r') as f:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
168 self.data = json.load(f)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
169
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
170 @property
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
171 def order(self) -> List[str]:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
172 """Return ordered list of model indexes."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
173 return self.data['order']
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
174
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
175 def get_plddt_for_rank(self, rank: int) -> List[float]:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
176 """Get pLDDT score for model instance."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
177 return self.data[self.context.plddt_key][self.data['order'][rank - 1]]
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
178
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
179 def get_rank_for_model(self, model_name: str) -> int:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
180 """Return 0-indexed rank for given model name.
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
181
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
182 Model names are expressed in result_model_*.pkl file names.
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
183 """
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
184 return self.data['order'].index(model_name)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
185
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
186
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
187 def write_confidence_scores(ranking: ResultRanking, context: ExecutionContext):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
188 """Write per-model confidence scores."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
189 path = context.settings.workdir / OUTPUTS['model_confidence_scores']
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
190 with open(path, 'w') as f:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
191 for rank in range(1, 6):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
192 score = ranking.get_plddt_for_rank(rank)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
193 f.write(f'ranked_{rank - 1}\t{score:.2f}\n')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
194
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
195
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
196 def write_per_residue_scores(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
197 ranking: ResultRanking,
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
198 context: ExecutionContext,
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
199 ):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
200 """Write per-residue plddts for each model.
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
201
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
202 A row of plddt values is written for each model in tabular format.
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
203 """
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
204 model_plddts = {}
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
205 for i, path in enumerate(context.model_pkl_paths):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
206 model = ResultModelPrediction(path, context)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
207 rank = ranking.get_rank_for_model(model.name)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
208 model_plddts[rank] = model.plddts
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
209
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
210 path = context.settings.workdir / OUTPUTS['plddts']
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
211 with open(path, 'w') as f:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
212 for i in sorted(list(model_plddts.keys())):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
213 row = [f'ranked_{i}'] + [
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
214 str(x) for x in model_plddts[i]
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
215 ]
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
216 f.write('\t'.join(row) + '\n')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
217
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
218
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
219 def rename_model_pkls(ranking: ResultRanking, context: ExecutionContext):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
220 """Rename model.pkl files so the rank order is implicit."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
221 for path in context.model_pkl_paths:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
222 model = ResultModelPrediction(path, context)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
223 rank = ranking.get_rank_for_model(model.name)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
224 new_path = (
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
225 context.settings.workdir
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
226 / OUTPUTS['model_pkl'].format(rank=rank)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
227 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
228 shutil.copyfile(path, new_path)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
229
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
230
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
231 def extract_pae_to_csv(ranking: ResultRanking, context: ExecutionContext):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
232 """Extract predicted alignment error matrix from pickle files.
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
233
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
234 Creates a CSV file for each of five ranked models.
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
235 """
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
236 for path in context.model_pkl_paths:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
237 model = ResultModelPrediction(path, context)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
238 rank = ranking.get_rank_for_model(model.name)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
239 with open(path, 'rb') as f:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
240 data = pk.load(f)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
241 if 'predicted_aligned_error' not in data:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
242 print("Skipping PAE output"
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
243 f" - not found in {path}."
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
244 " Running with model_preset=monomer?")
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
245 return
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
246 pae = data['predicted_aligned_error']
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
247 out_path = (
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
248 context.settings.workdir
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
249 / OUTPUTS['model_pae'].format(rank=rank)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
250 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
251 with open(out_path, 'w') as f:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
252 for row in pae:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
253 f.write(','.join([str(x) for x in row]) + '\n')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
254
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
255
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
256 def rekey_relax_metrics(ranking: ResultRanking, context: ExecutionContext):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
257 """Replace keys in relax_metrics.json with 0-indexed rank."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
258 with open(context.relax_metrics) as f:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
259 data = json.load(f)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
260 for k in list(data.keys()):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
261 rank = ranking.get_rank_for_model(k)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
262 data[f'ranked_{rank}'] = data.pop(k)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
263 new_path = context.settings.workdir / OUTPUTS['relax']
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
264 with open(new_path, 'w') as f:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
265 json.dump(data, f)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
266
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
267
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
268 def plddt_pae_plots(ranking: ResultRanking, context: ExecutionContext):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
269 """Generate a pLDDT + PAE plot for each model."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
270 for path in context.model_pkl_paths:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
271 num_plots = 2
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
272 model = ResultModelPrediction(path, context)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
273 rank = ranking.get_rank_for_model(model.name)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
274 png_path = (
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
275 context.settings.workdir
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
276 / OUTPUTS['model_plot'].format(rank=rank)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
277 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
278 plddts = model.data['plddt']
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
279 if 'predicted_aligned_error' in model.data:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
280 pae = model.data['predicted_aligned_error']
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
281 max_pae = model.data['max_predicted_aligned_error']
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
282 else:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
283 num_plots = 1
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
284
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
285 plt.figure(figsize=[8 * num_plots, 6])
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
286 plt.subplot(1, num_plots, 1)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
287 plt.plot(plddts)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
288 plt.title('Predicted LDDT')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
289 plt.xlabel('Residue')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
290 plt.ylabel('pLDDT')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
291
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
292 if num_plots == 2:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
293 plt.subplot(1, 2, 2)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
294 plt.imshow(pae, vmin=0., vmax=max_pae, cmap='Greens_r')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
295 plt.colorbar(fraction=0.046, pad=0.04)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
296 plt.title('Predicted Aligned Error')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
297 plt.xlabel('Scored residue')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
298 plt.ylabel('Aligned residue')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
299
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
300 plt.savefig(png_path)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
301
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
302
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
303 def main():
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
304 """Parse output files and generate additional output files."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
305 settings = Settings()
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
306 context = ExecutionContext(settings)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
307 ranking = ResultRanking(context)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
308 write_confidence_scores(ranking, context)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
309 rekey_relax_metrics(ranking, context)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
310
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
311 # Optional outputs
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
312 if settings.output_model_pkls:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
313 rename_model_pkls(ranking, context)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
314 if settings.output_model_plots:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
315 plddt_pae_plots(ranking, context)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
316 if settings.output_pae:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
317 # Only created by monomer_ptm and multimer models
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
318 extract_pae_to_csv(ranking, context)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
319 if settings.output_residue_scores:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
320 write_per_residue_scores(ranking, context)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
321
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
322
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
323 if __name__ == '__main__':
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents:
diff changeset
324 main()