alphafold2: scripts/outputs.py annotate

annotate scripts/outputs.py @ 22:3f188450ca4f draft default tip

planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d626bb28203543a70d3fc60d662cb054bc3cef7c

author	galaxy-australia
date	Wed, 30 Oct 2024 21:46:34 +0000
parents	e7f1b552a695
children

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
21 e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	19 import numpy as np
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	20 import os
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	21 import pickle as pk
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	22 import shutil
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	23 from pathlib import Path
21 e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	24 from typing import Dict, List
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	25
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	26 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	27
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	28 # Output file paths
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	29 OUTPUT_DIR = 'extra'
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	30 OUTPUTS = {
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	31 '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	32 '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	33 '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	34 '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	35 '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	36 'relax': OUTPUT_DIR + '/relax_metrics_ranked.json',
21 e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	37 'msa': OUTPUT_DIR + '/msa_coverage.png',
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	38 }
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	39
20 6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	40 HTML_PATH = Path(__file__).parent / "alphafold.html"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	41 HTML_OUTPUT_FILENAME = 'alphafold.html'
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	42 HTML_BUTTON_ATTR = 'class="btn" id="btn-ranked_{rank}"'
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	43 HTML_BUTTON_ATTR_DISABLED = (
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	44 'class="btn disabled" id="btn-ranked_{rank}" disabled')
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	45
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	46
21 e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	47 class PLDDT_KEY:
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	48 """Dict keys for accessing confidence data from JSON/pkl files."
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	49 Changes depending on which model PRESET was used.
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	50 """
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	51 monomer = 'plddts'
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	52 multimer = 'iptm+ptm'
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	53
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	54
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	55 class PRESETS:
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	56 monomer = 'monomer'
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	57 monomer_ptm = 'monomer_ptm'
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	58 multimer = 'multimer'
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	59
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	60
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	61 class Settings:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	62 """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	63 def __init__(self):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	64 self.workdir = None
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	65 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	66 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	67 self.is_multimer = False
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	68 self.parse()
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	69
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	70 def parse(self) -> None:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	71 parser = argparse.ArgumentParser()
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	72 parser.add_argument(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	73 "workdir",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	74 help="alphafold output directory",
21 e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	75 type=str,
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	76 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	77 parser.add_argument(
21 e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	78 "-s",
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	79 "--confidence-scores",
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	80 help="output per-residue confidence scores (pLDDTs)",
21 e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	81 action="store_true",
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	82 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	83 parser.add_argument(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	84 "--pkl",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	85 help="rename model pkl outputs with rank order",
21 e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	86 action="store_true",
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	87 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	88 parser.add_argument(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	89 "--pae",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	90 help="extract PAE from pkl files to CSV format",
21 e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	91 action="store_true",
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	92 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	93 parser.add_argument(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	94 "--plot",
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	95 help="Plot pLDDT and PAE for each model",
21 e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	96 action="store_true",
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	97 )
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	98 parser.add_argument(
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	99 "--plot-msa",
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	100 help="Plot multiple-sequence alignment coverage as a heatmap",
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	101 action="store_true",
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	102 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	103 args = parser.parse_args()
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	104 self.workdir = Path(args.workdir.rstrip('/'))
21 e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	105 self.output_residue_scores = args.confidence_scores
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	106 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	107 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	108 self.output_pae = args.pae
21 e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	109 self.plot_msa = args.plot_msa
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	110 self.model_preset = self._sniff_model_preset()
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	111 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	112 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	113
21 e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	114 def _sniff_model_preset(self) -> bool:
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	115 """Check if the run was multimer or monomer."""
22 3f188450ca4f planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d626bb28203543a70d3fc60d662cb054bc3cef7c galaxy-australia parents: 21 diff changeset	116 for path in self.workdir.glob('*.pkl'):
3f188450ca4f planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d626bb28203543a70d3fc60d662cb054bc3cef7c galaxy-australia parents: 21 diff changeset	117 if 'feature' not in path.name:
3f188450ca4f planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d626bb28203543a70d3fc60d662cb054bc3cef7c galaxy-australia parents: 21 diff changeset	118 if '_multimer_' in path.name:
3f188450ca4f planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d626bb28203543a70d3fc60d662cb054bc3cef7c galaxy-australia parents: 21 diff changeset	119 return PRESETS.multimer
3f188450ca4f planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d626bb28203543a70d3fc60d662cb054bc3cef7c galaxy-australia parents: 21 diff changeset	120 if '_ptm_' in path.name:
3f188450ca4f planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d626bb28203543a70d3fc60d662cb054bc3cef7c galaxy-australia parents: 21 diff changeset	121 return PRESETS.monomer_ptm
3f188450ca4f planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d626bb28203543a70d3fc60d662cb054bc3cef7c galaxy-australia parents: 21 diff changeset	122 return PRESETS.monomer
21 e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	123
16 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 class ExecutionContext:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	126 """Collect file paths etc."""
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	127 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	128 self.settings = settings
21 e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	129 if settings.model_preset == PRESETS.multimer:
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	130 self.plddt_key = PLDDT_KEY.multimer
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	131 else:
21 e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	132 self.plddt_key = PLDDT_KEY.monomer
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	133
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	134 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	135 """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	136
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	137 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	138 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	139 """
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	140 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	141 data = json.load(f)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	142 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	143 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	144 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	145 return k
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	146 return KeyError(
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	147 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	148 ' ranking_debug.json')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	149
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	150 @property
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	151 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	152 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	153
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	154 @property
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	155 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	156 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	157
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	158 @property
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	159 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	160 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	161
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	162 @property
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	163 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	164 return sorted([
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	165 self.settings.workdir / f
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	166 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	167 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	168 ])
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
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	171 class ResultModelPrediction:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	172 """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	173 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	174 self.context = context
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	175 self.path = path
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	176 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	177 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	178 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	179
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	180 @property
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	181 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	182 """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	183 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	184
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 class ResultRanking:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	187 """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	188
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	189 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	190 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	191 self.context = context
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	192 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	193 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	194
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	195 @property
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	196 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	197 """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	198 return self.data['order']
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 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	201 """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	202 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	203
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	204 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	205 """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	206
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	207 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	208 """
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	209 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	210
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	211
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	212 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	213 """Write per-model confidence scores."""
21 e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	214 outfile = context.settings.workdir / OUTPUTS['model_confidence_scores']
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	215 scores: Dict[str, list] = {}
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	216 header = ['model', context.plddt_key]
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	217
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	218 for i, path in enumerate(context.model_pkl_paths):
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	219 rank = int(path.name.split('model_')[-1][0])
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	220 scores_ls = [ranking.get_plddt_for_rank(rank)]
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	221 with open(path, 'rb') as f:
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	222 data = pk.load(f)
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	223 if 'ptm' in data:
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	224 scores_ls.append(data['ptm'])
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	225 if i == 0:
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	226 header += ['ptm']
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	227 if 'iptm' in data:
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	228 scores_ls.append(data['iptm'])
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	229 if i == 0:
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	230 header += ['iptm']
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	231 scores[rank] = scores_ls
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	232
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	233 with open(outfile, 'w') as f:
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	234 f.write('\t'.join(header) + '\n')
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	235 for rank, score_ls in scores.items():
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	236 row = [f"ranked_{rank - 1}"] + [str(x) for x in score_ls]
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	237 f.write('\t'.join(row) + '\n')
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	238
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	239
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	240 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	241 ranking: ResultRanking,
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	242 context: ExecutionContext,
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	243 ):
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	244 """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	245
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	246 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	247 """
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	248 model_plddts = {}
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	249 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	250 model = ResultModelPrediction(path, context)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	251 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	252 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	253
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	254 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	255 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	256 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	257 row = [f'ranked_{i}'] + [
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	258 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	259 ]
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	260 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	261
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	262
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	263 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	264 """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	265 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	266 model = ResultModelPrediction(path, context)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	267 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	268 new_path = (
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	269 context.settings.workdir
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	270 / 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	271 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	272 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	273
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	274
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	275 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	276 """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	277
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	278 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	279 """
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	280 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	281 model = ResultModelPrediction(path, context)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	282 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	283 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	284 data = pk.load(f)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	285 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	286 print("Skipping PAE output"
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	287 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	288 " 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	289 return
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	290 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	291 out_path = (
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	292 context.settings.workdir
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	293 / 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	294 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	295 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	296 for row in pae:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	297 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	298
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 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	301 """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	302 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	303 data = json.load(f)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	304 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	305 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	306 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	307 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	308 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	309 json.dump(data, f)
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
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	312 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	313 """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	314 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	315 num_plots = 2
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	316 model = ResultModelPrediction(path, context)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	317 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	318 png_path = (
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	319 context.settings.workdir
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	320 / 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	321 )
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	322 plddts = model.data['plddt']
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	323 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	324 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	325 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	326 else:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	327 num_plots = 1
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	328
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	329 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	330 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	331 plt.plot(plddts)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	332 plt.title('Predicted LDDT')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	333 plt.xlabel('Residue')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	334 plt.ylabel('pLDDT')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	335
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	336 if num_plots == 2:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	337 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	338 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	339 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	340 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	341 plt.xlabel('Scored residue')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	342 plt.ylabel('Aligned residue')
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	343
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	344 plt.savefig(png_path)
21 e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	345 plt.close()
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	346
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	347
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	348 def plot_msa(wdir: Path, dpi: int = 150):
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	349 """Plot MSA as a heatmap."""
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	350 with open(wdir / 'features.pkl', 'rb') as f:
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	351 features = pk.load(f)
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	352
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	353 msa = features.get('msa')
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	354 if msa is None:
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	355 print("Could not plot MSA coverage - 'msa' key not found in"
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	356 " features.pkl")
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	357 return
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	358 seqid = (np.array(msa[0] == msa).mean(-1))
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	359 seqid_sort = seqid.argsort()
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	360 non_gaps = (msa != 21).astype(float)
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	361 non_gaps[non_gaps == 0] = np.nan
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	362 final = non_gaps[seqid_sort] * seqid[seqid_sort, None]
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	363
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	364 plt.figure(figsize=(6, 4))
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	365 # plt.subplot(111)
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	366 plt.title("Sequence coverage")
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	367 plt.imshow(final,
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	368 interpolation='nearest', aspect='auto',
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	369 cmap="rainbow_r", vmin=0, vmax=1, origin='lower')
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	370 plt.plot((msa != 21).sum(0), color='black')
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	371 plt.xlim(-0.5, msa.shape[1] - 0.5)
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	372 plt.ylim(-0.5, msa.shape[0] - 0.5)
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	373 plt.colorbar(label="Sequence identity to query", )
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	374 plt.xlabel("Positions")
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	375 plt.ylabel("Sequences")
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	376 plt.tight_layout()
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	377 plt.savefig(wdir / OUTPUTS['msa'], dpi=dpi)
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	378 plt.close()
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	379
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	380
20 6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	381 def template_html(context: ExecutionContext):
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	382 """Template HTML file.
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	383
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	384 Remove buttons that are redundant with limited model outputs.
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	385 """
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	386 print("Templating HTML file...")
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	387 with open(HTML_PATH) as f:
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	388 html = f.read()
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	389 for i in range(len(context.model_pkl_paths), 5):
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	390 btn_id = HTML_BUTTON_ATTR.format(rank=i)
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	391 btn_attr_disabled = HTML_BUTTON_ATTR_DISABLED.format(rank=i)
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	392 html = html.replace(btn_id, btn_attr_disabled)
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	393 with open(context.settings.output_dir / HTML_OUTPUT_FILENAME, 'w') as f:
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	394 f.write(html)
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	395
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	396
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	397 def main():
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	398 """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	399 settings = Settings()
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	400 context = ExecutionContext(settings)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	401 ranking = ResultRanking(context)
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	402 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	403 rekey_relax_metrics(ranking, context)
20 6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty galaxy-australia parents: 16 diff changeset	404 template_html(context)
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	405
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	406 # Optional outputs
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	407 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	408 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	409 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	410 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	411 if settings.output_pae:
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	412 # 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	413 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	414 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	415 write_per_residue_scores(ranking, context)
21 e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	416 if settings.plot_msa:
e7f1b552a695 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty galaxy-australia parents: 20 diff changeset	417 plot_msa(context.settings.workdir)
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	418
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	419
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	420 if __name__ == '__main__':
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: diff changeset	421 main()

Mercurial > repos > galaxy-australia > alphafold2

annotate scripts/outputs.py @ 22:3f188450ca4f draft default tip