Mercurial > repos > galaxy-australia > alphafold2
annotate docker/alphafold/alphafold/data/msa_pairing.py @ 1:6c92e000d684 draft
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
author | galaxy-australia |
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date | Tue, 01 Mar 2022 02:53:05 +0000 |
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6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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1 # Copyright 2021 DeepMind Technologies Limited |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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2 # |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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3 # Licensed under the Apache License, Version 2.0 (the "License"); |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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4 # you may not use this file except in compliance with the License. |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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5 # You may obtain a copy of the License at |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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6 # |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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7 # http://www.apache.org/licenses/LICENSE-2.0 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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8 # |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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9 # Unless required by applicable law or agreed to in writing, software |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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10 # distributed under the License is distributed on an "AS IS" BASIS, |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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11 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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12 # See the License for the specific language governing permissions and |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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13 # limitations under the License. |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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14 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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15 """Pairing logic for multimer data pipeline.""" |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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16 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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17 import collections |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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18 import functools |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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19 import re |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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20 import string |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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21 from typing import Any, Dict, Iterable, List, Sequence |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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22 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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23 from alphafold.common import residue_constants |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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24 from alphafold.data import pipeline |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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25 import numpy as np |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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26 import pandas as pd |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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27 import scipy.linalg |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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28 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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29 ALPHA_ACCESSION_ID_MAP = {x: y for y, x in enumerate(string.ascii_uppercase)} |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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30 ALPHANUM_ACCESSION_ID_MAP = { |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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31 chr: num for num, chr in enumerate(string.ascii_uppercase + string.digits) |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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32 } # A-Z,0-9 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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33 NUM_ACCESSION_ID_MAP = {str(x): x for x in range(10)} # 0-9 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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34 |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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35 MSA_GAP_IDX = residue_constants.restypes_with_x_and_gap.index('-') |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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36 SEQUENCE_GAP_CUTOFF = 0.5 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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37 SEQUENCE_SIMILARITY_CUTOFF = 0.9 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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38 |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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39 MSA_PAD_VALUES = {'msa_all_seq': MSA_GAP_IDX, |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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40 'msa_mask_all_seq': 1, |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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41 'deletion_matrix_all_seq': 0, |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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42 'deletion_matrix_int_all_seq': 0, |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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43 'msa': MSA_GAP_IDX, |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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44 'msa_mask': 1, |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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45 'deletion_matrix': 0, |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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46 'deletion_matrix_int': 0} |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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47 |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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48 MSA_FEATURES = ('msa', 'msa_mask', 'deletion_matrix', 'deletion_matrix_int') |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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49 SEQ_FEATURES = ('residue_index', 'aatype', 'all_atom_positions', |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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50 'all_atom_mask', 'seq_mask', 'between_segment_residues', |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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51 'has_alt_locations', 'has_hetatoms', 'asym_id', 'entity_id', |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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52 'sym_id', 'entity_mask', 'deletion_mean', |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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53 'prediction_atom_mask', |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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54 'literature_positions', 'atom_indices_to_group_indices', |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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55 'rigid_group_default_frame') |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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56 TEMPLATE_FEATURES = ('template_aatype', 'template_all_atom_positions', |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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57 'template_all_atom_mask') |
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58 CHAIN_FEATURES = ('num_alignments', 'seq_length') |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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59 |
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60 |
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61 domain_name_pattern = re.compile( |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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62 r'''^(?P<pdb>[a-z\d]{4}) |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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63 \{(?P<bioassembly>[\d+(\+\d+)?])\} |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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64 (?P<chain>[a-zA-Z\d]+) |
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65 \{(?P<transform_index>\d+)\}$ |
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66 ''', re.VERBOSE) |
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67 |
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68 |
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69 def create_paired_features( |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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70 chains: Iterable[pipeline.FeatureDict], |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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71 prokaryotic: bool, |
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72 ) -> List[pipeline.FeatureDict]: |
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73 """Returns the original chains with paired NUM_SEQ features. |
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74 |
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75 Args: |
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76 chains: A list of feature dictionaries for each chain. |
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77 prokaryotic: Whether the target complex is from a prokaryotic organism. |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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78 Used to determine the distance metric for pairing. |
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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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79 |
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80 Returns: |
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81 A list of feature dictionaries with sequence features including only |
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82 rows to be paired. |
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83 """ |
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84 chains = list(chains) |
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85 chain_keys = chains[0].keys() |
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86 |
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87 if len(chains) < 2: |
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88 return chains |
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89 else: |
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90 updated_chains = [] |
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91 paired_chains_to_paired_row_indices = pair_sequences( |
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92 chains, prokaryotic) |
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93 paired_rows = reorder_paired_rows( |
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94 paired_chains_to_paired_row_indices) |
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95 |
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96 for chain_num, chain in enumerate(chains): |
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97 new_chain = {k: v for k, v in chain.items() if '_all_seq' not in k} |
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98 for feature_name in chain_keys: |
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99 if feature_name.endswith('_all_seq'): |
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100 feats_padded = pad_features(chain[feature_name], feature_name) |
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101 new_chain[feature_name] = feats_padded[paired_rows[:, chain_num]] |
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102 new_chain['num_alignments_all_seq'] = np.asarray( |
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103 len(paired_rows[:, chain_num])) |
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104 updated_chains.append(new_chain) |
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105 return updated_chains |
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106 |
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107 |
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108 def pad_features(feature: np.ndarray, feature_name: str) -> np.ndarray: |
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109 """Add a 'padding' row at the end of the features list. |
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110 |
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111 The padding row will be selected as a 'paired' row in the case of partial |
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112 alignment - for the chain that doesn't have paired alignment. |
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113 |
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114 Args: |
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115 feature: The feature to be padded. |
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116 feature_name: The name of the feature to be padded. |
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117 |
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118 Returns: |
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119 The feature with an additional padding row. |
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120 """ |
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121 assert feature.dtype != np.dtype(np.string_) |
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122 if feature_name in ('msa_all_seq', 'msa_mask_all_seq', |
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123 'deletion_matrix_all_seq', 'deletion_matrix_int_all_seq'): |
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124 num_res = feature.shape[1] |
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125 padding = MSA_PAD_VALUES[feature_name] * np.ones([1, num_res], |
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126 feature.dtype) |
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127 elif feature_name in ('msa_uniprot_accession_identifiers_all_seq', |
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128 'msa_species_identifiers_all_seq'): |
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129 padding = [b''] |
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130 else: |
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131 return feature |
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132 feats_padded = np.concatenate([feature, padding], axis=0) |
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133 return feats_padded |
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134 |
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135 |
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136 def _make_msa_df(chain_features: pipeline.FeatureDict) -> pd.DataFrame: |
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137 """Makes dataframe with msa features needed for msa pairing.""" |
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138 chain_msa = chain_features['msa_all_seq'] |
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139 query_seq = chain_msa[0] |
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140 per_seq_similarity = np.sum( |
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141 query_seq[None] == chain_msa, axis=-1) / float(len(query_seq)) |
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142 per_seq_gap = np.sum(chain_msa == 21, axis=-1) / float(len(query_seq)) |
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143 msa_df = pd.DataFrame({ |
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144 'msa_species_identifiers': |
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145 chain_features['msa_species_identifiers_all_seq'], |
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146 'msa_uniprot_accession_identifiers': |
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147 chain_features['msa_uniprot_accession_identifiers_all_seq'], |
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148 'msa_row': |
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149 np.arange(len( |
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150 chain_features['msa_uniprot_accession_identifiers_all_seq'])), |
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151 'msa_similarity': per_seq_similarity, |
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152 'gap': per_seq_gap |
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153 }) |
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154 return msa_df |
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155 |
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156 |
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157 def _create_species_dict(msa_df: pd.DataFrame) -> Dict[bytes, pd.DataFrame]: |
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158 """Creates mapping from species to msa dataframe of that species.""" |
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159 species_lookup = {} |
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160 for species, species_df in msa_df.groupby('msa_species_identifiers'): |
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161 species_lookup[species] = species_df |
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162 return species_lookup |
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163 |
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164 |
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165 @functools.lru_cache(maxsize=65536) |
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166 def encode_accession(accession_id: str) -> int: |
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167 """Map accession codes to the serial order in which they were assigned.""" |
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168 alpha = ALPHA_ACCESSION_ID_MAP # A-Z |
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169 alphanum = ALPHANUM_ACCESSION_ID_MAP # A-Z,0-9 |
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170 num = NUM_ACCESSION_ID_MAP # 0-9 |
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171 |
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172 coding = 0 |
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173 |
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174 # This is based on the uniprot accession id format |
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175 # https://www.uniprot.org/help/accession_numbers |
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176 if accession_id[0] in {'O', 'P', 'Q'}: |
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177 bases = (alpha, num, alphanum, alphanum, alphanum, num) |
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178 elif len(accession_id) == 6: |
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179 bases = (alpha, num, alpha, alphanum, alphanum, num) |
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180 elif len(accession_id) == 10: |
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181 bases = (alpha, num, alpha, alphanum, alphanum, num, alpha, alphanum, |
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182 alphanum, num) |
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183 |
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184 product = 1 |
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185 for place, base in zip(reversed(accession_id), reversed(bases)): |
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186 coding += base[place] * product |
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187 product *= len(base) |
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188 |
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189 return coding |
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190 |
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191 |
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192 def _calc_id_diff(id_a: bytes, id_b: bytes) -> int: |
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193 return abs(encode_accession(id_a.decode()) - encode_accession(id_b.decode())) |
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194 |
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195 |
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196 def _find_all_accession_matches(accession_id_lists: List[List[bytes]], |
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197 diff_cutoff: int = 20 |
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198 ) -> List[List[Any]]: |
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199 """Finds accession id matches across the chains based on their difference.""" |
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200 all_accession_tuples = [] |
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201 current_tuple = [] |
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202 tokens_used_in_answer = set() |
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203 |
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204 def _matches_all_in_current_tuple(inp: bytes, diff_cutoff: int) -> bool: |
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205 return all((_calc_id_diff(s, inp) < diff_cutoff for s in current_tuple)) |
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206 |
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207 def _all_tokens_not_used_before() -> bool: |
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208 return all((s not in tokens_used_in_answer for s in current_tuple)) |
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209 |
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210 def dfs(level, accession_id, diff_cutoff=diff_cutoff) -> None: |
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211 if level == len(accession_id_lists) - 1: |
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212 if _all_tokens_not_used_before(): |
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213 all_accession_tuples.append(list(current_tuple)) |
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214 for s in current_tuple: |
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215 tokens_used_in_answer.add(s) |
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216 return |
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217 |
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218 if level == -1: |
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219 new_list = accession_id_lists[level+1] |
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220 else: |
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221 new_list = [(_calc_id_diff(accession_id, s), s) for |
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222 s in accession_id_lists[level+1]] |
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223 new_list = sorted(new_list) |
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224 new_list = [s for d, s in new_list] |
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225 |
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226 for s in new_list: |
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227 if (_matches_all_in_current_tuple(s, diff_cutoff) and |
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228 s not in tokens_used_in_answer): |
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229 current_tuple.append(s) |
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230 dfs(level + 1, s) |
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231 current_tuple.pop() |
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232 dfs(-1, '') |
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233 return all_accession_tuples |
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234 |
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235 |
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236 def _accession_row(msa_df: pd.DataFrame, accession_id: bytes) -> pd.Series: |
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237 matched_df = msa_df[msa_df.msa_uniprot_accession_identifiers == accession_id] |
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238 return matched_df.iloc[0] |
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239 |
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240 |
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241 def _match_rows_by_genetic_distance( |
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242 this_species_msa_dfs: List[pd.DataFrame], |
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243 cutoff: int = 20) -> List[List[int]]: |
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244 """Finds MSA sequence pairings across chains within a genetic distance cutoff. |
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245 |
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246 The genetic distance between two sequences is approximated by taking the |
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247 difference in their UniProt accession ids. |
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248 |
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249 Args: |
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250 this_species_msa_dfs: a list of dataframes containing MSA features for |
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251 sequences for a specific species. If species is missing for a chain, the |
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252 dataframe is set to None. |
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253 cutoff: the genetic distance cutoff. |
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254 |
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255 Returns: |
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256 A list of lists, each containing M indices corresponding to paired MSA rows, |
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257 where M is the number of chains. |
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258 """ |
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259 num_examples = len(this_species_msa_dfs) # N |
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260 |
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261 accession_id_lists = [] # M |
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262 match_index_to_chain_index = {} |
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263 for chain_index, species_df in enumerate(this_species_msa_dfs): |
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264 if species_df is not None: |
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265 accession_id_lists.append( |
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266 list(species_df.msa_uniprot_accession_identifiers.values)) |
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267 # Keep track of which of the this_species_msa_dfs are not None. |
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268 match_index_to_chain_index[len(accession_id_lists) - 1] = chain_index |
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269 |
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270 all_accession_id_matches = _find_all_accession_matches( |
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271 accession_id_lists, cutoff) # [k, M] |
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272 |
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273 all_paired_msa_rows = [] # [k, N] |
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274 for accession_id_match in all_accession_id_matches: |
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275 paired_msa_rows = [] |
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276 for match_index, accession_id in enumerate(accession_id_match): |
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277 # Map back to chain index. |
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278 chain_index = match_index_to_chain_index[match_index] |
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279 seq_series = _accession_row( |
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280 this_species_msa_dfs[chain_index], accession_id) |
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281 |
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282 if (seq_series.msa_similarity > SEQUENCE_SIMILARITY_CUTOFF or |
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283 seq_series.gap > SEQUENCE_GAP_CUTOFF): |
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284 continue |
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285 else: |
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286 paired_msa_rows.append(seq_series.msa_row) |
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287 # If a sequence is skipped based on sequence similarity to the respective |
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288 # target sequence or a gap cuttoff, the lengths of accession_id_match and |
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289 # paired_msa_rows will be different. Skip this match. |
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290 if len(paired_msa_rows) == len(accession_id_match): |
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291 paired_and_non_paired_msa_rows = np.array([-1] * num_examples) |
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292 matched_chain_indices = list(match_index_to_chain_index.values()) |
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293 paired_and_non_paired_msa_rows[matched_chain_indices] = paired_msa_rows |
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294 all_paired_msa_rows.append(list(paired_and_non_paired_msa_rows)) |
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295 return all_paired_msa_rows |
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296 |
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297 |
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298 def _match_rows_by_sequence_similarity(this_species_msa_dfs: List[pd.DataFrame] |
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299 ) -> List[List[int]]: |
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300 """Finds MSA sequence pairings across chains based on sequence similarity. |
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301 |
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302 Each chain's MSA sequences are first sorted by their sequence similarity to |
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303 their respective target sequence. The sequences are then paired, starting |
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304 from the sequences most similar to their target sequence. |
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305 |
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306 Args: |
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307 this_species_msa_dfs: a list of dataframes containing MSA features for |
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308 sequences for a specific species. |
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309 |
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310 Returns: |
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311 A list of lists, each containing M indices corresponding to paired MSA rows, |
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312 where M is the number of chains. |
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313 """ |
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314 all_paired_msa_rows = [] |
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315 |
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316 num_seqs = [len(species_df) for species_df in this_species_msa_dfs |
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317 if species_df is not None] |
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318 take_num_seqs = np.min(num_seqs) |
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319 |
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320 sort_by_similarity = ( |
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321 lambda x: x.sort_values('msa_similarity', axis=0, ascending=False)) |
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322 |
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323 for species_df in this_species_msa_dfs: |
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324 if species_df is not None: |
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325 species_df_sorted = sort_by_similarity(species_df) |
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326 msa_rows = species_df_sorted.msa_row.iloc[:take_num_seqs].values |
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327 else: |
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328 msa_rows = [-1] * take_num_seqs # take the last 'padding' row |
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329 all_paired_msa_rows.append(msa_rows) |
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330 all_paired_msa_rows = list(np.array(all_paired_msa_rows).transpose()) |
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331 return all_paired_msa_rows |
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332 |
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333 |
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334 def pair_sequences(examples: List[pipeline.FeatureDict], |
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335 prokaryotic: bool) -> Dict[int, np.ndarray]: |
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336 """Returns indices for paired MSA sequences across chains.""" |
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337 |
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338 num_examples = len(examples) |
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339 |
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340 all_chain_species_dict = [] |
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341 common_species = set() |
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342 for chain_features in examples: |
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343 msa_df = _make_msa_df(chain_features) |
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344 species_dict = _create_species_dict(msa_df) |
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345 all_chain_species_dict.append(species_dict) |
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346 common_species.update(set(species_dict)) |
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347 |
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348 common_species = sorted(common_species) |
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349 common_species.remove(b'') # Remove target sequence species. |
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350 |
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351 all_paired_msa_rows = [np.zeros(len(examples), int)] |
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352 all_paired_msa_rows_dict = {k: [] for k in range(num_examples)} |
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353 all_paired_msa_rows_dict[num_examples] = [np.zeros(len(examples), int)] |
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354 |
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355 for species in common_species: |
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356 if not species: |
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357 continue |
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358 this_species_msa_dfs = [] |
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359 species_dfs_present = 0 |
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360 for species_dict in all_chain_species_dict: |
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361 if species in species_dict: |
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362 this_species_msa_dfs.append(species_dict[species]) |
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363 species_dfs_present += 1 |
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364 else: |
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365 this_species_msa_dfs.append(None) |
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366 |
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367 # Skip species that are present in only one chain. |
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368 if species_dfs_present <= 1: |
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369 continue |
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370 |
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371 if np.any( |
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372 np.array([len(species_df) for species_df in |
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373 this_species_msa_dfs if |
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374 isinstance(species_df, pd.DataFrame)]) > 600): |
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375 continue |
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376 |
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377 # In prokaryotes (and some eukaryotes), interacting genes are often |
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378 # co-located on the chromosome into operons. Because of that we can assume |
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379 # that if two proteins' intergenic distance is less than a threshold, they |
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380 # two proteins will form an an interacting pair. |
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381 # In most eukaryotes, a single protein's MSA can contain many paralogs. |
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382 # Two genes may interact even if they are not close by genomic distance. |
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383 # In case of eukaryotes, some methods pair MSA sequences using sequence |
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384 # similarity method. |
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385 # See Jinbo Xu's work: |
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386 # https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030867/#B28. |
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387 if prokaryotic: |
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388 paired_msa_rows = _match_rows_by_genetic_distance(this_species_msa_dfs) |
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389 |
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390 if not paired_msa_rows: |
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391 continue |
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392 else: |
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393 paired_msa_rows = _match_rows_by_sequence_similarity(this_species_msa_dfs) |
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394 all_paired_msa_rows.extend(paired_msa_rows) |
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395 all_paired_msa_rows_dict[species_dfs_present].extend(paired_msa_rows) |
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396 all_paired_msa_rows_dict = { |
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397 num_examples: np.array(paired_msa_rows) for |
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398 num_examples, paired_msa_rows in all_paired_msa_rows_dict.items() |
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399 } |
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400 return all_paired_msa_rows_dict |
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401 |
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402 |
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403 def reorder_paired_rows(all_paired_msa_rows_dict: Dict[int, np.ndarray] |
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404 ) -> np.ndarray: |
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405 """Creates a list of indices of paired MSA rows across chains. |
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406 |
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407 Args: |
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408 all_paired_msa_rows_dict: a mapping from the number of paired chains to the |
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409 paired indices. |
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410 |
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411 Returns: |
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412 a list of lists, each containing indices of paired MSA rows across chains. |
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413 The paired-index lists are ordered by: |
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414 1) the number of chains in the paired alignment, i.e, all-chain pairings |
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415 will come first. |
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416 2) e-values |
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417 """ |
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418 all_paired_msa_rows = [] |
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419 |
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420 for num_pairings in sorted(all_paired_msa_rows_dict, reverse=True): |
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421 paired_rows = all_paired_msa_rows_dict[num_pairings] |
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422 paired_rows_product = abs(np.array([np.prod(rows) for rows in paired_rows])) |
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423 paired_rows_sort_index = np.argsort(paired_rows_product) |
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424 all_paired_msa_rows.extend(paired_rows[paired_rows_sort_index]) |
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425 |
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426 return np.array(all_paired_msa_rows) |
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427 |
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428 |
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429 def block_diag(*arrs: np.ndarray, pad_value: float = 0.0) -> np.ndarray: |
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430 """Like scipy.linalg.block_diag but with an optional padding value.""" |
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431 ones_arrs = [np.ones_like(x) for x in arrs] |
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432 off_diag_mask = 1.0 - scipy.linalg.block_diag(*ones_arrs) |
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433 diag = scipy.linalg.block_diag(*arrs) |
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434 diag += (off_diag_mask * pad_value).astype(diag.dtype) |
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435 return diag |
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436 |
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437 |
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438 def _correct_post_merged_feats( |
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439 np_example: pipeline.FeatureDict, |
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440 np_chains_list: Sequence[pipeline.FeatureDict], |
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441 pair_msa_sequences: bool) -> pipeline.FeatureDict: |
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442 """Adds features that need to be computed/recomputed post merging.""" |
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443 |
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444 np_example['seq_length'] = np.asarray(np_example['aatype'].shape[0], |
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445 dtype=np.int32) |
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446 np_example['num_alignments'] = np.asarray(np_example['msa'].shape[0], |
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447 dtype=np.int32) |
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448 |
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449 if not pair_msa_sequences: |
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450 # Generate a bias that is 1 for the first row of every block in the |
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451 # block diagonal MSA - i.e. make sure the cluster stack always includes |
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452 # the query sequences for each chain (since the first row is the query |
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453 # sequence). |
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454 cluster_bias_masks = [] |
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455 for chain in np_chains_list: |
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456 mask = np.zeros(chain['msa'].shape[0]) |
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457 mask[0] = 1 |
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458 cluster_bias_masks.append(mask) |
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459 np_example['cluster_bias_mask'] = np.concatenate(cluster_bias_masks) |
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460 |
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461 # Initialize Bert mask with masked out off diagonals. |
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462 msa_masks = [np.ones(x['msa'].shape, dtype=np.float32) |
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463 for x in np_chains_list] |
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464 |
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465 np_example['bert_mask'] = block_diag( |
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466 *msa_masks, pad_value=0) |
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467 else: |
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468 np_example['cluster_bias_mask'] = np.zeros(np_example['msa'].shape[0]) |
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469 np_example['cluster_bias_mask'][0] = 1 |
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470 |
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471 # Initialize Bert mask with masked out off diagonals. |
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472 msa_masks = [np.ones(x['msa'].shape, dtype=np.float32) for |
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473 x in np_chains_list] |
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474 msa_masks_all_seq = [np.ones(x['msa_all_seq'].shape, dtype=np.float32) for |
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475 x in np_chains_list] |
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476 |
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477 msa_mask_block_diag = block_diag( |
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478 *msa_masks, pad_value=0) |
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479 msa_mask_all_seq = np.concatenate(msa_masks_all_seq, axis=1) |
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480 np_example['bert_mask'] = np.concatenate( |
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481 [msa_mask_all_seq, msa_mask_block_diag], axis=0) |
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482 return np_example |
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483 |
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484 |
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485 def _pad_templates(chains: Sequence[pipeline.FeatureDict], |
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486 max_templates: int) -> Sequence[pipeline.FeatureDict]: |
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487 """For each chain pad the number of templates to a fixed size. |
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488 |
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489 Args: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
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490 chains: A list of protein chains. |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
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491 max_templates: Each chain will be padded to have this many templates. |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
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492 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
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493 Returns: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
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changeset
|
494 The list of chains, updated to have template features padded to |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
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495 max_templates. |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
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496 """ |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
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497 for chain in chains: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
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498 for k, v in chain.items(): |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
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499 if k in TEMPLATE_FEATURES: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
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500 padding = np.zeros_like(v.shape) |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
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501 padding[0] = max_templates - v.shape[0] |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
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502 padding = [(0, p) for p in padding] |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
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changeset
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503 chain[k] = np.pad(v, padding, mode='constant') |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
504 return chains |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
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505 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
506 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
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507 def _merge_features_from_multiple_chains( |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
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508 chains: Sequence[pipeline.FeatureDict], |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
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509 pair_msa_sequences: bool) -> pipeline.FeatureDict: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
510 """Merge features from multiple chains. |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
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|
511 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
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512 Args: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
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513 chains: A list of feature dictionaries that we want to merge. |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
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514 pair_msa_sequences: Whether to concatenate MSA features along the |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
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515 num_res dimension (if True), or to block diagonalize them (if False). |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
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516 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
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517 Returns: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
518 A feature dictionary for the merged example. |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
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519 """ |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
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|
520 merged_example = {} |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
521 for feature_name in chains[0]: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
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|
522 feats = [x[feature_name] for x in chains] |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
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523 feature_name_split = feature_name.split('_all_seq')[0] |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
524 if feature_name_split in MSA_FEATURES: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
525 if pair_msa_sequences or '_all_seq' in feature_name: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
526 merged_example[feature_name] = np.concatenate(feats, axis=1) |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
527 else: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
528 merged_example[feature_name] = block_diag( |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
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529 *feats, pad_value=MSA_PAD_VALUES[feature_name]) |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
530 elif feature_name_split in SEQ_FEATURES: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
531 merged_example[feature_name] = np.concatenate(feats, axis=0) |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
532 elif feature_name_split in TEMPLATE_FEATURES: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
533 merged_example[feature_name] = np.concatenate(feats, axis=1) |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
534 elif feature_name_split in CHAIN_FEATURES: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
535 merged_example[feature_name] = np.sum(x for x in feats).astype(np.int32) |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
536 else: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
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|
537 merged_example[feature_name] = feats[0] |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
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|
538 return merged_example |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
539 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
540 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
541 def _merge_homomers_dense_msa( |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
542 chains: Iterable[pipeline.FeatureDict]) -> Sequence[pipeline.FeatureDict]: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
543 """Merge all identical chains, making the resulting MSA dense. |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
544 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
545 Args: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
546 chains: An iterable of features for each chain. |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
547 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
548 Returns: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
549 A list of feature dictionaries. All features with the same entity_id |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
550 will be merged - MSA features will be concatenated along the num_res |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
551 dimension - making them dense. |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
552 """ |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
553 entity_chains = collections.defaultdict(list) |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
554 for chain in chains: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
555 entity_id = chain['entity_id'][0] |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
556 entity_chains[entity_id].append(chain) |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
557 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
558 grouped_chains = [] |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
559 for entity_id in sorted(entity_chains): |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
560 chains = entity_chains[entity_id] |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
561 grouped_chains.append(chains) |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
562 chains = [ |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
563 _merge_features_from_multiple_chains(chains, pair_msa_sequences=True) |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
564 for chains in grouped_chains] |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
565 return chains |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
566 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
567 |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
568 def _concatenate_paired_and_unpaired_features( |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
569 example: pipeline.FeatureDict) -> pipeline.FeatureDict: |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
570 """Merges paired and block-diagonalised features.""" |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
571 features = MSA_FEATURES |
6c92e000d684
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents:
diff
changeset
|
572 for feature_name in features: |
6c92e000d684
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573 if feature_name in example: |
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574 feat = example[feature_name] |
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575 feat_all_seq = example[feature_name + '_all_seq'] |
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576 merged_feat = np.concatenate([feat_all_seq, feat], axis=0) |
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577 example[feature_name] = merged_feat |
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578 example['num_alignments'] = np.array(example['msa'].shape[0], |
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579 dtype=np.int32) |
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580 return example |
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581 |
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582 |
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583 def merge_chain_features(np_chains_list: List[pipeline.FeatureDict], |
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584 pair_msa_sequences: bool, |
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585 max_templates: int) -> pipeline.FeatureDict: |
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586 """Merges features for multiple chains to single FeatureDict. |
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587 |
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588 Args: |
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589 np_chains_list: List of FeatureDicts for each chain. |
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590 pair_msa_sequences: Whether to merge paired MSAs. |
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591 max_templates: The maximum number of templates to include. |
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592 |
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593 Returns: |
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594 Single FeatureDict for entire complex. |
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595 """ |
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596 np_chains_list = _pad_templates( |
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597 np_chains_list, max_templates=max_templates) |
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598 np_chains_list = _merge_homomers_dense_msa(np_chains_list) |
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599 # Unpaired MSA features will be always block-diagonalised; paired MSA |
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600 # features will be concatenated. |
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601 np_example = _merge_features_from_multiple_chains( |
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602 np_chains_list, pair_msa_sequences=False) |
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603 if pair_msa_sequences: |
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604 np_example = _concatenate_paired_and_unpaired_features(np_example) |
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605 np_example = _correct_post_merged_feats( |
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606 np_example=np_example, |
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607 np_chains_list=np_chains_list, |
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608 pair_msa_sequences=pair_msa_sequences) |
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609 |
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610 return np_example |
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611 |
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612 |
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613 def deduplicate_unpaired_sequences( |
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614 np_chains: List[pipeline.FeatureDict]) -> List[pipeline.FeatureDict]: |
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615 """Removes unpaired sequences which duplicate a paired sequence.""" |
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616 |
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617 feature_names = np_chains[0].keys() |
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618 msa_features = MSA_FEATURES |
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619 |
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620 for chain in np_chains: |
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621 sequence_set = set(tuple(s) for s in chain['msa_all_seq']) |
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622 keep_rows = [] |
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623 # Go through unpaired MSA seqs and remove any rows that correspond to the |
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624 # sequences that are already present in the paired MSA. |
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625 for row_num, seq in enumerate(chain['msa']): |
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626 if tuple(seq) not in sequence_set: |
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627 keep_rows.append(row_num) |
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628 for feature_name in feature_names: |
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629 if feature_name in msa_features: |
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630 if keep_rows: |
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631 chain[feature_name] = chain[feature_name][keep_rows] |
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632 else: |
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633 new_shape = list(chain[feature_name].shape) |
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634 new_shape[0] = 0 |
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635 chain[feature_name] = np.zeros(new_shape, |
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636 dtype=chain[feature_name].dtype) |
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637 chain['num_alignments'] = np.array(chain['msa'].shape[0], dtype=np.int32) |
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638 return np_chains |