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[pre-commit.ci] auto fixes from pre-commit.com hooks
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pre-commit-ci[bot] committed Oct 16, 2024
1 parent 77dd810 commit f72acf6
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3 changes: 2 additions & 1 deletion missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/kinase_schema.py
View file
Original file line number Diff line number Diff line change
@@ -1,9 +1,10 @@
import logging
import os
from enum import Enum, StrEnum

import pandas as pd
from typing_extensions import Self
from pydantic import BaseModel, ValidationError, constr, model_validator
from typing_extensions import Self

from missense_kinase_toolkit.databases.kincore import (
align_kincore2uniprot,
Expand Down
95 changes: 59 additions & 36 deletions missense_kinase_toolkit/databases/missense_kinase_toolkit/databases/klifs.py
View file
Original file line number Diff line number Diff line change
@@ -1,12 +1,16 @@
import logging
import re
from dataclasses import dataclass, field

import numpy as np
from bravado.client import SwaggerClient
from Bio import Align
from bravado.client import SwaggerClient

from missense_kinase_toolkit.databases.aligners import (
BL2UniProtAligner,
Kincore2UniProtAligner,
)
from missense_kinase_toolkit.databases.api_schema import SwaggerAPIClient
from missense_kinase_toolkit.databases.aligners import BL2UniProtAligner, Kincore2UniProtAligner

logger = logging.getLogger(__name__)

Expand Down Expand Up @@ -325,11 +329,9 @@ class KLIFSPocket:
list_klifs_substr_match: list[str | None] = field(default_factory=list)
list_substring_idxs: list[list[int | None] | None] = field(default_factory=list)


def __post_init__(self):
self.iterate_klifs_alignment()


@staticmethod
def remove_gaps_from_klifs(klifs_string: str) -> str:
"""Remove gaps from KLIFS pocket sequence.
Expand All @@ -348,10 +350,9 @@ def remove_gaps_from_klifs(klifs_string: str) -> str:
klifs_pocket_narm = "".join([i for i in klifs_string if i != "-"])
return klifs_pocket_narm


@staticmethod
def return_idx_of_substring_in_superstring(
superstring: str,
superstring: str,
substring: str,
) -> list[int] | None:
"""Returns the index where substring begins in superstring (does not require -1 offset).
Expand All @@ -374,7 +375,6 @@ def return_idx_of_substring_in_superstring(
]
return list_out


@staticmethod
def return_idx_of_alignment_match(
align: Align.PairwiseAlignments,
Expand Down Expand Up @@ -407,7 +407,6 @@ def return_idx_of_alignment_match(

return output


def select_correct_alignment(
self,
alignments: Align.PairwiseAlignments,
Expand All @@ -421,37 +420,48 @@ def select_correct_alignment(
Pairwise alignments
bool_bl : bool
If True, select correct alignment for b.l region; if False, select correct alignment for linker region
Returns
-------
list[int]
List of indices for correct alignment
"""
list_alignments = [re.findall(r"[A-Z]+", alignment[0, :]) \
for alignment in alignments]
list_alignments = [
re.findall(r"[A-Z]+", alignment[0, :]) for alignment in alignments
]

if bool_bl:
# manual review showed 2 matches + gap + 5 matches
list_idx = [idx for idx, i in enumerate(list_alignments) \
if len(i) == 2 and len(i[0]) == 2]
list_idx = [
idx
for idx, i in enumerate(list_alignments)
if len(i) == 2 and len(i[0]) == 2
]
region = "b.l"
else:
# manual review showed 1 matches + gap + 3 matches
list_idx = [idx for idx, i in enumerate(list_alignments) \
if len(i) == 2 and len(i[0]) == 1]
list_idx = [
idx
for idx, i in enumerate(list_alignments)
if len(i) == 2 and len(i[0]) == 1
]
region = "linker"

if len(list_idx) > 1:
logging.error(f"{len(list_idx)} correct alignments found for {region} region\n{list_alignments}")
logging.error(
f"{len(list_idx)} correct alignments found for {region} region\n{list_alignments}"
)
return None
# BUB1B and PIK3R4 have "-" in b.l region so will not obey heuristic in list_idx
elif len(list_idx) == 0:
if len(alignments) == 1:
alignment = alignments[0]
else:
logging.error(f"{len(alignments)} non-heuristic alignments found for {region} region\n"\
f"{[print(i) for i in alignments]}")
logging.error(
f"{len(alignments)} non-heuristic alignments found for {region} region\n"
f"{[print(i) for i in alignments]}"
)
return None
else:
alignment = alignments[list_idx[0]]
Expand All @@ -470,7 +480,6 @@ def select_correct_alignment(

return self.return_idx_of_alignment_match(alignment)


def align_klifs_pocket_to_uniprot_seq(
self,
idx_start: int,
Expand Down Expand Up @@ -503,7 +512,6 @@ def align_klifs_pocket_to_uniprot_seq(
)
return substring_klifs, list_idx


def find_start_or_end_idx_recursively(
self,
idx_in: int,
Expand Down Expand Up @@ -533,7 +541,9 @@ def find_start_or_end_idx_recursively(
if idx_temp is not None and len(idx_temp) == 1:
idx_out = idx_temp[0] + len(self.remove_gaps_from_klifs(str_temp))
else:
idx_out = self.find_start_or_end_idx_recursively(idx_in - 1, bool_start=True)
idx_out = self.find_start_or_end_idx_recursively(
idx_in - 1, bool_start=True
)
# if looking for subsequent region, start at idx_in + 1
else:
# if last region
Expand All @@ -548,12 +558,13 @@ def find_start_or_end_idx_recursively(
if idx_temp is not None and len(idx_temp) == 1:
idx_out = idx_temp[0]
else:
idx_out = self.find_start_or_end_idx_recursively(idx_in + 1, bool_start=False)
idx_out = self.find_start_or_end_idx_recursively(
idx_in + 1, bool_start=False
)

return idx_out


#TODO find_start_or_end_idx_recursively kwargs
# TODO find_start_or_end_idx_recursively kwargs
def return_partial_alignments(
self,
idx: int,
Expand All @@ -567,12 +578,12 @@ def return_partial_alignments(
Index of region (e.g., I is 0, g.l is 1, etc.)
align_fn : Align.PairwiseAligner | None
Alignment function; if none provided will use exact match
Returns
-------
tuple[int, int, Align.PairwiseAlignments | list[int | None] | None]
Start, end, and alignments (either indices or alignments or None) for region
"""
start_idx = self.find_start_or_end_idx_recursively(idx, bool_start=True)
end_idx = self.find_start_or_end_idx_recursively(idx, bool_start=False)
Expand All @@ -586,11 +597,12 @@ def return_partial_alignments(
if align_fn is not None:
aligned = align_fn.align(str_klifs, str_uniprot)
else:
aligned = self.return_idx_of_substring_in_superstring(str_uniprot, str_klifs)
aligned = self.return_idx_of_substring_in_superstring(
str_uniprot, str_klifs
)

return start_idx, end_idx, aligned


def iterate_klifs_alignment(
self,
) -> None:
Expand Down Expand Up @@ -639,7 +651,7 @@ def iterate_klifs_alignment(
):
len_offset = len(self.remove_gaps_from_klifs(str_klifs)) - len_klifs
list_substring_idx = [i + len_offset for i in list_substring_idx]

self.list_klifs_region.append(klifs_region_start + ":" + klifs_region_end)
self.list_klifs_substr_match.append(str_klifs)
self.list_substring_idxs.append(list_substring_idx)
Expand All @@ -664,31 +676,42 @@ def iterate_klifs_alignment(
if idx != idx_bl and substr_idx is not None and len(substr_idx) > 1:
start = self.find_start_or_end_idx_recursively(idx, bool_start=True)
end = self.find_start_or_end_idx_recursively(idx, bool_start=False)
self.list_substring_idxs[idx] = [i for i in substr_idx if i >= start and i <= end]
self.list_substring_idxs[idx] = [
i for i in substr_idx if i >= start and i <= end
]

# TODO: final partial alignment algorithm
for idx, substr_idx in enumerate(self.list_substring_idxs):
if substr_idx == []:
# check exact match
start_exact, _, align_exact = self.return_partial_alignments(idx=idx)
if align_exact != [] and len(align_exact) == 1:
self.list_substring_idxs[idx] = [i + start_exact for i in align_exact]
self.list_substring_idxs[idx] = [
i + start_exact for i in align_exact
]
# if no exact match, try local alignment
else:
start_local, _, align_local = self.return_partial_alignments(
idx=idx,
align_fn=Kincore2UniProtAligner(),
)
if len(align_local) == 1 and \
align_local[0].target == self.remove_gaps_from_klifs(align_local[0][0, :]):
if len(align_local) == 1 and align_local[
0
].target == self.remove_gaps_from_klifs(align_local[0][0, :]):
list_local = self.return_idx_of_alignment_match(align_local[0])
self.list_substring_idxs[idx] = [i + start_local for i in list_local]
self.list_substring_idxs[idx] = [
i + start_local for i in list_local
]
# if no exact match, try global alignment
else:
start_global, _, align_global = self.return_partial_alignments(
idx=idx,
align_fn=BL2UniProtAligner(),
)
# all that remains is linker region where some gaps (1 + 3) occur
list_global = self.select_correct_alignment(align_global, bool_bl=False)
self.list_substring_idxs[idx] = [i + start_global for i in list_global]
list_global = self.select_correct_alignment(
align_global, bool_bl=False
)
self.list_substring_idxs[idx] = [
i + start_global for i in list_global
]

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