cool-seq-tool 0.4.0.dev2__tar.gz → 0.4.1__tar.gz

{cool_seq_tool-0.4.0.dev2 → cool_seq_tool-0.4.1}/LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021-2023 Wagner Lab
+Copyright (c) 2021-2024 Wagner Lab
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

{cool_seq_tool-0.4.0.dev2/src/cool_seq_tool.egg-info → cool_seq_tool-0.4.1}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.1
 Name: cool_seq_tool
-Version: 0.4.0.dev2
+Version: 0.4.1
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
         
-        Copyright (c) 2021-2023 Wagner Lab
+        Copyright (c) 2021-2024 Wagner Lab
         
         Permission is hereby granted, free of charge, to any person obtaining a copy
         of this software and associated documentation files (the "Software"), to deal
@@ -26,7 +26,7 @@ License: MIT License
         SOFTWARE.
         
 Project-URL: Homepage, https://github.com/genomicmedlab/cool-seq-tool
-Project-URL: Documentation, https://coolseqtool.readthedocs.io/en/latest/index.html
+Project-URL: Documentation, https://coolseqtool.readthedocs.io/
 Project-URL: Changelog, https://github.com/genomicmedlab/cool-seq-tool/releases
 Project-URL: Source, https://github.com/genomicmedlab/cool-seq-tool
 Project-URL: Bug Tracker, https://github.com/genomicmedlab/cool-seq-tool/issues
@@ -39,30 +39,30 @@ Classifier: Intended Audience :: Developers
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.8
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: asyncpg
 Requires-Dist: aiofiles
 Requires-Dist: boto3
 Requires-Dist: agct>=0.1.0-dev1
-Requires-Dist: polars
+Requires-Dist: polars~=1.0
 Requires-Dist: hgvs
 Requires-Dist: biocommons.seqrepo
 Requires-Dist: pydantic==2.*
 Requires-Dist: uvicorn
 Requires-Dist: fastapi
 Requires-Dist: ga4gh.vrs
+Requires-Dist: wags-tails~=0.1.3
 Provides-Extra: dev
 Requires-Dist: pre-commit; extra == "dev"
 Requires-Dist: ipython; extra == "dev"
 Requires-Dist: ipykernel; extra == "dev"
 Requires-Dist: psycopg2-binary; extra == "dev"
-Requires-Dist: ruff>=0.1.14; extra == "dev"
+Requires-Dist: ruff==0.5.0; extra == "dev"
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: pytest-cov; extra == "tests"
@@ -81,8 +81,14 @@ Requires-Dist: sphinx-github-changelog==1.2.1; extra == "docs"
 CoolSeqTool
 </h1>
 
+[![image](https://img.shields.io/pypi/v/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/l/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/pyversions/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![Actions status](https://github.com/genomicmedlab/cool-seq-tool/actions/workflows/checks.yaml/badge.svg)](https://github.com/genomicmedlab/cool-seq-tool/actions/checks.yaml)
+
+---
+
 **[Documentation](https://coolseqtool.readthedocs.io/latest/)** · [Installation](https://coolseqtool.readthedocs.io/latest/install.html) · [Usage](https://coolseqtool.readthedocs.io/latest/usage.html) · [API reference](https://coolseqtool.readthedocs.io/latest/reference/index.html)
 
+---
+
 ## Overview
 
 <!-- description -->
@@ -113,6 +119,7 @@ All CoolSeqTool resources can be initialized by way of a top-level class instanc
 
 ```pycon
 >>> from cool_seq_tool.app import CoolSeqTool
+>>> from cool_seq_tool.schemas import AnnotationLayer, ResidueMode
 >>> cst = CoolSeqTool()
 >>> result = await cst.mane_transcript.get_mane_transcript(
 ...     "NP_004324.2",

{cool_seq_tool-0.4.0.dev2 → cool_seq_tool-0.4.1}/README.md

@@ -2,8 +2,14 @@
 CoolSeqTool
 </h1>
 
+[![image](https://img.shields.io/pypi/v/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/l/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![image](https://img.shields.io/pypi/pyversions/cool-seq-tool.svg)](https://pypi.python.org/pypi/cool-seq-tool) [![Actions status](https://github.com/genomicmedlab/cool-seq-tool/actions/workflows/checks.yaml/badge.svg)](https://github.com/genomicmedlab/cool-seq-tool/actions/checks.yaml)
+
+---
+
 **[Documentation](https://coolseqtool.readthedocs.io/latest/)** · [Installation](https://coolseqtool.readthedocs.io/latest/install.html) · [Usage](https://coolseqtool.readthedocs.io/latest/usage.html) · [API reference](https://coolseqtool.readthedocs.io/latest/reference/index.html)
 
+---
+
 ## Overview
 
 <!-- description -->
@@ -34,6 +40,7 @@ All CoolSeqTool resources can be initialized by way of a top-level class instanc
 
 ```pycon
 >>> from cool_seq_tool.app import CoolSeqTool
+>>> from cool_seq_tool.schemas import AnnotationLayer, ResidueMode
 >>> cst = CoolSeqTool()
 >>> result = await cst.mane_transcript.get_mane_transcript(
 ...     "NP_004324.2",

{cool_seq_tool-0.4.0.dev2 → cool_seq_tool-0.4.1}/pyproject.toml

@@ -17,12 +17,11 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 description = "Common Operation on Lots of Sequences Tool"
 license = {file = "LICENSE"}
 dependencies = [
@@ -30,18 +29,19 @@ dependencies = [
     "aiofiles",
     "boto3",
     "agct >= 0.1.0-dev1",
-    "polars",
+    "polars ~= 1.0",
     "hgvs",
     "biocommons.seqrepo",
     "pydantic == 2.*",
     "uvicorn",
     "fastapi",
     "ga4gh.vrs",
+    "wags-tails ~= 0.1.3"
 ]
 dynamic = ["version"]
 
 [project.optional-dependencies]
-dev = ["pre-commit", "ipython", "ipykernel", "psycopg2-binary", "ruff>=0.1.14"]
+dev = ["pre-commit", "ipython", "ipykernel", "psycopg2-binary", "ruff==0.5.0"]
 tests = ["pytest", "pytest-cov", "pytest-asyncio==0.18.3", "mock"]
 docs = [
     "sphinx==6.1.3",
@@ -55,13 +55,13 @@ docs = [
 
 [project.urls]
 Homepage = "https://github.com/genomicmedlab/cool-seq-tool"
-Documentation = "https://coolseqtool.readthedocs.io/en/latest/index.html"
+Documentation = "https://coolseqtool.readthedocs.io/"
 Changelog = "https://github.com/genomicmedlab/cool-seq-tool/releases"
 Source = "https://github.com/genomicmedlab/cool-seq-tool"
 "Bug Tracker" = "https://github.com/genomicmedlab/cool-seq-tool/issues"
 
 [build-system]
-requires = ["setuptools>=61.0"]
+requires = ["setuptools>=64"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools.dynamic]
@@ -75,7 +75,7 @@ version = {attr = "cool_seq_tool.version.__version__"}
 # where = ["src"]
 
 [tool.setuptools.package-data]
-"cool_seq_tool.data" = ["transcript_mapping.tsv"]
+"cool_seq_tool.resources" = ["transcript_mapping.tsv"]
 
 [tool.pytest.ini_options]
 addopts = "--cov=src --cov-report term-missing"
@@ -87,7 +87,7 @@ branch = true
 [tool.ruff]
 src = ["src"]
 exclude = ["docs/source/conf.py"]
-select = [
+lint.select = [
     "F",  # https://docs.astral.sh/ruff/rules/#pyflakes-f
     "E", "W",  # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
     "I",  # https://docs.astral.sh/ruff/rules/#isort-i
@@ -103,19 +103,25 @@ select = [
     "DTZ",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
     "T10",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
     "EM",  # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
+    "LOG",  # https://docs.astral.sh/ruff/rules/#flake8-logging-log
     "G",  # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
+    "INP",  # https://docs.astral.sh/ruff/rules/#flake8-no-pep420-inp
     "PIE",  # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
     "T20",  # https://docs.astral.sh/ruff/rules/#flake8-print-t20
     "PT",  # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
     "Q",  # https://docs.astral.sh/ruff/rules/#flake8-quotes-q
     "RSE",  # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
     "RET",  # https://docs.astral.sh/ruff/rules/#flake8-return-ret
+    "SLF",  # https://docs.astral.sh/ruff/rules/#flake8-self-slf
     "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
+    "ARG",  # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
     "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
     "PGH",  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
+    "PERF",  # https://docs.astral.sh/ruff/rules/#perflint-perf
+    "FURB",  # https://docs.astral.sh/ruff/rules/#refurb-furb
     "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
 ]
-fixable = [
+lint.fixable = [
     "I",
     "F401",
     "D",
@@ -123,16 +129,20 @@ fixable = [
     "ANN",
     "B",
     "C4",
+    "LOG",
     "G",
     "PIE",
     "PT",
     "RSE",
     "SIM",
+    "PERF",
+    "FURB",
     "RUF"
 ]
 
-# ANN101 - missing-type-self
 # ANN003 - missing-type-kwargs
+# ANN101 - missing-type-self
+# ANN102 - missing-type-cls
 # D203 - one-blank-line-before-class
 # D205 - blank-line-after-summary
 # D206 - indent-with-spaces*
@@ -147,24 +157,30 @@ fixable = [
 # W191 - tab-indentation*
 # S321 - suspicious-ftp-lib-usage
 # *ignored for compatibility with formatter
-ignore = [
-    "ANN101", "ANN003",
+lint.ignore = [
+    "ANN003", "ANN101", "ANN102",
     "D203", "D205", "D206", "D213", "D300", "D400", "D415",
     "E111", "E114", "E117", "E501",
     "W191",
     "S321",
 ]
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 # ANN001 - missing-type-function-argument
 # ANN2 - missing-return-type
 # ANN102 - missing-type-cls
 # N805 - invalid-first-argument-name-for-method
 # F821 - undefined-name
 # F401 - unused-import
-"tests/*" = ["ANN001", "ANN2", "ANN102", "S101"]
+# INP001 - implicit-namespace-package
+# SLF001 - private-member-access
+# ARG001 - unused-function-argument
+"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "INP001", "SLF001", "ARG001"]
 "*__init__.py" = ["F401"]
 "src/cool_seq_tool/schemas.py" = ["ANN201", "N805", "ANN001"]
 
 [tool.ruff.lint.flake8-bugbear]
 extend-immutable-calls = ["fastapi.Query"]
+
+[tool.ruff.format]
+docstring-code-format = true

{cool_seq_tool-0.4.0.dev2 → cool_seq_tool-0.4.1}/src/cool_seq_tool/__init__.py

@@ -1,8 +1,6 @@
 """The cool_seq_tool package"""
-import logging
-from pathlib import Path
 
-APP_ROOT = Path(__file__).resolve().parents[0]
+import logging
 
 logging.basicConfig(
     filename="cool_seq_tool.log",

{cool_seq_tool-0.4.0.dev2 → cool_seq_tool-0.4.1}/src/cool_seq_tool/api.py

@@ -1,5 +1,4 @@
 """Main application for FastAPI"""
-from typing import Dict
 
 from fastapi import FastAPI
 from fastapi.openapi.utils import get_openapi
@@ -19,7 +18,7 @@ app.include_router(mane.router)
 app.include_router(mappings.router)
 
 
-def custom_openapi() -> Dict:
+def custom_openapi() -> dict:
     """Generate custom fields for OpenAPI response."""
     if app.openapi_schema:
         return app.openapi_schema

{cool_seq_tool-0.4.0.dev2 → cool_seq_tool-0.4.1}/src/cool_seq_tool/app.py

@@ -1,24 +1,18 @@
 """Provides core CoolSeqTool class, which non-redundantly initializes all Cool-Seq-Tool
 data handler and mapping resources for straightforward access.
 """
+
 import logging
 from pathlib import Path
-from typing import Optional
 
 from biocommons.seqrepo import SeqRepo
 
-from cool_seq_tool.handlers.seqrepo_access import SeqRepoAccess
+from cool_seq_tool.handlers.seqrepo_access import SEQREPO_ROOT_DIR, SeqRepoAccess
 from cool_seq_tool.mappers import (
     AlignmentMapper,
     ExonGenomicCoordsMapper,
     ManeTranscript,
 )
-from cool_seq_tool.paths import (
-    LRG_REFSEQGENE_PATH,
-    MANE_SUMMARY_PATH,
-    SEQREPO_ROOT_DIR,
-    TRANSCRIPT_MAPPINGS_PATH,
-)
 from cool_seq_tool.sources.mane_transcript_mappings import ManeTranscriptMappings
 from cool_seq_tool.sources.transcript_mappings import TranscriptMappings
 from cool_seq_tool.sources.uta_database import UTA_DB_URL, UtaDatabase
@@ -37,26 +31,44 @@ class CoolSeqTool:
     * ``self.alignment_mapper``: :py:class:`AlignmentMapper <cool_seq_tool.mappers.alignment.AlignmentMapper>`
     * ``self.mane_transcript``: :py:class:`ManeTranscript <cool_seq_tool.mappers.mane_transcript.ManeTranscript>`
     * ``self.ex_g_coords_mapper``: :py:class:`ExonGenomicCoordsMapper <cool_seq_tool.mappers.exon_genomic_coords.ExonGenomicCoordsMapper>`
-
-    Initialization with default resource locations is straightforward:
-
-    .. code-block:: pycon
-
-       >>> from cool_seq_tool.app import CoolSeqTool
-       >>> cst = CoolSeqTool()
-
-    See the :ref:`configuration <configuration>` section for more information.
     """
 
     def __init__(
         self,
-        transcript_file_path: Path = TRANSCRIPT_MAPPINGS_PATH,
-        lrg_refseqgene_path: Path = LRG_REFSEQGENE_PATH,
-        mane_data_path: Path = MANE_SUMMARY_PATH,
+        transcript_file_path: Path | None = None,
+        lrg_refseqgene_path: Path | None = None,
+        mane_data_path: Path | None = None,
         db_url: str = UTA_DB_URL,
-        sr: Optional[SeqRepo] = None,
+        sr: SeqRepo | None = None,
+        force_local_files: bool = False,
     ) -> None:
-        """Initialize CoolSeqTool class
+        """Initialize CoolSeqTool class.
+
+        Initialization with default resource locations is straightforward:
+
+        >>> from cool_seq_tool.app import CoolSeqTool
+        >>> cst = CoolSeqTool()
+
+        By default, this will attempt to fetch the latest versions of static resources,
+        which means brief FTP and HTTPS requests to NCBI servers upon initialization.
+        To suppress this check and simply rely on the most recent locally-available
+        data:
+
+        >>> cst = CoolSeqTool(force_local_files=True)
+
+        Note that this will raise a FileNotFoundError if no locally-available data exists.
+
+        Paths to those files can also be explicitly passed to avoid checks as well:
+
+        >>> from pathlib import Path
+        >>> cst = CoolSeqTool(
+        ...     lrg_refseqgene_path=Path("lrg_refseqgene_20240625.tsv"),
+        ...     mane_data_path=Path("ncbi_mane_summary_1.3.txt"),
+        ... )
+
+        If not passed explicit arguments, these locations can also be set via
+        environment variables. See the :ref:`configuration <configuration>` section of
+        the docs for more information.
 
         :param transcript_file_path: The path to ``transcript_mapping.tsv``
         :param lrg_refseqgene_path: The path to the LRG_RefSeqGene file
@@ -64,6 +76,8 @@ class CoolSeqTool:
         :param db_url: PostgreSQL connection URL
             Format: ``driver://user:password@host/database/schema``
         :param sr: SeqRepo instance. If this is not provided, will create a new instance
+        :param force_local_files: if ``True``, don't check for or try to acquire latest
+            versions of static data files -- just use most recently available, if any
         """
         if not sr:
             sr = SeqRepo(root_dir=SEQREPO_ROOT_DIR)
@@ -71,9 +85,10 @@ class CoolSeqTool:
         self.transcript_mappings = TranscriptMappings(
             transcript_file_path=transcript_file_path,
             lrg_refseqgene_path=lrg_refseqgene_path,
+            from_local=force_local_files,
         )
         self.mane_transcript_mappings = ManeTranscriptMappings(
-            mane_data_path=mane_data_path
+            mane_data_path=mane_data_path, from_local=force_local_files
         )
         self.uta_db = UtaDatabase(db_url=db_url)
         self.alignment_mapper = AlignmentMapper(
@@ -86,5 +101,8 @@ class CoolSeqTool:
             self.uta_db,
         )
         self.ex_g_coords_mapper = ExonGenomicCoordsMapper(
-            self.uta_db, self.mane_transcript
+            self.seqrepo_access,
+            self.uta_db,
+            self.mane_transcript,
+            self.mane_transcript_mappings,
         )

{cool_seq_tool-0.4.0.dev2 → cool_seq_tool-0.4.1}/src/cool_seq_tool/handlers/__init__.py

@@ -1,2 +1,3 @@
 """Module for extending clients"""
+
 from .seqrepo_access import SeqRepoAccess

{cool_seq_tool-0.4.0.dev2 → cool_seq_tool-0.4.1}/src/cool_seq_tool/handlers/seqrepo_access.py

@@ -1,10 +1,10 @@
 """Wrap SeqRepo to provide additional lookup and identification methods on top of basic
 dereferencing functions.
 """
+
 import logging
 from os import environ
 from pathlib import Path
-from typing import List, Optional, Tuple, Union
 
 from ga4gh.vrs.dataproxy import SeqRepoDataProxy
 
@@ -14,6 +14,9 @@ from cool_seq_tool.utils import get_inter_residue_pos
 logger = logging.getLogger(__name__)
 
 
+SEQREPO_ROOT_DIR = environ.get("SEQREPO_ROOT_DIR", "/usr/local/share/seqrepo/latest")
+
+
 class SeqRepoAccess(SeqRepoDataProxy):
     """Provide a wrapper around the base SeqRepoDataProxy class from ``VRS-Python`` to
     provide additional lookup and identification methods.
@@ -24,10 +27,10 @@ class SeqRepoAccess(SeqRepoDataProxy):
     def get_reference_sequence(
         self,
         ac: str,
-        start: Optional[int] = None,
-        end: Optional[int] = None,
+        start: int | None = None,
+        end: int | None = None,
         residue_mode: ResidueMode = ResidueMode.RESIDUE,
-    ) -> Tuple[str, Optional[str]]:
+    ) -> tuple[str, str | None]:
         """Get reference sequence for an accession given a start and end position. If
         ``start`` and ``end`` are not given, returns the entire reference sequence.
 
@@ -93,8 +96,8 @@ class SeqRepoAccess(SeqRepoDataProxy):
             return sequence, None
 
     def translate_identifier(
-        self, ac: str, target_namespaces: Optional[Union[str, List[str]]] = None
-    ) -> Tuple[List[str], Optional[str]]:
+        self, ac: str, target_namespaces: str | list[str] | None = None
+    ) -> tuple[list[str], str | None]:
         """Return list of identifiers for accession.
 
         >>> from cool_seq_tool.handlers import SeqRepoAccess
@@ -120,9 +123,7 @@ class SeqRepoAccess(SeqRepoDataProxy):
         else:
             return ga4gh_identifiers, None
 
-    def translate_alias(
-        self, input_str: str
-    ) -> Tuple[List[Optional[str]], Optional[str]]:
+    def translate_alias(self, input_str: str) -> tuple[list[str | None], str | None]:
         """Get aliases for a given input.
 
         :param str input_str: Input to get aliases for
@@ -135,9 +136,7 @@ class SeqRepoAccess(SeqRepoDataProxy):
             logger.warning(msg)
             return [], msg
 
-    def chromosome_to_acs(
-        self, chromosome: str
-    ) -> Tuple[Optional[List[str]], Optional[str]]:
+    def chromosome_to_acs(self, chromosome: str) -> tuple[list[str] | None, str | None]:
         """Get accessions for a chromosome
 
         :param chromosome: Chromosome number. Must be either 1-22, X, or Y
@@ -148,13 +147,12 @@ class SeqRepoAccess(SeqRepoDataProxy):
             tmp_acs, _ = self.translate_identifier(
                 f"{assembly}:chr{chromosome}", target_namespaces="refseq"
             )
-            for ac in tmp_acs:
-                acs.append(ac.split("refseq:")[-1])
+            acs += [ac.split("refseq:")[-1] for ac in tmp_acs]
         if acs:
             return acs, None
         return None, f"{chromosome} is not a valid chromosome"
 
-    def ac_to_chromosome(self, ac: str) -> Tuple[Optional[str], Optional[str]]:
+    def ac_to_chromosome(self, ac: str) -> tuple[str | None, str | None]:
         """Get chromosome for accession.
 
         :param str ac: Accession

{cool_seq_tool-0.4.0.dev2 → cool_seq_tool-0.4.1}/src/cool_seq_tool/mappers/__init__.py

@@ -1,4 +1,5 @@
 """Module for mapping data"""
+
 from .alignment import AlignmentMapper  # noqa: I001
 from .mane_transcript import ManeTranscript
 from .exon_genomic_coords import ExonGenomicCoordsMapper

{cool_seq_tool-0.4.0.dev2 → cool_seq_tool-0.4.1}/src/cool_seq_tool/mappers/alignment.py

@@ -1,7 +1,6 @@
 """Module containing alignment methods for translating to and from different
 reference sequences.
 """
-from typing import Dict, Optional, Tuple
 
 from cool_seq_tool.handlers.seqrepo_access import SeqRepoAccess
 from cool_seq_tool.schemas import AnnotationLayer, Assembly, ResidueMode
@@ -34,7 +33,7 @@ class AlignmentMapper:
         p_start_pos: int,
         p_end_pos: int,
         residue_mode: ResidueMode = ResidueMode.RESIDUE,
-    ) -> Tuple[Optional[Dict], Optional[str]]:
+    ) -> tuple[dict | None, str | None]:
         """Translate protein representation to cDNA representation.
 
         :param p_ac: Protein RefSeq accession
@@ -83,7 +82,7 @@ class AlignmentMapper:
             "residue_mode": ResidueMode.INTER_RESIDUE.value,
         }, None
 
-    async def _get_cds_start(self, c_ac: str) -> Tuple[Optional[int], Optional[str]]:
+    async def _get_cds_start(self, c_ac: str) -> tuple[int | None, str | None]:
         """Get CDS start for a given cDNA RefSeq accession
 
         :param c_ac: cDNA RefSeq accession
@@ -105,10 +104,10 @@ class AlignmentMapper:
         c_ac: str,
         c_start_pos: int,
         c_end_pos: int,
-        cds_start: Optional[int] = None,
+        cds_start: int | None = None,
         residue_mode: ResidueMode = ResidueMode.RESIDUE,
         target_genome_assembly: bool = Assembly.GRCH38,
-    ) -> Tuple[Optional[Dict], Optional[str]]:
+    ) -> tuple[dict | None, str | None]:
         """Translate cDNA representation to genomic representation
 
         :param c_ac: cDNA RefSeq accession
@@ -212,7 +211,7 @@ class AlignmentMapper:
         p_end_pos: int,
         residue_mode: ResidueMode = ResidueMode.INTER_RESIDUE,
         target_genome_assembly: Assembly = Assembly.GRCH38,
-    ) -> Tuple[Optional[Dict], Optional[str]]:
+    ) -> tuple[dict | None, str | None]:
         """Translate protein representation to genomic representation, by way of
         intermediary conversion into cDNA coordinates.