cool-seq-tool 0.4.0.dev3__py3-none-any.whl → 0.5.0__py3-none-any.whl

cool_seq_tool/utils.py

@@ -1,17 +1,19 @@
 """Provide a small set of general helper functions."""
+
 import datetime
 import logging
-from typing import Tuple
 
+from bioutils.accessions import chr22XY
+
+from cool_seq_tool import __version__
 from cool_seq_tool.schemas import ResidueMode, ServiceMeta
-from cool_seq_tool.version import __version__
 
-logger = logging.getLogger(__name__)
+_logger = logging.getLogger(__name__)
 
 
 def get_inter_residue_pos(
     start_pos: int, end_pos: int, residue_mode: ResidueMode
-) -> Tuple[int, int]:
+) -> tuple[int, int]:
     """Return equivalent inter-residue position.
 
     Generally, we prefer to work with inter-residue coordinates where possible. Our
@@ -47,3 +49,41 @@ def service_meta() -> ServiceMeta:
         version=__version__,
         response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
     )
+
+
+def process_chromosome_input(chromosome: str, context: str = "") -> str:
+    """Perform processing on a chromosome arg.
+
+    E.g.
+
+    >>> from cool_seq_tool.utils import process_chromosome_input
+    >>> process_chromosome_input("7")
+    'chr7'
+    >>> process_chromosome_input("x")
+    'chrX'
+    >>> process_chromosome_input("chr7")
+    'chr7'
+
+    In the future, we could also use this method to be more opinionated about legal
+    chromosome values, or throw exceptions in the event of invalid or unrecognized
+    terms.
+
+    :param chromosome: user-provided chromosome input
+    :param context: calling context to provide in log
+    :return: processed chromosome value. Idempotent -- returns original value if no
+        changes needed.
+    """
+    original_chromosome_value = chromosome
+    if chromosome.lower().startswith("chr"):
+        chromosome = f"chr{chromosome[3:].upper()}"
+    else:
+        chromosome = chromosome.upper()
+    chromosome = chr22XY(chromosome)
+    if original_chromosome_value != chromosome:
+        _logger.warning(
+            "Transformed provided chromosome value from `%s` to `%s` in `%s`",
+            original_chromosome_value,
+            chromosome,
+            context if context else "cool_seq_tool",
+        )
+    return chromosome

{cool_seq_tool-0.4.0.dev3.dist-info → cool_seq_tool-0.5.0.dist-info}/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.dev3.dist-info → cool_seq_tool-0.5.0.dist-info}/METADATA

@@ -1,11 +1,11 @@
 Metadata-Version: 2.1
 Name: cool_seq_tool
-Version: 0.4.0.dev3
+Version: 0.5.0
 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
@@ -26,12 +26,11 @@ 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
 Classifier: Development Status :: 3 - Alpha
-Classifier: Framework :: FastAPI
 Classifier: Framework :: Pydantic
 Classifier: Framework :: Pydantic :: 2
 Classifier: Intended Audience :: Science/Research
@@ -39,30 +38,29 @@ 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
+Requires-Dist: bioutils
 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 ==0.2.0 ; extra == 'dev'
+Requires-Dist: ruff ==0.5.0 ; extra == 'dev'
 Provides-Extra: docs
 Requires-Dist: sphinx ==6.1.3 ; extra == 'docs'
 Requires-Dist: sphinx-autodoc-typehints ==1.22.0 ; extra == 'docs'
@@ -81,8 +79,14 @@ Requires-Dist: mock ; extra == 'tests'
 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 +117,7 @@ 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-0.5.0.dist-info/RECORD

@@ -0,0 +1,24 @@
+cool_seq_tool/__init__.py,sha256=fJmjglvv3Ylm0khQSD-XTqdyUA5YzEiS3iB8FGTOhIs,247
+cool_seq_tool/app.py,sha256=DJFcPVHQ5Ar9xdmHwrFKFMqbjDtx3L9gn84_wP63ARY,4982
+cool_seq_tool/schemas.py,sha256=hZ4pStUHgCarXPFLkuGU26znC0dooVDvixO_7eO5eUQ,16301
+cool_seq_tool/utils.py,sha256=mq_eGgqiILDcrtb1trMwRdsTERixuj8kDxHfgwsWsko,2914
+cool_seq_tool/handlers/__init__.py,sha256=KalQ46vX1MO4SJz2SlspKoIRy1n3c3Vp1t4Y2pIfqow,78
+cool_seq_tool/handlers/seqrepo_access.py,sha256=jKUn9mdyK0rHJk9I274N9H_B-M1m4r-hmOX7VwfjRC0,9135
+cool_seq_tool/mappers/__init__.py,sha256=O0JRxNFk8nWxD4v5ij47xelhvfVLdEXS43l2tzRuiUE,305
+cool_seq_tool/mappers/alignment.py,sha256=6Vk4XEar54ivuH8N7oBqa9gUa8E5GjWCI9hC1HCkM18,9552
+cool_seq_tool/mappers/exon_genomic_coords.py,sha256=Tvy0IQA9oAmq3dSYGnFHP-DlwFb1vwqehJ19NGg6Mpk,39160
+cool_seq_tool/mappers/liftover.py,sha256=lltx9zxfkrb5PHtJlKp3a39JCwPP4e0Zft-mQc1jXL8,3367
+cool_seq_tool/mappers/mane_transcript.py,sha256=iNkK8mtzXPmD1BROHzJ4vipr6oBbQv_BdUmvuOGFIMA,52823
+cool_seq_tool/resources/__init__.py,sha256=VwUC8YaucTS6SmRirToulZTF6CuvuLQRSxFfSfAovCc,77
+cool_seq_tool/resources/data_files.py,sha256=3lhu28tzlSoTs4vHZNu-hhoAWRrPGuZj_oIjqk2sYQM,3837
+cool_seq_tool/resources/status.py,sha256=L0KM-VG3N4Yuaqh3AKZd_2KPDLR0Y7rvW_OD6x8mF7A,5717
+cool_seq_tool/resources/transcript_mapping.tsv,sha256=AO3luYQAbFiCoRgiiPXotakb5pAwx1jDCeXpvGdIuac,24138769
+cool_seq_tool/sources/__init__.py,sha256=51QiymeptF7AeVGgV-tW_9f4pIUr0xtYbyzpvHOCneM,304
+cool_seq_tool/sources/mane_transcript_mappings.py,sha256=IQtaRWrIi3f1k0WiDtlmlfOlQQB6bTKSEAh2PHk-Lsw,4079
+cool_seq_tool/sources/transcript_mappings.py,sha256=903RKTMBO2rbKh6iTQ1BEWnY4C7saBFMPw2_4ATuudg,10054
+cool_seq_tool/sources/uta_database.py,sha256=TKMx_yoqWe5QVnqkZe_10x-Lp4PtKvArbMg5ufba0_Q,38353
+cool_seq_tool-0.5.0.dist-info/LICENSE,sha256=IpqC9A-tZW7XXXvCS8c4AVINqkmpxiVA-34Qe3CZSjo,1072
+cool_seq_tool-0.5.0.dist-info/METADATA,sha256=Ajjbvx2EZZUem5SVHY3qQHPRPx74c-VeHCMQdYcHB-o,6207
+cool_seq_tool-0.5.0.dist-info/WHEEL,sha256=Z4pYXqR_rTB7OWNDYFOm1qRk0RX6GFP2o8LgvP453Hk,91
+cool_seq_tool-0.5.0.dist-info/top_level.txt,sha256=cGuxdN6p3y16jQf6hCwWhE4OptwUeZPm_PNJlPb3b0k,14
+cool_seq_tool-0.5.0.dist-info/RECORD,,

{cool_seq_tool-0.4.0.dev3.dist-info → cool_seq_tool-0.5.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: setuptools (70.3.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

cool_seq_tool/api.py

@@ -1,42 +0,0 @@
-"""Main application for FastAPI"""
-from typing import Dict
-
-from fastapi import FastAPI
-from fastapi.openapi.utils import get_openapi
-
-from cool_seq_tool.routers import SERVICE_NAME, default, mane, mappings
-from cool_seq_tool.version import __version__
-
-app = FastAPI(
-    docs_url=f"/{SERVICE_NAME}",
-    openapi_url=f"/{SERVICE_NAME}/openapi.json",
-    swagger_ui_parameters={"tryItOutEnabled": True},
-)
-
-
-app.include_router(default.router)
-app.include_router(mane.router)
-app.include_router(mappings.router)
-
-
-def custom_openapi() -> Dict:
-    """Generate custom fields for OpenAPI response."""
-    if app.openapi_schema:
-        return app.openapi_schema
-    openapi_schema = get_openapi(
-        title="The GenomicMedLab Cool-Seq-Tool",
-        version=__version__,
-        description="Common Operations On Lots of Sequences Tool.",
-        routes=app.routes,
-    )
-
-    openapi_schema["info"]["contact"] = {
-        "name": "Alex H. Wagner",
-        "email": "Alex.Wagner@nationwidechildrens.org",
-        "url": "https://www.nationwidechildrens.org/specialties/institute-for-genomic-medicine/research-labs/wagner-lab",
-    }
-    app.openapi_schema = openapi_schema
-    return app.openapi_schema
-
-
-app.openapi = custom_openapi

cool_seq_tool/data/__init__.py

@@ -1,2 +0,0 @@
-"""Module for data"""
-from .data_downloads import DataDownload

cool_seq_tool/data/data_downloads.py

@@ -1,89 +0,0 @@
-"""Handle acquisition of external data."""
-import datetime
-import gzip
-import logging
-import shutil
-from ftplib import FTP
-from pathlib import Path
-
-from dateutil import parser
-
-from cool_seq_tool import APP_ROOT
-
-logger = logging.getLogger("cool_seq_tool")
-
-
-class DataDownload:
-    """Manage downloadable data files. Responsible for checking if files are available
-    under expected locations, and fetching them if not.
-
-    Relevant methods are called automatically by data classes; users should not have
-    to interact with this class under normal circumstances.
-    """
-
-    def __init__(self) -> None:
-        """Initialize downloadable data locations."""
-        self._data_dir = APP_ROOT / "data"
-
-    def get_mane_summary(self) -> Path:
-        """Identify latest MANE summary data. If unavailable locally, download from
-        `NCBI FTP server <https://ftp.ncbi.nlm.nih.gov/refseq/MANE/MANE_human/current/>`_.
-
-        :return: path to MANE summary file
-        """
-        with FTP("ftp.ncbi.nlm.nih.gov") as ftp:
-            ftp.login()
-            ftp.cwd("/refseq/MANE/MANE_human/current")
-            files = ftp.nlst()
-            mane_summary_file = [f for f in files if f.endswith(".summary.txt.gz")]
-            if not mane_summary_file:
-                msg = "Unable to download MANE summary data"
-                raise Exception(msg)
-            mane_summary_file = mane_summary_file[0]
-            self._mane_summary_path = self._data_dir / mane_summary_file[:-3]
-            mane_data_path = self._data_dir / mane_summary_file
-            if not self._mane_summary_path.exists():
-                logger.info("Downloading MANE summary file from NCBI.")
-                with mane_data_path.open("wb") as fp:
-                    ftp.retrbinary(f"RETR {mane_summary_file}", fp.write)
-                with gzip.open(
-                    mane_data_path, "rb"
-                ) as f_in, self._mane_summary_path.open("wb") as f_out:
-                    shutil.copyfileobj(f_in, f_out)
-                mane_data_path.unlink()
-                logger.info("MANE summary file download complete.")
-        return self._mane_summary_path
-
-    def get_lrg_refseq_gene_data(self) -> Path:
-        """Identify latest LRG RefSeq Gene file. If unavailable locally, download from
-        `NCBI FTP server <https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/>`_.
-
-        :return: path to acquired LRG RefSeq Gene data file
-        """
-        with FTP("ftp.ncbi.nlm.nih.gov") as ftp:
-            ftp.login()
-            lrg_refseqgene_file = "LRG_RefSeqGene"
-            ftp_dir_path = "/refseq/H_sapiens/RefSeqGene/"
-            ftp_file_path = f"{ftp_dir_path}{lrg_refseqgene_file}"
-            timestamp = ftp.voidcmd(f"MDTM {ftp_file_path}")[4:].strip()
-            date = str(parser.parse(timestamp)).split()[0]
-            version = (
-                datetime.datetime.strptime(date, "%Y-%m-%d")
-                .astimezone(tz=datetime.timezone.utc)
-                .strftime("%Y%m%d")
-            )
-            fn_versioned = f"{lrg_refseqgene_file}_{version}"
-            lrg_refseqgene_path = self._data_dir / lrg_refseqgene_file
-            self._lrg_refseqgene_path = self._data_dir / fn_versioned
-            if not self._lrg_refseqgene_path.exists():
-                logger.info("Downloading LRG RefSeq data from NCBI.")
-                ftp.cwd(ftp_dir_path)
-                with lrg_refseqgene_path.open("wb") as fp:
-                    ftp.retrbinary(f"RETR {lrg_refseqgene_file}", fp.write)
-                with lrg_refseqgene_path.open(
-                    "rb"
-                ) as f_in, self._lrg_refseqgene_path.open("wb") as f_out:
-                    shutil.copyfileobj(f_in, f_out)
-                lrg_refseqgene_path.unlink()
-                logger.info("LRG RefSeq data download complete.")
-        return self._lrg_refseqgene_path

cool_seq_tool/paths.py

@@ -1,28 +0,0 @@
-"""Provide paths to shared files, and trigger data acquisition if unavailable."""
-from os import environ
-from pathlib import Path
-
-from cool_seq_tool.data.data_downloads import DataDownload
-
-APP_ROOT = Path(__file__).resolve().parents[0]
-
-TRANSCRIPT_MAPPINGS_PATH = Path(
-    environ.get("TRANSCRIPT_MAPPINGS_PATH", f"{APP_ROOT}/data/transcript_mapping.tsv")
-)
-
-d = DataDownload()
-
-provided_mane_summary_path = environ.get("MANE_SUMMARY_PATH", "")
-if provided_mane_summary_path:
-    MANE_SUMMARY_PATH = Path(provided_mane_summary_path)
-else:
-    MANE_SUMMARY_PATH = d.get_mane_summary()
-
-provided_lrg_refseq_path = environ.get("LRG_REFSEQGENE_PATH", "")
-if provided_lrg_refseq_path:
-    LRG_REFSEQGENE_PATH = Path(provided_lrg_refseq_path)
-else:
-    LRG_REFSEQGENE_PATH = d.get_lrg_refseq_gene_data()
-
-
-SEQREPO_ROOT_DIR = environ.get("SEQREPO_ROOT_DIR", "/usr/local/share/seqrepo/latest")

cool_seq_tool/routers/__init__.py

@@ -1,16 +0,0 @@
-"""Module for routers"""
-from enum import Enum
-
-from cool_seq_tool.app import CoolSeqTool
-
-cool_seq_tool = CoolSeqTool()
-SERVICE_NAME = "cool_seq_tool"
-RESP_DESCR = "A response to a validly-formed query."
-UNHANDLED_EXCEPTION_MSG = "Unhandled exception occurred. Check logs for more details."
-
-
-class Tags(str, Enum):
-    """Define tags for endpoints"""
-
-    MANE_TRANSCRIPT = "MANE Transcript"
-    ALIGNMENT_MAPPER = "Alignment Mapper"

cool_seq_tool/routers/default.py

@@ -1,125 +0,0 @@
-"""Module containing default routes"""
-import logging
-import os
-import tempfile
-from pathlib import Path
-
-from fastapi import APIRouter, HTTPException, Query
-from fastapi.responses import FileResponse
-from starlette.background import BackgroundTasks
-
-from cool_seq_tool.routers import (
-    RESP_DESCR,
-    SERVICE_NAME,
-    UNHANDLED_EXCEPTION_MSG,
-    cool_seq_tool,
-)
-from cool_seq_tool.schemas import (
-    GenomicDataResponse,
-    GenomicRequestBody,
-    TranscriptRequestBody,
-)
-from cool_seq_tool.utils import service_meta
-
-logger = logging.getLogger("cool_seq_tool")
-
-router = APIRouter(prefix=f"/{SERVICE_NAME}")
-
-
-@router.post(
-    "/genomic_to_transcript_exon_coordinates",
-    summary="Get transcript exon data given genomic coordinate data",
-    response_description=RESP_DESCR,
-    description="Return transcript exon data",
-    response_model=GenomicDataResponse,
-)
-async def genomic_to_transcript_exon_coordinates(
-    request_body: GenomicRequestBody,
-) -> GenomicDataResponse:
-    """Get transcript exon data given genomic coordinate data
-
-    :param GenomicRequestBody request_body: Request body
-
-    Returns: GenomicDataResponse with data and warnings
-    """
-    request_body = request_body.model_dump()
-
-    response = GenomicDataResponse(
-        genomic_data=None, warnings=[], service_meta=service_meta()
-    )
-
-    try:
-        response = await cool_seq_tool.ex_g_coords_mapper.genomic_to_transcript_exon_coordinates(
-            **request_body
-        )
-    except Exception as e:
-        logger.error("genomic_to_transcript_exon_coordinates unhandled exception %s", e)
-        response.warnings.append(UNHANDLED_EXCEPTION_MSG)
-
-    return response
-
-
-@router.post(
-    "/transcript_to_genomic_coordinates",
-    summary="Get genomic coordinate data given transcript exon data",
-    response_description=RESP_DESCR,
-    description="Return genomic coordinate data",
-    response_model=GenomicDataResponse,
-)
-async def transcript_to_genomic_coordinates(
-    request_body: TranscriptRequestBody,
-) -> GenomicDataResponse:
-    """Get transcript exon data given genomic coordinate data
-
-    :param TranscriptRequestBody request_body: Request body
-
-    Returns: GenomicDataResponse with data and warnings
-    """
-    request_body = request_body.model_dump()
-
-    response = GenomicDataResponse(
-        genomic_data=None, warnings=[], service_meta=service_meta()
-    )
-
-    try:
-        response = (
-            await cool_seq_tool.ex_g_coords_mapper.transcript_to_genomic_coordinates(
-                **request_body
-            )
-        )
-    except Exception as e:
-        logger.error("transcript_to_genomic_coordinates unhandled exception %s", e)
-        response.warnings.append(UNHANDLED_EXCEPTION_MSG)
-
-    return response
-
-
-@router.get(
-    "/download_sequence",
-    summary="Get sequence for ID",
-    response_description=RESP_DESCR,
-    description="Given a known accession identifier, retrieve sequence data and return"
-    "as a FASTA file",
-    response_class=FileResponse,
-)
-async def get_sequence(
-    background_tasks: BackgroundTasks,
-    sequence_id: str = Query(
-        ..., description="ID of sequence to retrieve, sans namespace"
-    ),
-) -> FileResponse:
-    """Get sequence for requested sequence ID.
-    :param sequence_id: accession ID, sans namespace, eg `NM_152263.3`
-    :param background_tasks: Starlette background tasks object. Use to clean up
-        tempfile after get method returns.
-    :return: FASTA file if successful, or 404 if unable to find matching resource
-    """
-    _, path = tempfile.mkstemp(suffix=".fasta")
-    try:
-        cool_seq_tool.seqrepo_access.get_fasta_file(sequence_id, Path(path))
-    except KeyError as e:
-        raise HTTPException(
-            status_code=404, detail="No sequence available for requested identifier"
-        ) from e
-    background_tasks.add_task(lambda p: os.unlink(p), path)  # noqa: PTH108
-    return FileResponse(path)

cool_seq_tool/routers/mane.py

@@ -1,98 +0,0 @@
-"""Module containing routes related to MANE data"""
-import logging
-from typing import Optional
-
-from fastapi import APIRouter, Query
-
-from cool_seq_tool.routers import (
-    RESP_DESCR,
-    SERVICE_NAME,
-    UNHANDLED_EXCEPTION_MSG,
-    Tags,
-    cool_seq_tool,
-)
-from cool_seq_tool.schemas import AnnotationLayer, ManeDataService, ResidueMode
-from cool_seq_tool.utils import service_meta
-
-logger = logging.getLogger("cool_seq_tool")
-
-router = APIRouter(prefix=f"/{SERVICE_NAME}/mane")
-
-
-ref_descr = (
-    "Reference at position given during input. When this is set, it will "
-    "ensure that the reference sequences match for the final result."
-)
-try_longest_compatible_descr = (
-    "`True` if should try longest compatible remaining if"
-    " mane transcript was not compatible. `False` otherwise."
-)
-
-
-@router.get(
-    "/get_mane_data",
-    summary="Retrieve MANE data in inter-residue coordinates",
-    response_description=RESP_DESCR,
-    description="Return MANE Select, MANE Plus Clinical, or Longest Remaining "
-    "Transcript data in inter-residue coordinates. See our docs for "
-    "more information on transcript priority.",
-    response_model=ManeDataService,
-    tags=[Tags.MANE_TRANSCRIPT],
-)
-async def get_mane_data(
-    ac: str = Query(..., description="Accession"),
-    start_pos: int = Query(..., description="Start position"),
-    start_annotation_layer: AnnotationLayer = Query(
-        ..., description="Starting annotation layer for query"
-    ),
-    end_pos: Optional[int] = Query(
-        None, description="End position. If not set, will set to `start_pos`."
-    ),
-    gene: Optional[str] = Query(None, description="HGNC gene symbol"),
-    ref: Optional[str] = Query(None, description=ref_descr),
-    try_longest_compatible: bool = Query(
-        True, description=try_longest_compatible_descr
-    ),
-    residue_mode: ResidueMode = Query(
-        ResidueMode.RESIDUE, description="Residue mode for position(s)"
-    ),
-) -> ManeDataService:
-    """Return MANE or Longest Compatible Remaining Transcript data on inter-residue
-    coordinates
-
-    :param str ac: Accession
-    :param int start_pos: Start position
-    :param AnnotationLayer start_annotation_layer: Starting annotation layer for query
-    :param Optional[int] end_pos: End position. If `None` assumes
-        both  `start_pos` and `end_pos` have same values.
-    :param Optional[str] gene: Gene symbol
-    :param Optional[str] ref: Reference at position given during input
-    :param bool try_longest_compatible: `True` if should try longest
-        compatible remaining if mane transcript was not compatible.
-        `False` otherwise.
-    :param ResidueMode residue_mode: Starting residue mode for `start_pos`
-        and `end_pos`. Will always return coordinates in inter-residue
-    """
-    warnings = []
-    mane_data = None
-    try:
-        mane_data = await cool_seq_tool.mane_transcript.get_mane_transcript(
-            ac=ac,
-            start_pos=start_pos,
-            end_pos=end_pos,
-            start_annotation_layer=start_annotation_layer,
-            gene=gene,
-            ref=ref,
-            try_longest_compatible=try_longest_compatible,
-            residue_mode=residue_mode,
-        )
-
-        if not mane_data:
-            warnings.append("Unable to retrieve MANE data")
-    except Exception as e:
-        logger.exception("get_mane_data unhandled exception %s", e)
-        warnings.append(UNHANDLED_EXCEPTION_MSG)
-
-    return ManeDataService(
-        mane_data=mane_data, warnings=warnings, service_meta=service_meta()
-    )