cool-seq-tool 0.14.1__tar.gz → 0.14.2__tar.gz

{cool_seq_tool-0.14.1 → cool_seq_tool-0.14.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cool_seq_tool
-Version: 0.14.1
+Version: 0.14.2
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -45,15 +45,13 @@ 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~=1.0
-Requires-Dist: hgvs
 Requires-Dist: biocommons.seqrepo
 Requires-Dist: pydantic<3.0,>=2.0
 Requires-Dist: ga4gh.vrs<3.0,>=2.1.3
-Requires-Dist: wags-tails~=0.3.2
+Requires-Dist: wags-tails~=0.4.0
 Requires-Dist: bioutils
 Provides-Extra: dev
 Requires-Dist: pre-commit>=4.2.0; extra == "dev"
@@ -64,7 +62,7 @@ Requires-Dist: ruff==0.12.1; extra == "dev"
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: pytest-cov; extra == "tests"
-Requires-Dist: pytest-asyncio==0.18.3; extra == "tests"
+Requires-Dist: pytest-asyncio; extra == "tests"
 Requires-Dist: mock; extra == "tests"
 Provides-Extra: docs
 Requires-Dist: sphinx==6.1.3; extra == "docs"

{cool_seq_tool-0.14.1 → cool_seq_tool-0.14.2}/docs/source/reference/index.rst

@@ -55,6 +55,7 @@ Data Mappers
 
    cool_seq_tool.mappers.alignment
    cool_seq_tool.mappers.exon_genomic_coords
+   cool_seq_tool.mappers.feature_overlap
    cool_seq_tool.mappers.liftover
    cool_seq_tool.mappers.mane_transcript
 

{cool_seq_tool-0.14.1 → cool_seq_tool-0.14.2}/pyproject.toml

@@ -25,15 +25,13 @@ description = "Common Operation on Lots of Sequences Tool"
 license = {file = "LICENSE"}
 dependencies = [
     "asyncpg",
-    "aiofiles",
     "boto3",
     "agct >= 0.1.0-dev1",
     "polars ~= 1.0",
-    "hgvs",
     "biocommons.seqrepo",
     "pydantic >=2.0,<3.0",
     "ga4gh.vrs >=2.1.3,<3.0",
-    "wags-tails ~= 0.3.2",
+    "wags-tails ~= 0.4.0",
     "bioutils",
 ]
 dynamic = ["version"]
@@ -46,7 +44,7 @@ dev = [
     "psycopg2-binary",
     "ruff==0.12.1",
 ]
-tests = ["pytest", "pytest-cov", "pytest-asyncio==0.18.3", "mock"]
+tests = ["pytest", "pytest-cov", "pytest-asyncio", "mock"]
 docs = [
     "sphinx==6.1.3",
     "sphinx-autodoc-typehints==1.22.0",
@@ -81,6 +79,9 @@ build-backend = "setuptools.build_meta"
 "cool_seq_tool.resources" = ["transcript_mapping.tsv"]
 
 [tool.pytest.ini_options]
+asyncio_mode = "auto"
+asyncio_default_fixture_loop_scope = "session"
+asyncio_default_test_loop_scope = "session"
 addopts = "--cov=src --cov-report term-missing"
 testpaths = ["tests"]
 

{cool_seq_tool-0.14.1 → cool_seq_tool-0.14.2}/src/cool_seq_tool/mappers/__init__.py

@@ -4,6 +4,13 @@ from .alignment import AlignmentMapper  # noqa: I001
 from .liftover import LiftOver
 from .mane_transcript import ManeTranscript
 from .exon_genomic_coords import ExonGenomicCoordsMapper
+from .feature_overlap import FeatureOverlap
 
 
-__all__ = ["AlignmentMapper", "ExonGenomicCoordsMapper", "LiftOver", "ManeTranscript"]
+__all__ = [
+    "AlignmentMapper",
+    "ExonGenomicCoordsMapper",
+    "FeatureOverlap",
+    "LiftOver",
+    "ManeTranscript",
+]

cool_seq_tool-0.14.2/src/cool_seq_tool/mappers/feature_overlap.py

@@ -0,0 +1,251 @@
+"""Module for getting feature (gene/exon) overlap"""
+
+import re
+from pathlib import Path
+
+import polars as pl
+from ga4gh.core import ga4gh_identify
+from ga4gh.vrs.models import SequenceLocation, SequenceReference
+
+from cool_seq_tool.handlers import SeqRepoAccess
+from cool_seq_tool.resources.data_files import DataFile, get_data_file
+from cool_seq_tool.schemas import Assembly, CdsOverlap, CoordinateType
+
+# Pattern for chromosome
+CHR_PATTERN = r"X|Y|([1-9]|1[0-9]|2[0-2])"
+
+
+class FeatureOverlapError(Exception):
+    """Custom exception for the Feature Overlap class"""
+
+
+class FeatureOverlap:
+    """The class for getting feature overlap"""
+
+    def __init__(
+        self,
+        seqrepo_access: SeqRepoAccess,
+        mane_refseq_genomic_path: Path | None = None,
+        from_local: bool = False,
+    ) -> None:
+        """Initialize the FeatureOverlap class. Will load RefSeq data and store as df.
+
+        :param seqrepo_access: Client for accessing SeqRepo data
+        :param mane_refseq_genomic_path: Path to MANE RefSeq Genomic GFF data
+        :param from_local: if ``True``, don't check for or acquire latest version --
+            just provide most recent locally available file, if possible, and raise
+            error otherwise
+        """
+        if not mane_refseq_genomic_path:
+            mane_refseq_genomic_path = get_data_file(
+                DataFile.MANE_REFSEQ_GENOMIC, from_local
+            )
+        self.seqrepo_access = seqrepo_access
+        self.mane_refseq_genomic_path = mane_refseq_genomic_path
+        self.df = self._load_mane_refseq_gff_data()
+
+    def _load_mane_refseq_gff_data(self) -> pl.DataFrame:
+        """Load MANE RefSeq GFF data file into DataFrame.
+
+        :return: DataFrame containing MANE RefSeq Genomic GFF data for CDS. Columns
+            include `type`, `chromosome` (chromosome without 'chr' prefix), `cds_start`,
+            `cds_stop`, `info_name` (name of record), and `gene`. `cds_start` and
+            `cds_stop` use inter-residue coordinates.
+        """
+        df = pl.read_csv(
+            self.mane_refseq_genomic_path,
+            separator="\t",
+            has_header=False,
+            skip_rows=9,
+            columns=[0, 2, 3, 4, 8],
+        )
+        df.columns = ["chromosome", "type", "cds_start", "cds_stop", "info"]
+
+        # Restrict to only feature of interest: CDS (which has gene info)
+        df = df.filter(pl.col("type") == "CDS")
+
+        # Get name from the info field
+        # Get gene from the info field
+        # Get chromosome names without prefix and without suffix for alternate transcripts
+        # Convert start and stop to ints
+        # Convert to inter-residue coordinates
+        # Only return certain columns
+        return df.with_columns(
+            (pl.col("info").str.extract(r"Name=([^;]+)", 1).alias("info_name")),
+            (pl.col("info").str.extract(r"gene=([^;]+)", 1).alias("gene")),
+            (pl.col("chromosome").str.extract(r"^chr?([^_]+)", 1).alias("chromosome")),
+            (pl.col("cds_start").cast(pl.Int64) - 1).alias("cds_start"),
+            (pl.col("cds_stop").cast(pl.Int64).alias("cds_stop")),
+        ).select(
+            [
+                pl.col("type"),
+                pl.col("chromosome"),
+                pl.col("cds_start"),
+                pl.col("cds_stop"),
+                pl.col("info_name"),
+                pl.col("gene"),
+            ]
+        )
+
+    def _get_chr_from_alt_ac(self, identifier: str) -> str:
+        """Get chromosome given genomic identifier
+
+        :param identifier: Genomic identifier on GRCh38 assembly
+        :raises FeatureOverlapError: If unable to find associated GRCh38 chromosome
+        :return: Chromosome. 1..22, X, Y. No 'chr' prefix.
+        """
+        aliases, error_msg = self.seqrepo_access.translate_identifier(
+            identifier, Assembly.GRCH38.value
+        )
+
+        if error_msg:
+            raise FeatureOverlapError(str(error_msg))
+
+        if not aliases:
+            error_msg = (
+                f"Unable to find {Assembly.GRCH38.value} aliases for: {identifier}"
+            )
+            raise FeatureOverlapError(error_msg)
+
+        assembly_chr_pattern = (
+            rf"^{Assembly.GRCH38.value}:(?P<chromosome>{CHR_PATTERN})$"
+        )
+        for a in aliases:
+            chr_match = re.match(assembly_chr_pattern, a)
+            if chr_match:
+                break
+
+        if not chr_match:
+            error_msg = (
+                f"Unable to find {Assembly.GRCH38.value} chromosome for: {identifier}"
+            )
+            raise FeatureOverlapError(error_msg)
+
+        chr_groupdict = chr_match.groupdict()
+        return chr_groupdict["chromosome"]
+
+    def get_grch38_mane_gene_cds_overlap(
+        self,
+        start: int,
+        end: int,
+        chromosome: str | None = None,
+        identifier: str | None = None,
+        coordinate_type: CoordinateType = CoordinateType.RESIDUE,
+    ) -> dict[str, list[CdsOverlap]] | None:
+        """Given GRCh38 genomic data, find the overlapping MANE features (gene and cds).
+        The genomic data is specified as a sequence location by `chromosome`, `start`,
+        `end`. All CDS regions with which the input sequence location has nonzero base
+        pair overlap will be returned.
+
+        :param start: GRCh38 start position
+        :param end: GRCh38 end position
+        :param chromosome: Chromosome. 1..22, X, or Y. If not provided, must provide
+            `identifier`. If both `chromosome` and `identifier` are provided,
+            `chromosome` will be used.
+        :param identifier: Genomic identifier on GRCh38 assembly. If not provided, must
+            provide `chromosome`. If both `chromosome` and `identifier` are provided,
+            `chromosome` will be used.
+        :param coordinate_type: Coordinate type for ``start`` and ``end``
+        :raise FeatureOverlapError: If missing required fields or unable to find
+            associated ga4gh identifier
+        :return: MANE feature (gene/cds) overlap data represented as a dict. The
+            dictionary will be keyed by genes which overlap the input sequence location.
+            Each gene contains a list of the overlapping CDS regions with the beginning
+            and end of the input sequence location's overlap with each
+        """
+        ga4gh_seq_id = None
+        if chromosome:
+            if not re.match(f"^{CHR_PATTERN}$", chromosome):
+                error_msg = "`chromosome` must be 1, ..., 22, X, or Y"
+                raise FeatureOverlapError(error_msg)
+        else:
+            if identifier:
+                chromosome = self._get_chr_from_alt_ac(identifier)
+                if identifier.startswith("ga4gh:SQ."):
+                    ga4gh_seq_id = identifier
+            else:
+                error_msg = "Must provide either `chromosome` or `identifier`"
+                raise FeatureOverlapError(error_msg)
+
+        # Convert residue to inter-residue
+        if coordinate_type == CoordinateType.RESIDUE:
+            start -= 1
+
+        # Get feature dataframe (df uses inter-residue)
+        feature_df = self.df.filter(
+            (pl.col("chromosome") == chromosome)
+            & (pl.col("cds_start") <= end)
+            & (pl.col("cds_stop") >= start)
+        )
+
+        if feature_df.is_empty():
+            return None
+
+        # Add overlap columns
+        feature_df = feature_df.with_columns(
+            [
+                pl.when(pl.col("cds_start") < start)
+                .then(start)
+                .otherwise(pl.col("cds_start"))
+                .alias("overlap_start"),
+                pl.when(pl.col("cds_stop") > end)
+                .then(end)
+                .otherwise(pl.col("cds_stop"))
+                .alias("overlap_stop"),
+            ]
+        )
+
+        # Get ga4gh identifier for chromosome
+        if not ga4gh_seq_id:
+            grch38_chr = f"{Assembly.GRCH38.value}:{chromosome}"
+            ga4gh_aliases, error_msg = self.seqrepo_access.translate_identifier(
+                grch38_chr, "ga4gh"
+            )
+
+            # Errors should never happen but catching just in case
+            if error_msg:
+                raise FeatureOverlapError(str(error_msg))
+
+            if not ga4gh_aliases:
+                error_msg = f"Unable to find ga4gh identifier for: {grch38_chr}"
+                raise FeatureOverlapError(error_msg)
+
+            ga4gh_seq_id = ga4gh_aliases[0]
+
+        def _get_seq_loc(start_pos: int, stop_pos: int, refget_ac: str) -> dict:
+            """Get VRS Sequence Location represented as a dict
+
+            :param start_pos: Start position
+            :param stop_pos: Stop position
+            :param refget_ac: Refget Accession (SQ.)
+            :return: VRS Sequence Location represented as dictionary with the ga4gh ID
+                included
+            """
+            _sl = SequenceLocation(
+                sequenceReference=SequenceReference(
+                    refgetAccession=refget_ac,
+                ),
+                start=start_pos,
+                end=stop_pos,
+            )
+            ga4gh_identify(_sl)
+            return _sl.model_dump(exclude_none=True)
+
+        resp = {}
+        refget_ac = ga4gh_seq_id.split("ga4gh:")[-1]
+        for gene, group in feature_df.group_by("gene"):
+            gene = gene[0]
+            _gene_overlap_data = [
+                CdsOverlap(
+                    cds=_get_seq_loc(
+                        cds_row["cds_start"], cds_row["cds_stop"], refget_ac
+                    ),
+                    overlap=_get_seq_loc(
+                        cds_row["overlap_start"], cds_row["overlap_stop"], refget_ac
+                    ),
+                ).model_dump(by_alias=True, exclude_none=True)
+                for cds_row in group.iter_rows(named=True)
+            ]
+            resp[gene] = _gene_overlap_data
+
+        return resp

{cool_seq_tool-0.14.1 → cool_seq_tool-0.14.2}/src/cool_seq_tool/resources/data_files.py

@@ -6,7 +6,11 @@ from importlib import resources
 from os import environ
 from pathlib import Path
 
-from wags_tails import NcbiLrgRefSeqGeneData, NcbiManeSummaryData
+from wags_tails import (
+    NcbiLrgRefSeqGeneData,
+    NcbiManeRefSeqGenomicData,
+    NcbiManeSummaryData,
+)
 
 _logger = logging.getLogger(__name__)
 
@@ -16,6 +20,7 @@ class DataFile(str, Enum):
 
     TRANSCRIPT_MAPPINGS = "transcript_mappings"
     MANE_SUMMARY = "mane_summary"
+    MANE_REFSEQ_GENOMIC = "mane_refseq_genomic"
     LRG_REFSEQGENE = "lrg_refseqgene"
 
     def lower(self) -> str:
@@ -37,6 +42,12 @@ _resource_acquisition_params = {
             from_local=from_local
         )[0],
     ),
+    DataFile.MANE_REFSEQ_GENOMIC: (
+        "MANE_REFSEQ_GENOMIC_PATH",
+        lambda from_local: NcbiManeRefSeqGenomicData(silent=True).get_latest(
+            from_local=from_local
+        )[0],
+    ),
     DataFile.LRG_REFSEQGENE: (
         "LRG_REFSEQGENE_PATH",
         lambda from_local: NcbiLrgRefSeqGeneData(silent=True).get_latest(
@@ -53,6 +64,7 @@ def get_data_file(resource: DataFile, from_local: bool = False) -> Path:
 
     * ``Resource.TRANSCRIPT_MAPPINGS`` -> ``TRANSCRIPT_MAPPINGS_PATH``
     * ``Resource.MANE_SUMMARY`` -> ``MANE_SUMMARY_PATH``
+    * ``Resource.MANE_REFSEQ_GENOMIC`` -> ``MANE_REFSEQ_GENOMIC_PATH``
     * ``Resource.LRG_REFSEQGENE`` -> ``LRG_REFSEQGENE_PATH``
 
     Otherwise, this function falls back on default expected locations:

{cool_seq_tool-0.14.1 → cool_seq_tool-0.14.2}/src/cool_seq_tool/schemas.py

@@ -4,6 +4,7 @@ import datetime
 from enum import Enum, IntEnum
 from typing import Literal
 
+from ga4gh.vrs.models import SequenceLocation
 from pydantic import (
     BaseModel,
     ConfigDict,
@@ -167,3 +168,37 @@ class ServiceMeta(BaseModelForbidExtra):
             }
         }
     )
+
+
+class CdsOverlap(BaseModelForbidExtra):
+    """Create model for representing CDS start/stop and Overlap start/stop"""
+
+    cds: SequenceLocation
+    overlap: SequenceLocation
+
+    model_config = ConfigDict(
+        json_schema_extra={
+            "example": {
+                "cds": {
+                    "id": "ga4gh:SL.fYRYzNIAoe6UQF9MT1XaYsFscoU68ZJv",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
+                        "type": "SequenceReference",
+                    },
+                    "start": 140726493,
+                    "end": 140726516,
+                },
+                "overlap": {
+                    "id": "ga4gh:SL.fYRYzNIAoe6UQF9MT1XaYsFscoU68ZJv",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
+                        "type": "SequenceReference",
+                    },
+                    "start": 140726493,
+                    "end": 140726516,
+                },
+            }
+        }
+    )

{cool_seq_tool-0.14.1 → cool_seq_tool-0.14.2}/src/cool_seq_tool.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cool_seq_tool
-Version: 0.14.1
+Version: 0.14.2
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -45,15 +45,13 @@ 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~=1.0
-Requires-Dist: hgvs
 Requires-Dist: biocommons.seqrepo
 Requires-Dist: pydantic<3.0,>=2.0
 Requires-Dist: ga4gh.vrs<3.0,>=2.1.3
-Requires-Dist: wags-tails~=0.3.2
+Requires-Dist: wags-tails~=0.4.0
 Requires-Dist: bioutils
 Provides-Extra: dev
 Requires-Dist: pre-commit>=4.2.0; extra == "dev"
@@ -64,7 +62,7 @@ Requires-Dist: ruff==0.12.1; extra == "dev"
 Provides-Extra: tests
 Requires-Dist: pytest; extra == "tests"
 Requires-Dist: pytest-cov; extra == "tests"
-Requires-Dist: pytest-asyncio==0.18.3; extra == "tests"
+Requires-Dist: pytest-asyncio; extra == "tests"
 Requires-Dist: mock; extra == "tests"
 Provides-Extra: docs
 Requires-Dist: sphinx==6.1.3; extra == "docs"

{cool_seq_tool-0.14.1 → cool_seq_tool-0.14.2}/src/cool_seq_tool.egg-info/SOURCES.txt

@@ -39,6 +39,7 @@ src/cool_seq_tool/handlers/seqrepo_access.py
 src/cool_seq_tool/mappers/__init__.py
 src/cool_seq_tool/mappers/alignment.py
 src/cool_seq_tool/mappers/exon_genomic_coords.py
+src/cool_seq_tool/mappers/feature_overlap.py
 src/cool_seq_tool/mappers/liftover.py
 src/cool_seq_tool/mappers/mane_transcript.py
 src/cool_seq_tool/resources/__init__.py
@@ -51,6 +52,7 @@ src/cool_seq_tool/sources/transcript_mappings.py
 src/cool_seq_tool/sources/uta_database.py
 tests/conftest.py
 tests/test_utils.py
+tests/handlers/test_feature_overlap.py
 tests/handlers/test_seqrepo_access.py
 tests/mappers/test_alignment.py
 tests/mappers/test_exon_genomic_coords.py

{cool_seq_tool-0.14.1 → cool_seq_tool-0.14.2}/src/cool_seq_tool.egg-info/requires.txt

@@ -1,13 +1,11 @@
 asyncpg
-aiofiles
 boto3
 agct>=0.1.0-dev1
 polars~=1.0
-hgvs
 biocommons.seqrepo
 pydantic<3.0,>=2.0
 ga4gh.vrs<3.0,>=2.1.3
-wags-tails~=0.3.2
+wags-tails~=0.4.0
 bioutils
 
 [dev]
@@ -29,5 +27,5 @@ sphinx-github-changelog==1.2.1
 [tests]
 pytest
 pytest-cov
-pytest-asyncio==0.18.3
+pytest-asyncio
 mock

{cool_seq_tool-0.14.1 → cool_seq_tool-0.14.2}/tests/conftest.py

@@ -1,7 +1,5 @@
 """Provide utilities for test cases."""
 
-import asyncio
-
 import pytest
 
 from cool_seq_tool import CoolSeqTool
@@ -10,14 +8,6 @@ from cool_seq_tool.schemas import ManeGeneData, Strand
 from cool_seq_tool.sources.uta_database import GenomicAlnData, GenomicTxMetadata
 
 
-@pytest.fixture(scope="session")
-def event_loop(request):
-    """Create an instance of the default event loop for each test case."""
-    loop = asyncio.get_event_loop_policy().new_event_loop()
-    yield loop
-    loop.close()
-
-
 @pytest.fixture(scope="session")
 def test_cool_seq_tool():
     """Create CoolSeqTool test fixture"""

cool_seq_tool-0.14.2/tests/handlers/test_feature_overlap.py

@@ -0,0 +1,492 @@
+"""Module for testing Feature Overlap class"""
+
+import polars as pl
+import pytest
+
+from cool_seq_tool.mappers.feature_overlap import (
+    FeatureOverlap,
+    FeatureOverlapError,
+)
+from cool_seq_tool.schemas import CoordinateType
+
+
+@pytest.fixture(scope="module")
+def test_feature_overlap(test_seqrepo_access):
+    """Build Feature Overlap test fixture"""
+    return FeatureOverlap(test_seqrepo_access)
+
+
+def test_df(test_feature_overlap):
+    """Test that the dataframe contains correct data"""
+    # We only store CDS data
+    assert list(test_feature_overlap.df["type"].unique()) == ["CDS"]
+
+    assert set(test_feature_overlap.df.columns) == {
+        "type",
+        "chromosome",
+        "cds_start",
+        "cds_stop",
+        "info_name",
+        "gene",
+    }
+
+    assert test_feature_overlap.df["cds_start"].dtype == pl.Int64
+    assert test_feature_overlap.df["cds_stop"].dtype == pl.Int64
+
+    assert set(test_feature_overlap.df["chromosome"].unique()) == {
+        "1",
+        "2",
+        "3",
+        "4",
+        "5",
+        "6",
+        "7",
+        "8",
+        "9",
+        "10",
+        "11",
+        "12",
+        "13",
+        "14",
+        "15",
+        "16",
+        "17",
+        "18",
+        "19",
+        "20",
+        "21",
+        "22",
+        "X",
+        "Y",
+    }
+
+
+def test_get_chr_from_alt_ac(test_feature_overlap):
+    """Test that _get_chr_from_alt_ac works correctly"""
+    resp = test_feature_overlap._get_chr_from_alt_ac("NC_000001.11")
+    assert resp == "1"
+
+    resp = test_feature_overlap._get_chr_from_alt_ac("NC_000023.11")
+    assert resp == "X"
+
+    # identifier is invalid (no version)
+    with pytest.raises(FeatureOverlapError) as e:
+        test_feature_overlap._get_chr_from_alt_ac("NC_000001")
+    assert str(e.value) == "SeqRepo unable to get translated identifiers for NC_000001"
+
+    # identifier is grch37
+    with pytest.raises(FeatureOverlapError) as e:
+        test_feature_overlap._get_chr_from_alt_ac("NC_000001.10")
+    assert str(e.value) == "Unable to find GRCh38 aliases for: NC_000001.10"
+
+
+def test_get_grch38_cds_overlap(test_feature_overlap):
+    """Test that get_grch38_mane_gene_cds_overlap works correctly"""
+    # Variant fully contains exon (negative strand)
+    resp = test_feature_overlap.get_grch38_mane_gene_cds_overlap(
+        140726490, 140726520, identifier="ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul"
+    )
+    assert resp == {
+        "BRAF": [
+            {
+                "cds": {
+                    "id": "ga4gh:SL.fYRYzNIAoe6UQF9MT1XaYsFscoU68ZJv",
+                    "digest": "fYRYzNIAoe6UQF9MT1XaYsFscoU68ZJv",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
+                        "type": "SequenceReference",
+                    },
+                    "start": 140726493,
+                    "end": 140726516,
+                },
+                "overlap": {
+                    "id": "ga4gh:SL.fYRYzNIAoe6UQF9MT1XaYsFscoU68ZJv",
+                    "digest": "fYRYzNIAoe6UQF9MT1XaYsFscoU68ZJv",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
+                        "type": "SequenceReference",
+                    },
+                    "start": 140726493,
+                    "end": 140726516,
+                },
+            }
+        ]
+    }
+
+    expected = {
+        "BRAF": [
+            {
+                "cds": {
+                    "id": "ga4gh:SL.fYRYzNIAoe6UQF9MT1XaYsFscoU68ZJv",
+                    "digest": "fYRYzNIAoe6UQF9MT1XaYsFscoU68ZJv",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
+                        "type": "SequenceReference",
+                    },
+                    "start": 140726493,
+                    "end": 140726516,
+                },
+                "overlap": {
+                    "id": "ga4gh:SL.rMJlP7STVHBdvcCMgHkA4XJXXIdXnsix",
+                    "digest": "rMJlP7STVHBdvcCMgHkA4XJXXIdXnsix",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
+                        "type": "SequenceReference",
+                    },
+                    "start": 140726500,
+                    "end": 140726501,
+                },
+            }
+        ]
+    }
+
+    # Using residue (start == stop)
+    resp = test_feature_overlap.get_grch38_mane_gene_cds_overlap(
+        140726501,
+        140726501,
+        identifier="ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
+        coordinate_type=CoordinateType.RESIDUE,
+    )
+    assert resp == expected
+
+    # Using inter-residue
+    resp = test_feature_overlap.get_grch38_mane_gene_cds_overlap(
+        140726500,
+        140726501,
+        identifier="ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
+        coordinate_type=CoordinateType.INTER_RESIDUE,
+    )
+    assert resp == expected
+
+    # Variant is fully contained within exon (positive strand)
+    resp = test_feature_overlap.get_grch38_mane_gene_cds_overlap(
+        55019308, 55019341, chromosome="7"
+    )
+    assert resp == {
+        "EGFR": [
+            {
+                "cds": {
+                    "id": "ga4gh:SL.vjxcgicBFEkN8b8AXhagvUDC7FZgZgCp",
+                    "digest": "vjxcgicBFEkN8b8AXhagvUDC7FZgZgCp",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
+                        "type": "SequenceReference",
+                    },
+                    "start": 55019277,
+                    "end": 55019365,
+                },
+                "overlap": {
+                    "id": "ga4gh:SL.a_MHSA9TJ5zMkxd52eBuRUNb5ZIXHH7T",
+                    "digest": "a_MHSA9TJ5zMkxd52eBuRUNb5ZIXHH7T",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
+                        "type": "SequenceReference",
+                    },
+                    "start": 55019307,
+                    "end": 55019341,
+                },
+            }
+        ]
+    }
+
+    # Variant partially overlaps with exon, from the exon's start side (negative strand)
+    resp = test_feature_overlap.get_grch38_mane_gene_cds_overlap(
+        140726503, 140726520, chromosome="7"
+    )
+    assert resp == {
+        "BRAF": [
+            {
+                "cds": {
+                    "id": "ga4gh:SL.fYRYzNIAoe6UQF9MT1XaYsFscoU68ZJv",
+                    "digest": "fYRYzNIAoe6UQF9MT1XaYsFscoU68ZJv",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
+                        "type": "SequenceReference",
+                    },
+                    "start": 140726493,
+                    "end": 140726516,
+                },
+                "overlap": {
+                    "id": "ga4gh:SL.MdSOBEGp0l8wT3y1taeRvVIEi_XDBIGK",
+                    "digest": "MdSOBEGp0l8wT3y1taeRvVIEi_XDBIGK",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
+                        "type": "SequenceReference",
+                    },
+                    "start": 140726502,
+                    "end": 140726516,
+                },
+            }
+        ]
+    }
+
+    # Variant partially overlaps with exon, from the exon's stop side (negative strand)
+    resp = test_feature_overlap.get_grch38_mane_gene_cds_overlap(
+        140726490, 140726505, identifier="NC_000007.14"
+    )
+    assert resp == {
+        "BRAF": [
+            {
+                "cds": {
+                    "id": "ga4gh:SL.fYRYzNIAoe6UQF9MT1XaYsFscoU68ZJv",
+                    "digest": "fYRYzNIAoe6UQF9MT1XaYsFscoU68ZJv",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
+                        "type": "SequenceReference",
+                    },
+                    "start": 140726493,
+                    "end": 140726516,
+                },
+                "overlap": {
+                    "id": "ga4gh:SL.Rjvup1y8hPgveXiYnj7dipqYkt3BaFZE",
+                    "digest": "Rjvup1y8hPgveXiYnj7dipqYkt3BaFZE",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
+                        "type": "SequenceReference",
+                    },
+                    "start": 140726493,
+                    "end": 140726505,
+                },
+            }
+        ]
+    }
+
+    # Variant overlaps with multiple exons (positive strand)
+    resp = test_feature_overlap.get_grch38_mane_gene_cds_overlap(
+        21522390, 21523491, chromosome="Y"
+    )
+    assert resp == {
+        "RBMY1B": [
+            {
+                "cds": {
+                    "id": "ga4gh:SL.3fbgdG4Z2a1fqkqkY8M2bQMfBhJsVr_i",
+                    "digest": "3fbgdG4Z2a1fqkqkY8M2bQMfBhJsVr_i",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5",
+                        "type": "SequenceReference",
+                    },
+                    "start": 21522382,
+                    "end": 21522493,
+                },
+                "overlap": {
+                    "id": "ga4gh:SL.XSqmOKSXECFtfjhcvVDmga72xQ0jVGO7",
+                    "digest": "XSqmOKSXECFtfjhcvVDmga72xQ0jVGO7",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5",
+                        "type": "SequenceReference",
+                    },
+                    "start": 21522389,
+                    "end": 21522493,
+                },
+            },
+            {
+                "cds": {
+                    "id": "ga4gh:SL.wi_fCVQHmZCOUf--3UPKm6johAu3zQYJ",
+                    "digest": "wi_fCVQHmZCOUf--3UPKm6johAu3zQYJ",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5",
+                        "type": "SequenceReference",
+                    },
+                    "start": 21522934,
+                    "end": 21523045,
+                },
+                "overlap": {
+                    "id": "ga4gh:SL.wi_fCVQHmZCOUf--3UPKm6johAu3zQYJ",
+                    "digest": "wi_fCVQHmZCOUf--3UPKm6johAu3zQYJ",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5",
+                        "type": "SequenceReference",
+                    },
+                    "start": 21522934,
+                    "end": 21523045,
+                },
+            },
+            {
+                "cds": {
+                    "id": "ga4gh:SL.cnULzfdHZPiY6rSQP2Prfzocf1_YOBGA",
+                    "digest": "cnULzfdHZPiY6rSQP2Prfzocf1_YOBGA",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5",
+                        "type": "SequenceReference",
+                    },
+                    "start": 21523479,
+                    "end": 21523590,
+                },
+                "overlap": {
+                    "id": "ga4gh:SL.kHLoQs5cjOqjztK9yZyyVR9ScKCM1S8f",
+                    "digest": "kHLoQs5cjOqjztK9yZyyVR9ScKCM1S8f",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5",
+                        "type": "SequenceReference",
+                    },
+                    "start": 21523479,
+                    "end": 21523491,
+                },
+            },
+        ]
+    }
+
+    # Variant overlaps with multiple exons (negative strand)
+    resp = test_feature_overlap.get_grch38_mane_gene_cds_overlap(
+        154779177, 154781317, chromosome="X"
+    )
+    assert resp == {
+        "MPP1": [
+            {
+                "cds": {
+                    "id": "ga4gh:SL.dnHzxh-VwjVdanLcvKkI1otKhZeY223-",
+                    "digest": "dnHzxh-VwjVdanLcvKkI1otKhZeY223-",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP",
+                        "type": "SequenceReference",
+                    },
+                    "start": 154781238,
+                    "end": 154781313,
+                },
+                "overlap": {
+                    "id": "ga4gh:SL.dnHzxh-VwjVdanLcvKkI1otKhZeY223-",
+                    "digest": "dnHzxh-VwjVdanLcvKkI1otKhZeY223-",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP",
+                        "type": "SequenceReference",
+                    },
+                    "start": 154781238,
+                    "end": 154781313,
+                },
+            },
+            {
+                "cds": {
+                    "id": "ga4gh:SL.Z4jQtiT0-FplZWGVA1wNhdCaCMKGQ17D",
+                    "digest": "Z4jQtiT0-FplZWGVA1wNhdCaCMKGQ17D",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP",
+                        "type": "SequenceReference",
+                    },
+                    "start": 154779176,
+                    "end": 154779353,
+                },
+                "overlap": {
+                    "id": "ga4gh:SL.Z4jQtiT0-FplZWGVA1wNhdCaCMKGQ17D",
+                    "digest": "Z4jQtiT0-FplZWGVA1wNhdCaCMKGQ17D",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP",
+                        "type": "SequenceReference",
+                    },
+                    "start": 154779176,
+                    "end": 154779353,
+                },
+            },
+        ]
+    }
+
+    # Variant overlap with cds in multiple genes and alt chromosome accession
+    # chr19_KI270930v1_alt with exact start/stop CDS
+    resp = test_feature_overlap.get_grch38_mane_gene_cds_overlap(
+        135329, 135381, chromosome="19"
+    )
+    expected = {
+        "KIR2DL5B": [
+            {
+                "cds": {
+                    "id": "ga4gh:SL.tR0TL0hHD3udyK9at0snGQ3zNSmhCz6K",
+                    "digest": "tR0TL0hHD3udyK9at0snGQ3zNSmhCz6K",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl",
+                        "type": "SequenceReference",
+                    },
+                    "start": 135328,
+                    "end": 135381,
+                },
+                "overlap": {
+                    "id": "ga4gh:SL.tR0TL0hHD3udyK9at0snGQ3zNSmhCz6K",
+                    "digest": "tR0TL0hHD3udyK9at0snGQ3zNSmhCz6K",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl",
+                        "type": "SequenceReference",
+                    },
+                    "start": 135328,
+                    "end": 135381,
+                },
+            }
+        ],
+        "FCGBP": [
+            {
+                "cds": {
+                    "id": "ga4gh:SL.3G3gZfvJ56-y-TRWNSAUHUmyPi_8X3qK",
+                    "digest": "3G3gZfvJ56-y-TRWNSAUHUmyPi_8X3qK",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl",
+                        "type": "SequenceReference",
+                    },
+                    "start": 135263,
+                    "end": 135807,
+                },
+                "overlap": {
+                    "id": "ga4gh:SL.tR0TL0hHD3udyK9at0snGQ3zNSmhCz6K",
+                    "digest": "tR0TL0hHD3udyK9at0snGQ3zNSmhCz6K",
+                    "type": "SequenceLocation",
+                    "sequenceReference": {
+                        "refgetAccession": "SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl",
+                        "type": "SequenceReference",
+                    },
+                    "start": 135328,
+                    "end": 135381,
+                },
+            }
+        ],
+    }
+    assert resp == expected
+
+    # Using inter-residue (start != stop)
+    resp = test_feature_overlap.get_grch38_mane_gene_cds_overlap(
+        135328, 135381, chromosome="19", coordinate_type=CoordinateType.INTER_RESIDUE
+    )
+    assert resp == expected
+
+    # No overlap found
+    resp = test_feature_overlap.get_grch38_mane_gene_cds_overlap(1, 2, chromosome="19")
+    assert resp is None
+
+    # Testing invalid
+
+    # chromosome does not match regex pattern
+    with pytest.raises(FeatureOverlapError) as e:
+        test_feature_overlap.get_grch38_mane_gene_cds_overlap(
+            154779177, 154781317, chromosome="chrX"
+        )
+    assert str(e.value) == "`chromosome` must be 1, ..., 22, X, or Y"
+
+    # identifier is GRCh37
+    with pytest.raises(FeatureOverlapError) as e:
+        test_feature_overlap.get_grch38_mane_gene_cds_overlap(
+            154779177, 154781317, identifier="NC_000023.10"
+        )
+    assert str(e.value) == "Unable to find GRCh38 aliases for: NC_000023.10"
+
+    # no identifier or chromosome provided
+    with pytest.raises(FeatureOverlapError) as e:
+        test_feature_overlap.get_grch38_mane_gene_cds_overlap(154779177, 154781317)
+    assert str(e.value) == "Must provide either `chromosome` or `identifier`"

{cool_seq_tool-0.14.1 → cool_seq_tool-0.14.2}/tests/mappers/test_mane_transcript.py

@@ -298,8 +298,8 @@ async def test_g_to_c(
 
 def test_set_liftover(test_mane_transcript, genomic_tx_data):
     """Test that _set_liftover works correctly."""
-    cpy = genomic_tx_data.copy(deep=True)
-    expected = genomic_tx_data.copy(deep=True)
+    cpy = genomic_tx_data.model_copy(deep=True)
+    expected = genomic_tx_data.model_copy(deep=True)
     test_mane_transcript._set_liftover(cpy, "alt_pos_range", "chr7", "GRCh38")
     expected.alt_pos_range = (140739811, 140739946)
     assert cpy == expected
@@ -311,8 +311,8 @@ def test_set_liftover(test_mane_transcript, genomic_tx_data):
 @pytest.mark.asyncio
 async def test_liftover_to_38(test_mane_transcript, genomic_tx_data):
     """Test that liftover_to_38 works correctly."""
-    cpy = genomic_tx_data.copy(deep=True)
-    expected = genomic_tx_data.copy(deep=True)
+    cpy = genomic_tx_data.model_copy(deep=True)
+    expected = genomic_tx_data.model_copy(deep=True)
     await test_mane_transcript._liftover_to_38(cpy)
     expected.alt_ac = "NC_000007.14"
     expected.alt_pos_change_range = (140739903, 140739903)
@@ -675,7 +675,7 @@ async def test_g_to_grch38(test_mane_transcript, grch38_egfr, grch38_braf):
     resp = await test_mane_transcript.g_to_grch38(
         "NC_000007.13", 55259515, 55259515, get_mane_genes=False
     )
-    grch38_egfr_no_genes = grch38_egfr.copy()
+    grch38_egfr_no_genes = grch38_egfr.model_copy()
     grch38_egfr_no_genes.mane_genes = []
     assert resp == grch38_egfr_no_genes