cool-seq-tool 0.5.1__py3-none-any.whl → 0.7.0__py3-none-any.whl

cool_seq_tool/schemas.py

@@ -9,7 +9,6 @@ from pydantic import (
     ConfigDict,
     StrictInt,
     StrictStr,
-    model_validator,
 )
 
 from cool_seq_tool import __version__
@@ -20,9 +19,9 @@ _now = str(datetime.datetime.now(tz=datetime.timezone.utc))
 class AnnotationLayer(str, Enum):
     """Create enum for supported annotation layers"""
 
-    PROTEIN: Literal["p"] = "p"
-    CDNA: Literal["c"] = "c"
-    GENOMIC: Literal["g"] = "g"
+    PROTEIN = "p"
+    CDNA = "c"
+    GENOMIC = "g"
 
 
 class Strand(IntEnum):
@@ -53,15 +52,17 @@ class TranscriptPriority(str, Enum):
     GRCH38 = "grch38"
 
 
-class ResidueMode(str, Enum):
-    """Create Enum for residue modes.
+class CoordinateType(str, Enum):
+    """Create Enum for coordinate types.
 
-    We typically prefer to operate in inter-residue coordinates, but users should be
+    It is preferred to operate in inter-residue coordinates, but users should be
     careful to define the coordinate mode of their data when calling ``cool-seq-tool``
     functions.
 
+    ``RESIDUE`` means 1-indexed, residue coordinates and ``INTER_RESIDUE`` means
+    0-indexed, inter-residue coordinates.
+
                       |   | C |   | T |   | G |   |
-    ZERO              |   | 0 |   | 1 |   | 2 |   |
     RESIDUE           |   | 1 |   | 2 |   | 3 |   |
     INTER_RESIDUE     | 0 |   | 1 |   | 2 |   | 3 |
 
@@ -77,14 +78,6 @@ class ResidueMode(str, Enum):
          -
          - G
          -
-       * - ``ZERO``
-         -
-         - 0
-         -
-         - 1
-         -
-         - 2
-         -
        * - ``RESIDUE``
          -
          - 1
@@ -107,7 +100,6 @@ class ResidueMode(str, Enum):
     `Variation Representation Schema (VRS) paper <https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/35311178/>`_ for further discussion.
     """
 
-    ZERO = "zero"
     RESIDUE = "residue"
     INTER_RESIDUE = "inter-residue"
 
@@ -116,157 +108,35 @@ class BaseModelForbidExtra(BaseModel, extra="forbid"):
     """Base Pydantic model class with extra values forbidden."""
 
 
-class GenomicRequestBody(BaseModelForbidExtra):
-    """Define constraints for genomic to transcript exon coordinates request body"""
-
-    chromosome: StrictStr | StrictInt
-    start: StrictInt | None = None
-    end: StrictInt | None = None
-    strand: Strand | None = None
-    transcript: StrictStr | None = None
-    gene: StrictStr | None = None
-    residue_mode: ResidueMode = ResidueMode.RESIDUE
-
-    @model_validator(mode="after")
-    def check_start_and_end(cls, values):
-        """Check that at least one of {``start``, ``end``} is set"""
-        start, end = values.start, values.end
-        if not start or end:
-            msg = "Must provide either `start` or `end`"
-            raise ValueError(msg)
-        return values
-
-    model_config = ConfigDict(
-        json_schema_extra={
-            "example": {
-                "chromosome": "NC_000001.11",
-                "start": 154192135,
-                "end": None,
-                "strand": Strand.NEGATIVE,
-                "transcript": "NM_152263.3",
-                "gene": "TPM3",
-                "residue_mode": "residue",
-            }
-        }
-    )
-
-
-class TranscriptRequestBody(BaseModelForbidExtra):
-    """Define constraints for transcript exon to genomic coordinates request body"""
+class GenomicTxData(BaseModelForbidExtra):
+    """Represent aligned genomic/transcript exon data"""
 
-    transcript: StrictStr
-    gene: StrictStr | None = None
-    exon_start: StrictInt | None = None
-    exon_start_offset: StrictInt | None = 0
-    exon_end: StrictInt | None = None
-    exon_end_offset: StrictInt | None = 0
-
-    @model_validator(mode="after")
-    def check_exon_start_and_exon_end(cls, values):
-        """Check that at least one of {``exon_start``, ``exon_end``} is set"""
-        exon_start, exon_end = values.exon_start, values.exon_end
-        if not exon_start or exon_end:
-            msg = "Must provide either `exon_start` or `exon_end`"
-            raise ValueError(msg)
-        return values
-
-    model_config = ConfigDict(
-        json_schema_extra={
-            "example": {
-                "gene": "TPM3",
-                "transcript": "NM_152263.3",
-                "exon_start": 1,
-                "exon_start_offset": 1,
-                "exon_end": None,
-                "exon_end_offset": None,
-            }
-        }
-    )
-
-
-class TranscriptExonData(BaseModelForbidExtra):
-    """Model containing transcript exon data."""
-
-    transcript: StrictStr
-    pos: StrictInt
-    exon: StrictInt
-    exon_offset: StrictInt = 0
-    gene: StrictStr
-    chr: StrictStr
+    gene: str
     strand: Strand
+    tx_pos_range: tuple[int, int]
+    alt_pos_range: tuple[int, int]
+    alt_aln_method: str
+    tx_exon_id: int
+    alt_exon_id: int
 
-    model_config = ConfigDict(
-        json_schema_extra={
-            "example": {
-                "chr": "NC_000001.11",
-                "gene": "TPM3",
-                "pos": 154192135,
-                "exon": 1,
-                "exon_offset": 0,
-                "transcript": "NM_152263.3",
-                "strand": Strand.NEGATIVE,
-            }
-        }
-    )
 
+class GenomicTxMetadata(GenomicTxData):
+    """Store relevant metadata for genomic and transcript accessions"""
 
-class GenomicData(BaseModelForbidExtra):
-    """Model containing genomic and transcript exon data."""
+    tx_ac: str
+    alt_ac: str
+    coding_start_site: int = 0
+    coding_end_site: int = 0
+    alt_pos_change_range: tuple[int, int]
+    pos_change: tuple[int, int] | None
 
-    gene: StrictStr
-    chr: StrictStr
-    start: StrictInt | None = None  # Genomic start position
-    end: StrictInt | None = None  # Genomic end position
-    exon_start: StrictInt | None = None
-    exon_start_offset: StrictInt | None = 0
-    exon_end: StrictInt | None = None
-    exon_end_offset: StrictInt | None = 0
-    transcript: StrictStr
-    strand: Strand
 
-    @model_validator(mode="after")
-    def check_start_end(cls, values):
-        """Check that at least one of {``start``, ``end``} is set.
-        Check that at least one of {``exon_start``, ``exon_end``} is set.
-        If not set, set corresponding offset to ``None``
-        """
-        start = values.start
-        end = values.end
-        if not start and not end:
-            msg = "Missing values for `start` or `end`"
-            raise ValueError(msg)
-
-        if start:
-            if not values.exon_start:
-                msg = "Missing value `exon_start`"
-                raise ValueError(msg)
-        else:
-            values.exon_start_offset = None
-
-        if end:
-            if not values.exon_end:
-                msg = "Missing value `exon_end`"
-                raise ValueError(msg)
-        else:
-            values.exon_end_offset = None
-        return values
+class ManeGeneData(BaseModel, extra="forbid"):
+    """Define minimal object model for representing a MANE gene"""
 
-    model_config = ConfigDict(
-        json_schema_extra={
-            "example": {
-                "gene": "TPM3",
-                "chr": "NC_000001.11",
-                "start": 154192135,
-                "end": None,
-                "exon_start": 1,
-                "exon_end": None,
-                "exon_start_offset": 0,
-                "exon_end_offset": None,
-                "transcript": "NM_152263.3",
-                "strand": Strand.NEGATIVE,
-            }
-        }
-    )
+    ncbi_gene_id: StrictInt
+    hgnc_id: StrictInt | None
+    symbol: StrictStr
 
 
 class ServiceMeta(BaseModelForbidExtra):
@@ -289,281 +159,3 @@ class ServiceMeta(BaseModelForbidExtra):
             }
         }
     )
-
-
-class TranscriptExonDataResponse(BaseModelForbidExtra):
-    """Response model for Transcript Exon Data"""
-
-    transcript_exon_data: TranscriptExonData | None = None
-    warnings: list[StrictStr] = []
-    service_meta: ServiceMeta
-
-    model_config = ConfigDict(
-        json_schema_extra={
-            "example": {
-                "transcript_exon_data": {
-                    "chr": "NC_000001.11",
-                    "gene": "TPM3",
-                    "pos": 154192135,
-                    "exon": 1,
-                    "exon_offset": 0,
-                    "transcript": "NM_152263.3",
-                    "strand": Strand.NEGATIVE,
-                },
-                "warnings": [],
-                "service_meta": {
-                    "name": "cool_seq_tool",
-                    "version": __version__,
-                    "response_datetime": _now,
-                    "url": "https://github.com/GenomicMedLab/cool-seq-tool",
-                },
-            }
-        }
-    )
-
-
-class GenomicDataResponse(BaseModelForbidExtra):
-    """Response model for Genomic Data"""
-
-    genomic_data: GenomicData | None = None
-    warnings: list[StrictStr] = []
-    service_meta: ServiceMeta
-
-    model_config = ConfigDict(
-        json_schema_extra={
-            "example": {
-                "genomic_data": {
-                    "gene": "TPM3",
-                    "chr": "NC_000001.11",
-                    "start": 154192135,
-                    "end": None,
-                    "exon_start": 1,
-                    "exon_end": None,
-                    "exon_start_offset": 0,
-                    "exon_end_offset": None,
-                    "transcript": "NM_152263.3",
-                    "strand": Strand.NEGATIVE,
-                },
-                "warnings": [],
-                "service_meta": {
-                    "name": "cool_seq_tool",
-                    "version": __version__,
-                    "response_datetime": _now,
-                    "url": "https://github.com/GenomicMedLab/cool-seq-tool",
-                },
-            }
-        }
-    )
-
-
-class MappedManeData(BaseModel):
-    """Define mapped mane data fields"""
-
-    gene: StrictStr
-    refseq: StrictStr
-    ensembl: StrictStr | None = None
-    strand: Strand
-    status: TranscriptPriority
-    alt_ac: StrictStr
-    assembly: Assembly
-
-    model_config = ConfigDict(
-        json_schema_extra={
-            "example": {
-                "gene": "BRAF",
-                "refseq": "NM_001374258.1",
-                "ensembl": "ENST00000644969.2",
-                "strand": Strand.NEGATIVE,
-                "status": TranscriptPriority.MANE_PLUS_CLINICAL,
-                "alt_ac": "NC_000007.13",
-                "assembly": Assembly.GRCH37,
-            }
-        }
-    )
-
-
-class MappedManeDataService(BaseModelForbidExtra):
-    """Service model response for mapped mane data"""
-
-    mapped_mane_data: MappedManeData | None = None
-    warnings: list[StrictStr] = []
-    service_meta: ServiceMeta
-
-    model_config = ConfigDict(
-        json_schema_extra={
-            "example": {
-                "mapped_mane_data": {
-                    "gene": "BRAF",
-                    "refseq": "NM_001374258.1",
-                    "ensembl": "ENST00000644969.2",
-                    "strand": Strand.NEGATIVE,
-                    "status": TranscriptPriority.MANE_PLUS_CLINICAL,
-                    "alt_ac": "NC_000007.13",
-                    "assembly": Assembly.GRCH37,
-                },
-                "warnings": [],
-                "service_meta": {
-                    "name": "cool_seq_tool",
-                    "version": __version__,
-                    "response_datetime": _now,
-                    "url": "https://github.com/GenomicMedLab/cool-seq-tool",
-                },
-            }
-        }
-    )
-
-
-class ManeData(BaseModel):
-    """Define mane data fields"""
-
-    gene: StrictStr | None = None
-    refseq: StrictStr | None = None
-    ensembl: StrictStr | None = None
-    pos: tuple[int, int]
-    strand: Strand
-    status: TranscriptPriority
-
-    model_config = ConfigDict(
-        json_schema_extra={
-            "example": {
-                "gene": "BRAF",
-                "refseq": "NP_004324.2",
-                "ensembl": "ENSP00000493543.1",
-                "pos": (598, 598),
-                "strand": Strand.NEGATIVE,
-                "status": TranscriptPriority.MANE_SELECT,
-            }
-        }
-    )
-
-
-class ManeDataService(BaseModelForbidExtra):
-    """Service model response for getting mane data"""
-
-    mane_data: ManeData | None = None
-    warnings: list[StrictStr] = []
-    service_meta: ServiceMeta
-
-    model_config = ConfigDict(
-        json_schema_extra={
-            "example": {
-                "mane_data": {
-                    "gene": "BRAF",
-                    "refseq": "NP_004324.2",
-                    "ensembl": "ENSP00000493543.1",
-                    "pos": (598, 598),
-                    "strand": Strand.NEGATIVE,
-                    "status": TranscriptPriority.MANE_SELECT,
-                },
-                "warnings": [],
-                "service_meta": {
-                    "name": "cool_seq_tool",
-                    "version": __version__,
-                    "response_datetime": _now,
-                    "url": "https://github.com/GenomicMedLab/cool-seq-tool",
-                },
-            }
-        }
-    )
-
-
-# ALIGNMENT MAPPER SERVICE SCHEMAS
-
-
-class CdnaRepresentation(BaseModelForbidExtra):
-    """Model response for cDNA representation"""
-
-    c_ac: StrictStr
-    c_start_pos: StrictInt
-    c_end_pos: StrictInt
-    cds_start: StrictInt
-    residue_mode: Literal[ResidueMode.INTER_RESIDUE] = ResidueMode.INTER_RESIDUE.value
-
-    model_config = ConfigDict(
-        json_schema_extra={
-            "example": {
-                "c_ac": "NM_004333.6",
-                "c_start_pos": 1797,
-                "c_end_pos": 1800,
-                "cds_start": 226,
-                "residue_mode": ResidueMode.INTER_RESIDUE,
-            }
-        }
-    )
-
-
-class ToCdnaService(BaseModelForbidExtra):
-    """Service model response for protein -> cDNA"""
-
-    c_data: CdnaRepresentation | None = None
-    warnings: list[StrictStr] = []
-    service_meta: ServiceMeta
-
-    model_config = ConfigDict(
-        json_schema_extra={
-            "example": {
-                "c_data": {
-                    "c_ac": "NM_004333.6",
-                    "c_start_pos": 1797,
-                    "c_end_pos": 1800,
-                    "cds_start": 226,
-                    "residue_mode": ResidueMode.INTER_RESIDUE,
-                },
-                "warnings": [],
-                "service_meta": {
-                    "name": "cool_seq_tool",
-                    "version": __version__,
-                    "response_datetime": _now,
-                    "url": "https://github.com/GenomicMedLab/cool-seq-tool",
-                },
-            }
-        }
-    )
-
-
-class GenomicRepresentation(BaseModelForbidExtra):
-    """Model response for genomic representation"""
-
-    g_ac: str
-    g_start_pos: int
-    g_end_pos: int
-    residue_mode: Literal[ResidueMode.INTER_RESIDUE] = ResidueMode.INTER_RESIDUE.value
-
-    model_config = ConfigDict(
-        json_schema_extra={
-            "example": {
-                "g_ac": "NC_000007.13",
-                "g_start_pos": 140453134,
-                "g_end_pos": 140453137,
-                "residue_mode": ResidueMode.INTER_RESIDUE,
-            }
-        }
-    )
-
-
-class ToGenomicService(BaseModelForbidExtra):
-    """Service model response for cDNA -> genomic"""
-
-    g_data: GenomicRepresentation | None = None
-    warnings: list[StrictStr] = []
-    service_meta: ServiceMeta
-
-    model_config = ConfigDict(
-        json_schema_extra={
-            "example": {
-                "g_data": {
-                    "g_ac": "NC_000007.13",
-                    "g_start_pos": 140453134,
-                    "g_end_pos": 140453137,
-                    "residue_mode": ResidueMode.INTER_RESIDUE,
-                },
-                "warnings": [],
-                "service_meta": {
-                    "name": "cool_seq_tool",
-                    "version": __version__,
-                    "response_datetime": _now,
-                    "url": "https://github.com/GenomicMedLab/cool-seq-tool",
-                },
-            }
-        }
-    )

cool_seq_tool/sources/mane_transcript_mappings.py

@@ -8,6 +8,7 @@ from pathlib import Path
 import polars as pl
 
 from cool_seq_tool.resources.data_files import DataFile, get_data_file
+from cool_seq_tool.schemas import ManeGeneData
 
 _logger = logging.getLogger(__name__)
 
@@ -103,3 +104,37 @@ class ManeTranscriptMappings:
 
         mane_rows = mane_rows.sort(by="MANE_status", descending=True)
         return mane_rows.to_dicts()
+
+    def get_genomic_mane_genes(
+        self, ac: str, start: int, end: int
+    ) -> list[ManeGeneData]:
+        """Get MANE gene(s) for genomic location
+
+        :param ac: RefSeq genomic accession
+        :param start: Genomic start position. Assumes residue coordinates.
+        :param end: Genomic end position. Assumes residue coordinates.
+        :return: Unique MANE gene(s) found for a genomic location
+        """
+        mane_rows = self.df.filter(
+            (start >= pl.col("chr_start"))
+            & (end <= pl.col("chr_end"))
+            & (pl.col("GRCh38_chr") == ac)
+        ).unique(subset=["#NCBI_GeneID"])
+
+        if len(mane_rows) == 0:
+            return []
+
+        mane_rows = mane_rows.with_columns(
+            pl.col("#NCBI_GeneID")
+            .str.split_exact(":", 1)
+            .struct.field("field_1")
+            .cast(pl.Int32)
+            .alias("ncbi_gene_id"),
+            pl.col("HGNC_ID")
+            .str.split_exact(":", 1)
+            .struct.field("field_1")
+            .cast(pl.Int32)
+            .alias("hgnc_id"),
+        )
+        mane_rows = mane_rows.select(["ncbi_gene_id", "hgnc_id", "symbol"])
+        return [ManeGeneData(**mane_gene) for mane_gene in mane_rows.to_dicts()]