cool-seq-tool 0.5.0__py3-none-any.whl → 0.6.0__py3-none-any.whl

cool_seq_tool/mappers/exon_genomic_coords.py

@@ -962,7 +962,7 @@ class ExonGenomicCoordsMapper:
             exon = tx_exons_genomic_coords[i]
             next_exon = tx_exons_genomic_coords[i + 1]
             bp = start if start else end
-            if strand == strand.POSITIVE:
+            if strand == Strand.POSITIVE:
                 lte_exon = exon
                 gte_exon = next_exon
             else:

cool_seq_tool/mappers/mane_transcript.py

@@ -25,6 +25,7 @@ from cool_seq_tool.mappers.liftover import LiftOver
 from cool_seq_tool.schemas import (
     AnnotationLayer,
     Assembly,
+    ManeGeneData,
     ResidueMode,
     Strand,
     TranscriptPriority,
@@ -71,10 +72,10 @@ class CdnaRepresentation(DataRepresentation):
 class GenomicRepresentation(BaseModel):
     """Define object model for genomic representation"""
 
-    refseq: str
     pos: tuple[int, int]
-    status: TranscriptPriority
-    alt_ac: str
+    mane_genes: list[ManeGeneData] = []
+    status: Literal["grch38"] = TranscriptPriority.GRCH38.value
+    ac: str
 
 
 class ProteinAndCdnaRepresentation(BaseModel):
@@ -108,7 +109,7 @@ class ManeTranscript:
 
         >>> import asyncio
         >>> result = asyncio.run(mane_mapper.g_to_grch38("NC_000001.11", 100, 200))
-        >>> result["ac"]
+        >>> result.ac
         'NC_000001.11'
 
         See the :ref:`Usage section <async_note>` for more information.
@@ -128,7 +129,7 @@ class ManeTranscript:
         self.liftover = liftover
 
     @staticmethod
-    def _get_reading_frame(pos: int) -> int:
+    def get_reading_frame(pos: int) -> int:
         """Return reading frame number. Only used on c. coordinate.
 
         :param pos: cDNA position
@@ -531,8 +532,8 @@ class ManeTranscript:
         """
         for pos, pos_index in [(start_pos, 0), (end_pos, 1)]:
             if pos is not None:
-                og_rf = self._get_reading_frame(pos)
-                new_rf = self._get_reading_frame(transcript_data.pos[pos_index])
+                og_rf = self.get_reading_frame(pos)
+                new_rf = self.get_reading_frame(transcript_data.pos[pos_index])
 
                 if og_rf != new_rf:
                     _logger.warning(
@@ -618,7 +619,7 @@ class ManeTranscript:
 
         return True
 
-    def _validate_index(
+    def validate_index(
         self, ac: str, pos: tuple[int, int], coding_start_site: int
     ) -> bool:
         """Validate that positions actually exist on accession
@@ -910,7 +911,7 @@ class ManeTranscript:
                 ac = lcr_result.refseq or lcr_result.ensembl
                 pos = lcr_result.pos
 
-                if not self._validate_index(ac, pos, coding_start_site):
+                if not self.validate_index(ac, pos, coding_start_site):
                     _logger.warning(
                         "%s are not valid positions on %s with coding start site %s",
                         pos,
@@ -936,7 +937,7 @@ class ManeTranscript:
                 cds = lcr_result_dict[k].get("coding_start_site", 0)
                 ac = lcr_result_dict[k]["refseq"] or lcr_result_dict[k]["ensembl"]
                 pos = lcr_result_dict[k]["pos"]
-                if not self._validate_index(ac, pos, cds):
+                if not self.validate_index(ac, pos, cds):
                     valid = False
                     _logger.warning(
                         "%s are not valid positions on %s with coding start site %s",
@@ -962,7 +963,16 @@ class ManeTranscript:
         residue_mode: Literal[ResidueMode.RESIDUE]
         | Literal[ResidueMode.INTER_RESIDUE] = ResidueMode.RESIDUE,
     ) -> DataRepresentation | CdnaRepresentation | None:
-        """Return MANE transcript.
+        """Return MANE representation
+
+        If ``start_annotation_layer`` is ``AnnotationLayer.PROTEIN``, will return
+            ``AnnotationLayer.PROTEIN`` representation.
+        If ``start_annotation_layer`` is ``AnnotationLayer.CDNA``, will return
+            ``AnnotationLayer.CDNA`` representation.
+        If ``start_annotation_layer`` is ``AnnotationLayer.GENOMIC`` will return
+            ``AnnotationLayer.CDNA`` representation if ``gene`` is provided and
+            ``AnnotationLayer.GENOMIC`` GRCh38 representation if ``gene`` is NOT
+            provided.
 
         >>> from cool_seq_tool.app import CoolSeqTool
         >>> from cool_seq_tool.schemas import AnnotationLayer, ResidueMode
@@ -983,7 +993,11 @@ class ManeTranscript:
         :param start_pos: Start position change
         :param end_pos: End position change
         :param start_annotation_layer: Starting annotation layer.
-        :param gene: HGNC gene symbol
+        :param gene: HGNC gene symbol.
+            If ``gene`` is not provided and ``start_annotation_layer`` is
+            ``AnnotationLayer.GENOMIC``, will return GRCh38 representation.
+            If ``gene`` is provided and ``start_annotation_layer`` is
+            ``AnnotationLayer.GENOMIC``, will return cDNA representation.
         :param ref: Reference at position given during input
         :param try_longest_compatible: ``True`` if should try longest compatible remaining
             if mane transcript was not compatible. ``False`` otherwise.
@@ -1093,29 +1107,56 @@ class ManeTranscript:
                 )
             return None
         if start_annotation_layer == AnnotationLayer.GENOMIC:
+            if not gene:
+                return await self.g_to_grch38(
+                    ac,
+                    start_pos,
+                    end_pos,
+                    get_mane_genes=True,
+                    residue_mode=residue_mode,
+                )
+
             return await self.g_to_mane_c(
-                ac, start_pos, end_pos, gene=gene, residue_mode=residue_mode
+                ac, start_pos, end_pos, gene, residue_mode=residue_mode
             )
         _logger.warning("Annotation layer not supported: %s", start_annotation_layer)
         return None
 
-    async def g_to_grch38(self, ac: str, start_pos: int, end_pos: int) -> dict | None:
+    async def g_to_grch38(
+        self,
+        ac: str,
+        start_pos: int,
+        end_pos: int,
+        get_mane_genes: bool = False,
+        residue_mode: ResidueMode = ResidueMode.RESIDUE,
+    ) -> GenomicRepresentation | None:
         """Return genomic coordinate on GRCh38 when not given gene context.
 
         :param ac: Genomic accession
         :param start_pos: Genomic start position
         :param end_pos: Genomic end position
-        :return: NC accession, start and end pos on GRCh38 assembly
+        :param get_mane_genes: ``True`` if mane genes for genomic position should be
+            included in response. ``False``, otherwise.
+        :param residue_mode: Residue mode for ``start_pos`` and ``end_pos``
+        :return: GRCh38 genomic representation (accession and start/end inter-residue
+            position)
         """
-        if end_pos is None:
-            end_pos = start_pos
+        start_pos, end_pos = get_inter_residue_pos(start_pos, end_pos, residue_mode)
 
         # Checking to see what chromosome and assembly we're on
         descr = await self.uta_db.get_chr_assembly(ac)
         if not descr:
             # Already GRCh38 assembly
-            if self._validate_index(ac, (start_pos, end_pos), 0):
-                return {"ac": ac, "pos": (start_pos, end_pos)}
+            if self.validate_index(ac, (start_pos, end_pos), 0):
+                return GenomicRepresentation(
+                    ac=ac,
+                    pos=(start_pos, end_pos),
+                    mane_genes=self.mane_transcript_mappings.get_genomic_mane_genes(
+                        ac, start_pos + 1, end_pos
+                    )
+                    if get_mane_genes
+                    else [],
+                )
             return None
         chromosome, assembly = descr
         is_same_pos = start_pos == end_pos
@@ -1145,8 +1186,16 @@ class ManeTranscript:
         newest_ac = await self.uta_db.get_newest_assembly_ac(ac)
         if newest_ac:
             ac = newest_ac[0]
-            if self._validate_index(ac, (start_pos, end_pos), 0):
-                return {"ac": ac, "pos": (start_pos, end_pos)}
+            if self.validate_index(ac, (start_pos, end_pos), 0):
+                return GenomicRepresentation(
+                    ac=ac,
+                    pos=(start_pos, end_pos),
+                    mane_genes=self.mane_transcript_mappings.get_genomic_mane_genes(
+                        ac, start_pos + 1, end_pos
+                    )
+                    if get_mane_genes
+                    else [],
+                )
         return None
 
     @staticmethod
@@ -1176,14 +1225,11 @@ class ManeTranscript:
         ac: str,
         start_pos: int,
         end_pos: int,
-        gene: str | None = None,
+        gene: str,
         residue_mode: ResidueMode = ResidueMode.RESIDUE,
-    ) -> GenomicRepresentation | CdnaRepresentation | None:
+    ) -> CdnaRepresentation | None:
         """Return MANE Transcript on the c. coordinate.
 
-        If an arg for ``gene`` is provided, lifts to GRCh38, then gets MANE cDNA
-        representation.
-
         >>> import asyncio
         >>> from cool_seq_tool.app import CoolSeqTool
         >>> cst = CoolSeqTool()
@@ -1198,34 +1244,17 @@ class ManeTranscript:
         <TranscriptPriority.MANE_SELECT: 'mane_select'>
         >>> del cst
 
-        Locating a MANE transcript requires a ``gene`` symbol argument -- if none is
-        given, this method will only lift over to genomic coordinates on GRCh38.
-
         :param ac: Transcript accession on g. coordinate
         :param start_pos: genomic start position
         :param end_pos: genomic end position
         :param gene: HGNC gene symbol
         :param residue_mode: Starting residue mode for ``start_pos`` and ``end_pos``.
             Will always return coordinates in inter-residue.
-        :return: MANE Transcripts with cDNA change on c. coordinate if gene
-            is provided. Else, GRCh38 data
+        :return: MANE Transcripts with cDNA change on c. coordinate
         """
         start_pos, end_pos = get_inter_residue_pos(start_pos, end_pos, residue_mode)
         residue_mode = ResidueMode.INTER_RESIDUE
 
-        # If gene not provided, return GRCh38
-        if not gene:
-            grch38 = await self.g_to_grch38(ac, start_pos, end_pos)
-            if not grch38:
-                return None
-
-            return GenomicRepresentation(
-                refseq=grch38["ac"],
-                pos=grch38["pos"],
-                status=TranscriptPriority.GRCH38,
-                alt_ac=grch38["ac"],
-            )
-
         if not await self.uta_db.validate_genomic_ac(ac):
             _logger.warning("Genomic accession does not exist: %s", ac)
             return None
@@ -1238,12 +1267,14 @@ class ManeTranscript:
             mane_c_ac = current_mane_data["RefSeq_nuc"]
 
             # Liftover to GRCh38
-            grch38 = await self.g_to_grch38(ac, start_pos, end_pos)
+            grch38 = await self.g_to_grch38(
+                ac, start_pos, end_pos, get_mane_genes=False, residue_mode=residue_mode
+            )
             mane_tx_genomic_data = None
             if grch38:
                 # GRCh38 -> MANE C
                 mane_tx_genomic_data = await self.uta_db.get_mane_c_genomic_data(
-                    mane_c_ac, grch38["ac"], grch38["pos"][0], grch38["pos"][1]
+                    mane_c_ac, grch38.ac, grch38.pos[0], grch38.pos[1]
                 )
 
             if not grch38 or not mane_tx_genomic_data:
@@ -1261,9 +1292,7 @@ class ManeTranscript:
                 mane_tx_genomic_data, coding_start_site
             )
 
-            if not self._validate_index(
-                mane_c_ac, mane_c_pos_change, coding_start_site
-            ):
+            if not self.validate_index(mane_c_ac, mane_c_pos_change, coding_start_site):
                 _logger.warning(
                     "%s are not valid positions on %s with coding start site %s",
                     mane_c_pos_change,
@@ -1284,7 +1313,7 @@ class ManeTranscript:
                 ),
                 refseq_c_ac=current_mane_data["RefSeq_nuc"],
                 ensembl_c_ac=current_mane_data["Ensembl_nuc"],
-                alt_ac=grch38["ac"] if grch38 else None,
+                alt_ac=grch38.ac if grch38 else None,
             )
         return None
 
@@ -1351,9 +1380,7 @@ class ManeTranscript:
             )
 
             # Validate MANE C positions
-            if not self._validate_index(
-                mane_c_ac, mane_c_pos_change, coding_start_site
-            ):
+            if not self.validate_index(mane_c_ac, mane_c_pos_change, coding_start_site):
                 _logger.warning(
                     "%s are not valid positions on %s with coding start site %s",
                     mane_c_pos_change,

cool_seq_tool/schemas.py

@@ -116,72 +116,12 @@ 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"""
+class ManeGeneData(BaseModel, extra="forbid"):
+    """Define minimal object model for representing a MANE gene"""
 
-    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"""
-
-    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,
-            }
-        }
-    )
+    ncbi_gene_id: StrictInt
+    hgnc_id: StrictInt | None
+    symbol: StrictStr
 
 
 class TranscriptExonData(BaseModelForbidExtra):
@@ -354,216 +294,3 @@ class GenomicDataResponse(BaseModelForbidExtra):
             }
         }
     )
-
-
-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()]

{cool_seq_tool-0.5.0.dist-info → cool_seq_tool-0.6.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cool_seq_tool
-Version: 0.5.0
+Version: 0.6.0
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -56,7 +56,7 @@ 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: pre-commit >=3.7.1 ; extra == 'dev'
 Requires-Dist: ipython ; extra == 'dev'
 Requires-Dist: ipykernel ; extra == 'dev'
 Requires-Dist: psycopg2-binary ; extra == 'dev'
@@ -69,11 +69,11 @@ Requires-Dist: sphinx-copybutton ==0.5.2 ; extra == 'docs'
 Requires-Dist: sphinxext-opengraph ==0.8.2 ; extra == 'docs'
 Requires-Dist: furo ==2023.3.27 ; extra == 'docs'
 Requires-Dist: sphinx-github-changelog ==1.2.1 ; extra == 'docs'
-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: mock ; extra == 'tests'
+Provides-Extra: test
+Requires-Dist: pytest ; extra == 'test'
+Requires-Dist: pytest-cov ; extra == 'test'
+Requires-Dist: pytest-asyncio ==0.18.3 ; extra == 'test'
+Requires-Dist: mock ; extra == 'test'
 
 <h1 align="center">
 CoolSeqTool

{cool_seq_tool-0.5.0.dist-info → cool_seq_tool-0.6.0.dist-info}/RECORD

@@ -1,24 +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/schemas.py,sha256=OfRoEEB-bJPvPtSh8GKDBMs_wdGljrSCkg9vPVqFeIw,8033
 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/exon_genomic_coords.py,sha256=McLXZcnDLdLSKR3eHnY4xJ0iLfCmSwAwK_RQXBV1AYQ,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/mappers/mane_transcript.py,sha256=Iv6J2Tjwt9cYAqoiEQ-XNEc8iRI3tXOONA6YjOv2huU,54241
 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/mane_transcript_mappings.py,sha256=E_pj7FEBcB6HUR8yhSVibB0beMMlKJ62pK0qvl4y5nw,5358
 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-0.6.0.dist-info/LICENSE,sha256=IpqC9A-tZW7XXXvCS8c4AVINqkmpxiVA-34Qe3CZSjo,1072
+cool_seq_tool-0.6.0.dist-info/METADATA,sha256=9q0VK-zTlDxBI5jOG3d4w02n9SevWbGdHSO5HP0-U8M,6210
+cool_seq_tool-0.6.0.dist-info/WHEEL,sha256=Wyh-_nZ0DJYolHNn1_hMa4lM7uDedD_RGVwbmTjyItk,91
+cool_seq_tool-0.6.0.dist-info/top_level.txt,sha256=cGuxdN6p3y16jQf6hCwWhE4OptwUeZPm_PNJlPb3b0k,14
+cool_seq_tool-0.6.0.dist-info/RECORD,,

{cool_seq_tool-0.5.0.dist-info → cool_seq_tool-0.6.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (70.3.0)
+Generator: setuptools (71.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any