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

cool_seq_tool/sources/uta_database.py

@@ -12,8 +12,16 @@ import boto3
 import polars as pl
 from asyncpg.exceptions import InterfaceError, InvalidAuthorizationSpecificationError
 from botocore.exceptions import ClientError
-
-from cool_seq_tool.schemas import AnnotationLayer, Assembly, Strand
+from pydantic import Field, StrictInt, StrictStr
+
+from cool_seq_tool.schemas import (
+    AnnotationLayer,
+    Assembly,
+    BaseModelForbidExtra,
+    GenomicTxData,
+    GenomicTxMetadata,
+    Strand,
+)
 
 # use `bound` to upper-bound UtaDatabase or child classes
 UTADatabaseType = TypeVar("UTADatabaseType", bound="UtaDatabase")
@@ -25,6 +33,52 @@ UTA_DB_URL = environ.get(
 _logger = logging.getLogger(__name__)
 
 
+class DbConnectionArgs(BaseModelForbidExtra):
+    """Represent database connection arguments"""
+
+    host: str
+    port: int
+    user: str
+    password: str
+    database: str
+
+
+class GenomicAlnData(BaseModelForbidExtra):
+    """Represent genomic alignment data from UTA tx_exon_aln_v view"""
+
+    hgnc: StrictStr = Field(..., description="HGNC gene symbol.")
+    ord: StrictInt = Field(..., description="Exon number. 0-based.")
+    alt_ac: StrictStr = Field(..., description="RefSeq genomic accession.")
+    alt_start_i: StrictInt = Field(
+        ...,
+        description="`alt_ac`'s start index of the exon using inter-residue coordinates.",
+    )
+    alt_end_i: StrictInt = Field(
+        ...,
+        description="`alt_ac`'s end index of the exon using inter-residue coordinates.",
+    )
+    alt_strand: Strand = Field(..., description="Strand.")
+
+
+class TxExonAlnData(GenomicAlnData):
+    """Represent data from UTA tx_exon_aln_v view"""
+
+    tx_ac: StrictStr = Field(..., description="Transcript accession.")
+    tx_start_i: StrictInt = Field(
+        ...,
+        description="`tx_ac`'s start index of the exon using inter-residue coordinates.",
+    )
+    tx_end_i: StrictInt = Field(
+        ...,
+        description="`tx_ac`'s end index of the exon using inter-residue coordinates.",
+    )
+    alt_aln_method: StrictStr = Field(
+        ..., description="The alignment method used to compare sequences."
+    )
+    tx_exon_id: StrictInt = Field(..., description="`tx_ac` exon identifier.")
+    alt_exon_id: StrictInt = Field(..., description="`alt_ac` exon identifier.")
+
+
 class UtaDatabase:
     """Provide transcript lookup and metadata tools via the Universal Transcript Archive
     (UTA) database.
@@ -51,11 +105,11 @@ class UtaDatabase:
         self.db_url = db_url.replace(original_pwd, quote(original_pwd))
         self.args = self._get_conn_args()
 
-    def _get_conn_args(self) -> dict:
+    def _get_conn_args(self) -> DbConnectionArgs:
         """Return connection arguments.
 
         :param db_url: raw connection URL
-        :return: Database credentials
+        :return: Database connection arguments
         """
         if "UTA_DB_PROD" in environ:
             secret = ast.literal_eval(self.get_secret())
@@ -72,23 +126,24 @@ class UtaDatabase:
             environ["UTA_DB_URL"] = (
                 f"postgresql://{username}@{host}:{port}/{database}/{schema}"
             )
-            return {
-                "host": host,
-                "port": int(port),
-                "database": database,
-                "user": username,
-                "password": password,
-            }
+            return DbConnectionArgs(
+                host=host,
+                port=int(port),
+                database=database,
+                user=username,
+                password=password,
+            )
+
         url = ParseResult(urlparse(self.db_url))
         self.schema = url.schema
         password = unquote(url.password) if url.password else ""
-        return {
-            "host": url.hostname,
-            "port": url.port,
-            "database": url.database,
-            "user": url.username,
-            "password": password,
-        }
+        return DbConnectionArgs(
+            host=url.hostname,
+            port=url.port,
+            database=url.database,
+            user=url.username,
+            password=password,
+        )
 
     async def create_pool(self) -> None:
         """Create connection pool if not already created."""
@@ -100,11 +155,11 @@ class UtaDatabase:
                     max_size=10,
                     max_inactive_connection_lifetime=3,
                     command_timeout=60,
-                    host=self.args["host"],
-                    port=self.args["port"],
-                    user=self.args["user"],
-                    password=self.args["password"],
-                    database=self.args["database"],
+                    host=self.args.host,
+                    port=self.args.port,
+                    user=self.args.user,
+                    password=self.args.password,
+                    database=self.args.database,
                 )
             except InterfaceError as e:
                 _logger.error(
@@ -215,156 +270,21 @@ class UtaDatabase:
         """
         return [list(i) for i in li]
 
-    async def get_genes_and_alt_acs(
-        self,
-        pos: int,
-        strand: Strand | None = None,
-        chromosome: int | None = None,
-        alt_ac: str | None = None,
-        gene: str | None = None,
-    ) -> tuple[dict | None, str | None]:
-        """Return genes and genomic accessions for a position on a chromosome or alt_ac
-
-        :param pos: Genomic position
-        :param strand: Strand
-        :param chromosome: Chromosome. Must give chromosome without a prefix
-            (i.e. ``1`` or ``X``). If not provided, must provide ``alt_ac``.
-            If ``alt_ac`` is also provided, ``alt_ac`` will be used.
-        :param alt_ac: Genomic accession (i.e. ``NC_000001.11``). If not provided,
-            must provide ``chromosome``. If ``chromosome`` is also provided, ``alt_ac``
-            will be used.
-        :param gene: Gene symbol
-        :return: Dictionary containing genes and genomic accessions and warnings if found
-        """
-        alt_ac_cond = (
-            f"WHERE alt_ac = '{alt_ac}'"
-            if alt_ac
-            else f"WHERE alt_ac ~ '^NC_[0-9]+0{chromosome}.[0-9]+$'"
-        )
-        strand_cond = f"AND alt_strand = '{strand.value}'" if strand else ""
-        gene_cond = f"AND hgnc = '{gene}'" if gene else ""
-
-        query = f"""
-            SELECT hgnc, alt_ac
-            FROM {self.schema}.tx_exon_aln_v
-            {alt_ac_cond}
-            AND alt_aln_method = 'splign'
-            AND {pos} BETWEEN alt_start_i AND alt_end_i
-            {strand_cond}
-            {gene_cond};
-            """  # noqa: S608
-
-        results = await self.execute_query(query)
-        if not results:
-            msg = (
-                f"Unable to find a result for chromosome "
-                f"{alt_ac or chromosome} where genomic coordinate {pos}"
-                f" is mapped between an exon's start and end coordinates"
-            )
-            if strand:
-                msg += (
-                    f" on the "
-                    f"{'positive' if strand == Strand.POSITIVE else 'negative'} strand"
-                )
-            if gene:
-                msg += f" and on gene {gene}"
-            return None, msg
-
-        results = self._transform_list(results)
-        genes = set()
-        alt_acs = set()
-        for r in results:
-            genes.add(r[0])
-            alt_acs.add(r[1])
-        return {"genes": genes, "alt_acs": alt_acs}, None
-
-    async def get_tx_exons(
-        self, tx_ac: str, alt_ac: str | None = None
-    ) -> tuple[list[tuple[int, int]] | None, str | None]:
-        """Get list of transcript exons start/end coordinates.
-
-        :param tx_ac: Transcript accession
-        :param alt_ac: Genomic accession
-        :return: List of a transcript's accessions and warnings if found
-        """
-        if alt_ac:
-            # We know what assembly we're looking for since we have the
-            # genomic accession
-            query = f"""
-                SELECT DISTINCT tx_start_i, tx_end_i
-                FROM {self.schema}.tx_exon_aln_v
-                WHERE tx_ac = '{tx_ac}'
-                AND alt_aln_method = 'splign'
-                AND alt_ac = '{alt_ac}'
-                """  # noqa: S608
-        else:
-            # Use GRCh38 by default if no genomic accession is provided
-            query = f"""
-                SELECT DISTINCT tx_start_i, tx_end_i
-                FROM {self.schema}.tx_exon_aln_v as t
-                INNER JOIN {self.schema}._seq_anno_most_recent as s
-                ON t.alt_ac = s.ac
-                WHERE s.descr = ''
-                AND t.tx_ac = '{tx_ac}'
-                AND t.alt_aln_method = 'splign'
-                AND t.alt_ac like 'NC_000%'
-                """  # noqa: S608
-        result = await self.execute_query(query)
-
-        if not result:
-            msg = f"Unable to get exons for {tx_ac}"
-            _logger.warning(msg)
-            return None, msg
-        tx_exons = [(r["tx_start_i"], r["tx_end_i"]) for r in result]
-        return tx_exons, None
-
-    async def get_tx_exons_genomic_coords(
-        self,
-        tx_ac: str,
-        alt_ac: str,
-    ) -> tuple[tuple[int, int, int, int, int] | None, str | None]:
-        """Get exon number, transcript coordinates, and genomic coordinates
-
-        :param tx_ac: Transcript accession
-        :param alt_ac: RefSeq genomic accession
-        :return: Tuple of exon numbers, transcript and genomic coordinates,
-            and warnings if found
-        """
-        query = f"""
-            SELECT DISTINCT ord, tx_start_i, tx_end_i, alt_start_i, alt_end_i
-            FROM {self.schema}.tx_exon_aln_v
-            WHERE tx_ac = '{tx_ac}'
-            AND alt_ac = '{alt_ac}'
-            """  # noqa: S608
-        result = await self.execute_query(query)
-
-        if not result:
-            msg = f"Unable to get exons and genomic coordinates for {tx_ac} on {alt_ac}"
-            _logger.warning(msg)
-            return None, msg
-        tx_exons_genomic_coords = [
-            (r["ord"], r["tx_start_i"], r["tx_end_i"], r["alt_start_i"], r["alt_end_i"])
-            for r in result
-        ]
-        return tx_exons_genomic_coords, None
-
     async def get_alt_ac_start_or_end(
         self, tx_ac: str, tx_exon_start: int, tx_exon_end: int, gene: str | None
-    ) -> tuple[tuple[str, str, int, int, int] | None, str | None]:
+    ) -> tuple[GenomicAlnData | None, str | None]:
         """Get genomic data for related transcript exon start or end.
 
         :param tx_ac: Transcript accession
         :param tx_exon_start: Transcript's exon start coordinate
         :param tx_exon_end: Transcript's exon end coordinate
         :param gene: HGNC gene symbol
-        :return: [hgnc symbol, genomic accession for chromosome,
-            aligned genomic start coordinate, aligned genomic end coordinate, strand],
-            and warnings if found
+        :return: Genomic alignment data and warnings if found
         """
         gene_query = f"AND T.hgnc = '{gene}'" if gene else ""
 
         query = f"""
-            SELECT T.hgnc, T.alt_ac, T.alt_start_i, T.alt_end_i, T.alt_strand
+            SELECT T.hgnc, T.alt_ac, T.alt_start_i, T.alt_end_i, T.alt_strand, T.ord
             FROM {self.schema}._cds_exons_fp_v as C
             JOIN {self.schema}.tx_exon_aln_v as T ON T.tx_ac = C.tx_ac
             WHERE T.tx_ac = '{tx_ac}'
@@ -387,8 +307,7 @@ class UtaDatabase:
                 msg += f" on gene {gene}"
             _logger.warning(msg)
             return None, msg
-        result = result[0]
-        return (result[0], result[1], result[2], result[3], result[4]), None
+        return GenomicAlnData(**result[0]), None
 
     async def get_cds_start_end(self, tx_ac: str) -> tuple[int, int] | None:
         """Get coding start and end site
@@ -497,7 +416,7 @@ class UtaDatabase:
         alt_ac: str | None = None,
         use_tx_pos: bool = True,
         like_tx_ac: bool = False,
-    ) -> list:
+    ) -> list[TxExonAlnData]:
         """Return queried data from tx_exon_aln_v table.
 
         :param tx_ac: accession on c. coordinate
@@ -511,11 +430,8 @@ class UtaDatabase:
         :param like_tx_ac: ``True`` if tx_ac condition should be a like statement.
             This is used when you want to query an accession regardless of its version
             ``False`` if tx_condition will be exact match
-        :return: List of tx_exon_aln_v data
+        :return: List of transcript exon alignment data
         """
-        if end_pos is None:
-            end_pos = start_pos
-
         if tx_ac.startswith("EN"):
             temp_ac = tx_ac.split(".")[0]
             aln_method = f"AND alt_aln_method='genebuild'"  # noqa: F541
@@ -543,7 +459,7 @@ class UtaDatabase:
 
         query = f"""
             SELECT hgnc, tx_ac, tx_start_i, tx_end_i, alt_ac, alt_start_i,
-                alt_end_i, alt_strand, alt_aln_method, tx_exon_id, alt_exon_id
+                alt_end_i, alt_strand, alt_aln_method, ord, tx_exon_id, alt_exon_id
             FROM {self.schema}.tx_exon_aln_v
             {tx_q}
             {alt_ac_q}
@@ -562,22 +478,17 @@ class UtaDatabase:
                 temp_ac,
                 alt_ac,
             )
-        return [list(r) for r in result]
+        return [TxExonAlnData(**r) for r in result]
 
     @staticmethod
-    def data_from_result(result: list) -> dict | None:
+    def data_from_result(result: TxExonAlnData) -> GenomicTxData | None:
         """Return data found from result.
 
-        :param result: Data from tx_exon_aln_v table
-        :return: Gene, strand, and position ranges for tx and alt_ac
+        :param result: Transcript exon alignment data
+        :return: Aligned genomic / transcript exon data
         """
-        gene = result[0]
-        tx_pos_range = result[2], result[3]
-        alt_pos_range = result[5], result[6]
-        strand = Strand(result[7])
-        alt_aln_method = result[8]
-        tx_exon_id = result[9]
-        alt_exon_id = result[10]
+        tx_pos_range = result.tx_start_i, result.tx_end_i
+        alt_pos_range = result.alt_start_i, result.alt_end_i
 
         if (tx_pos_range[1] - tx_pos_range[0]) != (alt_pos_range[1] - alt_pos_range[0]):
             _logger.warning(
@@ -587,19 +498,19 @@ class UtaDatabase:
             )
             return None
 
-        return {
-            "gene": gene,
-            "strand": strand,
-            "tx_pos_range": tx_pos_range,
-            "alt_pos_range": alt_pos_range,
-            "alt_aln_method": alt_aln_method,
-            "tx_exon_id": tx_exon_id,
-            "alt_exon_id": alt_exon_id,
-        }
+        return GenomicTxData(
+            gene=result.hgnc,
+            strand=Strand(result.alt_strand),
+            tx_pos_range=tx_pos_range,
+            alt_pos_range=alt_pos_range,
+            alt_aln_method=result.alt_aln_method,
+            tx_exon_id=result.tx_exon_id,
+            alt_exon_id=result.alt_exon_id,
+        )
 
     async def get_mane_c_genomic_data(
         self, ac: str, alt_ac: str | None, start_pos: int, end_pos: int
-    ) -> dict | None:
+    ) -> GenomicTxMetadata | None:
         """Get MANE transcript and genomic data. Used when going from g. to MANE c.
         representation.
 
@@ -623,7 +534,8 @@ class UtaDatabase:
             be set to ``None`` if unavailable.
         :param start_pos: Genomic start position
         :param end_pos: Genomic end position change
-        :return: MANE transcript results if successful
+        :return: Metadata for MANE genomic and transcript accessions results if
+            successful
         """
         results = await self.get_tx_exon_aln_v_data(
             ac, start_pos, end_pos, alt_ac=alt_ac, use_tx_pos=False
@@ -632,8 +544,8 @@ class UtaDatabase:
             return None
         result = results[0]
 
-        data = self.data_from_result(result)
-        if not data:
+        genomic_tx_data = self.data_from_result(result)
+        if not genomic_tx_data:
             return None
 
         coding_start_site = await self.get_cds_start_end(ac)
@@ -641,25 +553,30 @@ class UtaDatabase:
             _logger.warning("Accession %s not found in UTA", ac)
             return None
 
-        data["tx_ac"] = result[1]
-        data["alt_ac"] = result[4]
-        data["coding_start_site"] = coding_start_site[0]
-        data["coding_end_site"] = coding_start_site[1]
+        coding_start_site, coding_end_site = coding_start_site
 
-        if data["strand"] == Strand.NEGATIVE:
-            data["alt_pos_change_range"] = (end_pos, start_pos)
-            data["alt_pos_change"] = (
-                data["alt_pos_range"][1] - data["alt_pos_change_range"][0],
-                data["alt_pos_change_range"][1] - data["alt_pos_range"][0],
+        if genomic_tx_data.strand == Strand.NEGATIVE:
+            alt_pos_change_range = (end_pos, start_pos)
+            pos_change = (
+                genomic_tx_data.alt_pos_range[1] - alt_pos_change_range[0],
+                alt_pos_change_range[1] - genomic_tx_data.alt_pos_range[0],
             )
         else:
-            data["alt_pos_change_range"] = (start_pos, end_pos)
-            data["alt_pos_change"] = (
-                data["alt_pos_change_range"][0] - data["alt_pos_range"][0],
-                data["alt_pos_range"][1] - data["alt_pos_change_range"][1],
+            alt_pos_change_range = (start_pos, end_pos)
+            pos_change = (
+                alt_pos_change_range[0] - genomic_tx_data.alt_pos_range[0],
+                genomic_tx_data.alt_pos_range[1] - alt_pos_change_range[1],
             )
 
-        return data
+        return GenomicTxMetadata(
+            **genomic_tx_data.model_dump(),
+            pos_change=pos_change,
+            tx_ac=result.tx_ac,
+            alt_ac=result.alt_ac,
+            coding_start_site=coding_start_site,
+            coding_end_site=coding_end_site,
+            alt_pos_change_range=alt_pos_change_range,
+        )
 
     async def get_genomic_tx_data(
         self,
@@ -669,7 +586,7 @@ class UtaDatabase:
         | Literal[AnnotationLayer.GENOMIC] = AnnotationLayer.CDNA,
         alt_ac: str | None = None,
         target_genome_assembly: Assembly = Assembly.GRCH38,
-    ) -> dict | None:
+    ) -> GenomicTxMetadata | None:
         """Get transcript mapping to genomic data.
 
         :param tx_ac: Accession on c. coordinate
@@ -678,8 +595,7 @@ class UtaDatabase:
         :param alt_ac: Accession on g. coordinate
         :param target_genome_assembly: Genome assembly to get genomic data for.
             If ``alt_ac`` is provided, it will return the associated assembly.
-        :return: Gene, Transcript accession and position change,
-            Altered transcript accession and position change, Strand
+        :return: Metadata for genomic and transcript accessions
         """
         results = await self.get_tx_exon_aln_v_data(
             tx_ac,
@@ -696,35 +612,39 @@ class UtaDatabase:
         else:
             result = results[0]
 
-        data = self.data_from_result(result)
-        if not data:
+        genomic_tx_data = self.data_from_result(result)
+        if not genomic_tx_data:
             return None
-        data["tx_ac"] = result[1]
-        data["alt_ac"] = result[4]
 
-        data["pos_change"] = (
-            pos[0] - data["tx_pos_range"][0],
-            data["tx_pos_range"][1] - pos[1],
+        pos_change = (
+            pos[0] - genomic_tx_data.tx_pos_range[0],
+            genomic_tx_data.tx_pos_range[1] - pos[1],
         )
 
         if annotation_layer == AnnotationLayer.CDNA:
-            if data["strand"] == Strand.NEGATIVE:
-                data["alt_pos_change_range"] = (
-                    data["alt_pos_range"][1] - data["pos_change"][0],
-                    data["alt_pos_range"][0] + data["pos_change"][1],
+            if genomic_tx_data.strand == Strand.NEGATIVE:
+                alt_pos_change_range = (
+                    genomic_tx_data.alt_pos_range[1] - pos_change[0],
+                    genomic_tx_data.alt_pos_range[0] + pos_change[1],
                 )
             else:
-                data["alt_pos_change_range"] = (
-                    data["alt_pos_range"][0] + data["pos_change"][0],
-                    data["alt_pos_range"][1] - data["pos_change"][1],
+                alt_pos_change_range = (
+                    genomic_tx_data.alt_pos_range[0] + pos_change[0],
+                    genomic_tx_data.alt_pos_range[1] - pos_change[1],
                 )
         else:
-            if data["strand"] == Strand.NEGATIVE:
-                data["alt_pos_change_range"] = (pos[1], pos[0])
+            if genomic_tx_data.strand == Strand.NEGATIVE:
+                alt_pos_change_range = (pos[1], pos[0])
             else:
-                data["alt_pos_change_range"] = pos
-
-        return data
+                alt_pos_change_range = pos
+
+        return GenomicTxMetadata(
+            **genomic_tx_data.model_dump(),
+            tx_ac=result.tx_ac,
+            alt_ac=result.alt_ac,
+            pos_change=pos_change,
+            alt_pos_change_range=alt_pos_change_range,
+        )
 
     async def get_ac_from_gene(self, gene: str) -> list[str]:
         """Return genomic accession(s) associated to a gene.

cool_seq_tool/utils.py

@@ -6,35 +6,35 @@ import logging
 from bioutils.accessions import chr22XY
 
 from cool_seq_tool import __version__
-from cool_seq_tool.schemas import ResidueMode, ServiceMeta
+from cool_seq_tool.schemas import CoordinateType, ServiceMeta
 
 _logger = logging.getLogger(__name__)
 
 
 def get_inter_residue_pos(
-    start_pos: int, end_pos: int, residue_mode: ResidueMode
+    start_pos: int, end_pos: int, coordinate_type: CoordinateType
 ) -> tuple[int, int]:
     """Return equivalent inter-residue position.
 
-    Generally, we prefer to work with inter-residue coordinates where possible. Our
+    Residue coordinates start with 1, whereas inter-residue coordinates start with 0.
+
+    It is preferred to work with inter-residue coordinates where possible. Our
     rationale is detailed in an appendix to the
     `VRS docs <https://vrs.ga4gh.org/en/stable/appendices/design_decisions.html#inter-residue-coordinates>`_.
     This function is used internally to shift user-provided coordinates accordingly.
 
     >>> from cool_seq_tool.utils import get_inter_residue_pos
-    >>> from cool_seq_tool.schemas import ResidueMode
-    >>> get_inter_residue_pos(10, ResidueMode.RESIDUE)
+    >>> from cool_seq_tool.schemas import CoordinateType
+    >>> get_inter_residue_pos(10, CoordinateType.RESIDUE)
     ((9, 9), None)
 
     :param start_pos: Start position
     :param end_pos: End position
-    :param residue_mode: Residue mode for `start_pos` and `end_pos`
+    :param coordinate_type: Coordinate type for `start_pos` and `end_pos`
     :return: Inter-residue coordinates
     """
-    if residue_mode == ResidueMode.RESIDUE:
+    if coordinate_type == CoordinateType.RESIDUE:
         start_pos -= 1
-    elif residue_mode == ResidueMode.ZERO:
-        end_pos += 1
     return start_pos, end_pos
 
 

{cool_seq_tool-0.5.1.dist-info → cool_seq_tool-0.7.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cool_seq_tool
-Version: 0.5.1
+Version: 0.7.0
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -52,7 +52,7 @@ Requires-Dist: polars ~=1.0
 Requires-Dist: hgvs
 Requires-Dist: biocommons.seqrepo
 Requires-Dist: pydantic ==2.*
-Requires-Dist: ga4gh.vrs
+Requires-Dist: ga4gh.vrs ~=2.0.0a10
 Requires-Dist: wags-tails ~=0.1.3
 Requires-Dist: bioutils
 Provides-Extra: dev
@@ -83,7 +83,7 @@ CoolSeqTool
 
 ---
 
-**[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)
+**[Documentation](https://coolseqtool.readthedocs.io/stable/)** · [Installation](https://coolseqtool.readthedocs.io/stable/install.html) · [Usage](https://coolseqtool.readthedocs.io/stable/usage.html) · [API reference](https://coolseqtool.readthedocs.io/stable/reference/index.html)
 
 ---
 
@@ -107,7 +107,7 @@ CoolSeqTool is available on [PyPI](https://pypi.org/project/cool-seq-tool)
 python3 -m pip install cool-seq-tool
 ```
 
-See the [installation instructions](https://coolseqtool.readthedocs.io/latest/install.html) in the documentation for a description of dependency setup requirements.
+See the [installation instructions](https://coolseqtool.readthedocs.io/stable/install.html) in the documentation for a description of dependency setup requirements.
 
 ---
 
@@ -116,14 +116,14 @@ See the [installation instructions](https://coolseqtool.readthedocs.io/latest/in
 All CoolSeqTool resources can be initialized by way of a top-level class instance:
 
 ```pycon
->>> from cool_seq_tool.app import CoolSeqTool
->>> from cool_seq_tool.schemas import AnnotationLayer, ResidueMode
+>>> from cool_seq_tool import CoolSeqTool
+>>> from cool_seq_tool.schemas import AnnotationLayer, CoordinateType
 >>> cst = CoolSeqTool()
 >>> result = await cst.mane_transcript.get_mane_transcript(
 ...     "NP_004324.2",
 ...     599,
 ...     AnnotationLayer.PROTEIN,
-...     residue_mode=ResidueMode.INTER_RESIDUE,
+...     coordinate_type=CoordinateType.INTER_RESIDUE,
 ... )
 >>> result.gene, result.refseq, result.status
 ('EGFR', 'NM_005228.5', <TranscriptPriority.MANE_SELECT: 'mane_select'>)
@@ -133,4 +133,4 @@ All CoolSeqTool resources can be initialized by way of a top-level class instanc
 
 ## Feedback and contributing
 
-We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The [documentation](https://coolseqtool.readthedocs.io/latest/contributing.html) contains guidance for submitting feedback and contributing new code.
+We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The [documentation](https://coolseqtool.readthedocs.io/stable/contributing.html) contains guidance for submitting feedback and contributing new code.

cool_seq_tool-0.7.0.dist-info/RECORD

@@ -0,0 +1,24 @@
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+cool_seq_tool/app.py,sha256=vyqlQRffC8sWZXMm-f_f-8WuTTWo3oRNfPUa_qdPV2M,4944
+cool_seq_tool/schemas.py,sha256=HInmKpsujybVR6pRmkKNOIzPCBqk9Ni5q1ZKNFtip50,3945
+cool_seq_tool/utils.py,sha256=kesu7UnOplDzvNBg_G-_m1xMM22979nmsi4yWtweetU,2959
+cool_seq_tool/handlers/__init__.py,sha256=KalQ46vX1MO4SJz2SlspKoIRy1n3c3Vp1t4Y2pIfqow,78
+cool_seq_tool/handlers/seqrepo_access.py,sha256=Jd19jbdUvPRPn_XWozL67ph-nSIxpb4_UUimapDrsm4,9162
+cool_seq_tool/mappers/__init__.py,sha256=O0JRxNFk8nWxD4v5ij47xelhvfVLdEXS43l2tzRuiUE,305
+cool_seq_tool/mappers/alignment.py,sha256=nV6PS3mhkQ2MD1GcpNBujBOqd3AKxYSYA9BCusFOa1o,9636
+cool_seq_tool/mappers/exon_genomic_coords.py,sha256=hfzfuxsNwMvj6y9thwWCj4WcOXamdnqvvd29gmX19Bo,48261
+cool_seq_tool/mappers/liftover.py,sha256=lltx9zxfkrb5PHtJlKp3a39JCwPP4e0Zft-mQc1jXL8,3367
+cool_seq_tool/mappers/mane_transcript.py,sha256=nirxlf3EGVInFYG4fsAqiEmDdTc_h1XuPyX2ul-a7Rk,54368
+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=E_pj7FEBcB6HUR8yhSVibB0beMMlKJ62pK0qvl4y5nw,5358
+cool_seq_tool/sources/transcript_mappings.py,sha256=903RKTMBO2rbKh6iTQ1BEWnY4C7saBFMPw2_4ATuudg,10054
+cool_seq_tool/sources/uta_database.py,sha256=gc5wsKOIhvzhwFmPmqOY0hhaVfRkRSzYNa9tpBt81_U,35017
+cool_seq_tool-0.7.0.dist-info/LICENSE,sha256=IpqC9A-tZW7XXXvCS8c4AVINqkmpxiVA-34Qe3CZSjo,1072
+cool_seq_tool-0.7.0.dist-info/METADATA,sha256=UrSjQTJOgl4sqFvMG_p_TpeZW2R0GE6lMGus9NQhUew,6226
+cool_seq_tool-0.7.0.dist-info/WHEEL,sha256=Mdi9PDNwEZptOjTlUcAth7XJDFtKrHYaQMPulZeBCiQ,91
+cool_seq_tool-0.7.0.dist-info/top_level.txt,sha256=cGuxdN6p3y16jQf6hCwWhE4OptwUeZPm_PNJlPb3b0k,14
+cool_seq_tool-0.7.0.dist-info/RECORD,,