cool-seq-tool 0.4.1__py3-none-any.whl → 0.5.1__py3-none-any.whl

cool_seq_tool/sources/uta_database.py

@@ -1,7 +1,6 @@
 """Provide transcript lookup and metadata tools via the UTA database."""
 
 import ast
-import base64
 import logging
 from os import environ
 from typing import Any, Literal, TypeVar
@@ -11,7 +10,6 @@ from urllib.parse import quote, unquote, urlparse
 import asyncpg
 import boto3
 import polars as pl
-from agct import Converter, Genome
 from asyncpg.exceptions import InterfaceError, InvalidAuthorizationSpecificationError
 from botocore.exceptions import ClientError
 
@@ -20,46 +18,11 @@ from cool_seq_tool.schemas import AnnotationLayer, Assembly, Strand
 # use `bound` to upper-bound UtaDatabase or child classes
 UTADatabaseType = TypeVar("UTADatabaseType", bound="UtaDatabase")
 
-# Environment variables for paths to chain files for agct
-LIFTOVER_CHAIN_37_TO_38 = environ.get("LIFTOVER_CHAIN_37_TO_38")
-LIFTOVER_CHAIN_38_TO_37 = environ.get("LIFTOVER_CHAIN_38_TO_37")
-
 UTA_DB_URL = environ.get(
     "UTA_DB_URL", "postgresql://uta_admin:uta@localhost:5432/uta/uta_20210129b"
 )
 
-logger = logging.getLogger(__name__)
-
-
-def get_liftover(
-    chain_file_37_to_38: str | None = None, chain_file_38_to_37: str | None = None
-) -> tuple[Converter, Converter]:
-    """Fetch Converter instances between GRCh37 and 38.
-
-    Factored out of the UTA Database initialization method to support less expensive
-    status check-type operations.
-
-    :param chain_file_37_to_38: Optional path to chain file for 37 to 38 assembly.
-        This is used for ``agct``. If this is not provided, will check to see
-        if ``LIFTOVER_CHAIN_37_TO_38`` env var is set. If neither is provided, will
-        allow ``agct`` to download a chain file from UCSC
-    :param chain_file_38_to_37: Optional path to chain file for 38 to 37 assembly.
-        This is used for ``agct``. If this is not provided, will check to see
-        if ``LIFTOVER_CHAIN_38_TO_37`` env var is set. If neither is provided, will
-        allow ``agct`` to download a chain file from UCSC
-    :return: converters (37->38, 38->37)
-    """
-    chain_file_37_to_38 = chain_file_37_to_38 or LIFTOVER_CHAIN_37_TO_38
-    if chain_file_37_to_38:
-        converter_37_to_38 = Converter(chainfile=chain_file_37_to_38)
-    else:
-        converter_37_to_38 = Converter(from_db=Genome.HG19, to_db=Genome.HG38)
-    chain_file_38_to_37 = chain_file_38_to_37 or LIFTOVER_CHAIN_38_TO_37
-    if chain_file_38_to_37:
-        converter_38_to_37 = Converter(chainfile=chain_file_38_to_37)
-    else:
-        converter_38_to_37 = Converter(from_db=Genome.HG38, to_db=Genome.HG19)
-    return (converter_37_to_38, converter_38_to_37)
+_logger = logging.getLogger(__name__)
 
 
 class UtaDatabase:
@@ -75,34 +38,18 @@ class UtaDatabase:
     >>> uta_db = asyncio.run(UtaDatabase.create())
     """
 
-    def __init__(
-        self,
-        db_url: str = UTA_DB_URL,
-        chain_file_37_to_38: str | None = None,
-        chain_file_38_to_37: str | None = None,
-    ) -> None:
+    def __init__(self, db_url: str = UTA_DB_URL) -> None:
         """Initialize DB class. Should only be used by ``create()`` method, and not
         be called directly by a user.
 
         :param db_url: PostgreSQL connection URL
             Format: ``driver://user:password@host/database/schema``
-        :param chain_file_37_to_38: Optional path to chain file for 37 to 38 assembly.
-            This is used for ``agct``. If this is not provided, will check to see
-            if ``LIFTOVER_CHAIN_37_TO_38`` env var is set. If neither is provided, will
-            allow ``agct`` to download a chain file from UCSC
-        :param chain_file_38_to_37: Optional path to chain file for 38 to 37 assembly.
-            This is used for ``agct``. If this is not provided, will check to see
-            if ``LIFTOVER_CHAIN_38_TO_37`` env var is set. If neither is provided, will
-            allow ``agct`` to download a chain file from UCSC
         """
         self.schema = None
         self._connection_pool = None
         original_pwd = db_url.split("//")[-1].split("@")[0].split(":")[-1]
         self.db_url = db_url.replace(original_pwd, quote(original_pwd))
         self.args = self._get_conn_args()
-        self.liftover_37_to_38, self.liftover_38_to_37 = get_liftover(
-            chain_file_37_to_38, chain_file_38_to_37
-        )
 
     def _get_conn_args(self) -> dict:
         """Return connection arguments.
@@ -160,7 +107,7 @@ class UtaDatabase:
                     database=self.args["database"],
                 )
             except InterfaceError as e:
-                logger.error(
+                _logger.error(
                     "While creating connection pool, encountered exception %s", e
                 )
                 msg = "Could not create connection pool"
@@ -223,7 +170,7 @@ class UtaDatabase:
         genomic_table_exists = await self.execute_query(check_table_exists)
         genomic_table_exists = genomic_table_exists[0].get("exists")
         if genomic_table_exists is None:
-            logger.critical(
+            _logger.critical(
                 "SELECT EXISTS query in UtaDatabase._create_genomic_table "
                 "returned invalid response"
             )
@@ -284,7 +231,7 @@ class UtaDatabase:
             (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``
+            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
@@ -366,7 +313,7 @@ class UtaDatabase:
 
         if not result:
             msg = f"Unable to get exons for {tx_ac}"
-            logger.warning(msg)
+            _logger.warning(msg)
             return None, msg
         tx_exons = [(r["tx_start_i"], r["tx_end_i"]) for r in result]
         return tx_exons, None
@@ -393,7 +340,7 @@ class UtaDatabase:
 
         if not result:
             msg = f"Unable to get exons and genomic coordinates for {tx_ac} on {alt_ac}"
-            logger.warning(msg)
+            _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"])
@@ -438,7 +385,7 @@ class UtaDatabase:
             )
             if gene_query:
                 msg += f" on gene {gene}"
-            logger.warning(msg)
+            _logger.warning(msg)
             return None, msg
         result = result[0]
         return (result[0], result[1], result[2], result[3], result[4]), None
@@ -462,7 +409,7 @@ class UtaDatabase:
             if cds_start_end[0] is not None and cds_start_end[1] is not None:  # noqa: RET503
                 return cds_start_end[0], cds_start_end[1]
         else:
-            logger.warning(
+            _logger.warning(
                 "Unable to get coding start/end site for accession: %s", tx_ac
             )
             return None
@@ -535,7 +482,7 @@ class UtaDatabase:
             """  # noqa: S608
         result = await self.execute_query(query)
         if not result:
-            logger.warning("Accession %s does not have a description", ac)
+            _logger.warning("Accession %s does not have a description", ac)
             return None
         result = result[0][0]
         if result == "":
@@ -607,10 +554,10 @@ class UtaDatabase:
             """  # noqa: S608
         result = await self.execute_query(query)
         if not result:
-            logger.warning("Unable to find transcript alignment for query: %s", query)
+            _logger.warning("Unable to find transcript alignment for query: %s", query)
             return []
         if alt_ac and not use_tx_pos and len(result) > 1:
-            logger.debug(
+            _logger.debug(
                 "Found more than one match for tx_ac %s and alt_ac = %s",
                 temp_ac,
                 alt_ac,
@@ -633,7 +580,7 @@ class UtaDatabase:
         alt_exon_id = result[10]
 
         if (tx_pos_range[1] - tx_pos_range[0]) != (alt_pos_range[1] - alt_pos_range[0]):
-            logger.warning(
+            _logger.warning(
                 "tx_pos_range %s is not the same length as alt_pos_range %s.",
                 tx_pos_range,
                 alt_pos_range,
@@ -691,7 +638,7 @@ class UtaDatabase:
 
         coding_start_site = await self.get_cds_start_end(ac)
         if coding_start_site is None:
-            logger.warning("Accession %s not found in UTA", ac)
+            _logger.warning("Accession %s not found in UTA", ac)
             return None
 
         data["tx_ac"] = result[1]
@@ -833,12 +780,12 @@ class UtaDatabase:
             """  # noqa: S608
         results = await self.execute_query(query)
         if not results:
-            logger.warning(
+            _logger.warning(
                 "Unable to find gene between %s and %s on %s", start_pos, end_pos, ac
             )
             return None
         if len(results) > 1:
-            logger.info(
+            _logger.info(
                 "Found more than one gene between %s and %s on %s",
                 start_pos,
                 end_pos,
@@ -922,16 +869,26 @@ class UtaDatabase:
         results = [
             (r["pro_ac"], r["tx_ac"], r["alt_ac"], r["cds_start_i"]) for r in results
         ]
-        results_df = pl.DataFrame(results, schema=schema)
+        results_df = pl.DataFrame(results, schema=schema, orient="row")
         if results:
             results_df = results_df.unique()
         return results_df
 
-    async def get_chr_assembly(self, ac: str) -> tuple[str, str] | None:
+    async def get_chr_assembly(self, ac: str) -> tuple[str, Assembly] | None:
         """Get chromosome and assembly for NC accession if not in GRCh38.
 
-        :param ac: NC accession
-        :return: Chromosome and Assembly accession is on
+        >>> import asyncio
+        >>> from cool_seq_tool.sources.uta_database import UtaDatabase
+        >>> uta_db = asyncio.run(UtaDatabase.create())
+        >>> result = asyncio.run(uta_db.get_chr_assembly("NC_000007.13"))
+        >>> result
+        ('chr7', <Assembly.GRCH37: 'GRCh37'>)
+
+        Returns ``None`` if unable to find (either unrecognized/invalid, or
+        a GRCh38 accession).
+
+        :param ac: RefSeq NC accession, eg ``"NC_000007.13"``
+        :return: Chromosome and assembly that accession is on, if available.
         """
         descr = await self.get_ac_descr(ac)
         if not descr:
@@ -941,135 +898,14 @@ class UtaDatabase:
         chromosome = f"chr{descr[0].split()[-1]}"
         assembly = f"GRCh{descr[1].split('.')[0].split('GRCh')[-1]}"
 
-        if assembly not in ["GRCh37", "GRCh38"]:
-            logger.warning(
-                "Assembly not supported: %s. Only GRCh37 and GRCh38 are supported.",
-                assembly,
-            )
+        try:
+            assembly = Assembly(assembly)
+        except ValueError as e:
+            _logger.error(e)
             return None
 
         return chromosome, assembly
 
-    async def liftover_to_38(self, genomic_tx_data: dict) -> None:
-        """Liftover genomic_tx_data to hg38 assembly.
-
-        :param genomic_tx_data: Dictionary containing gene, nc_accession, alt_pos, and
-            strand
-        """
-        descr = await self.get_chr_assembly(genomic_tx_data["alt_ac"])
-        if descr is None:
-            # already grch38
-            return
-        chromosome, _ = descr
-
-        query = f"""
-            SELECT DISTINCT alt_ac
-            FROM {self.schema}.tx_exon_aln_v
-            WHERE tx_ac = '{genomic_tx_data['tx_ac']}';
-            """  # noqa: S608
-        nc_acs = await self.execute_query(query)
-        nc_acs = [nc_ac[0] for nc_ac in nc_acs]
-        if nc_acs == [genomic_tx_data["alt_ac"]]:
-            logger.warning(
-                "UTA does not have GRCh38 assembly for %s",
-                genomic_tx_data["alt_ac"].split(".")[0],
-            )
-            return
-
-        # Get most recent assembly version position
-        # Liftover range
-        self._set_liftover(
-            genomic_tx_data, "alt_pos_range", chromosome, Assembly.GRCH38
-        )
-
-        # Liftover changes range
-        self._set_liftover(
-            genomic_tx_data, "alt_pos_change_range", chromosome, Assembly.GRCH38
-        )
-
-        # Change alt_ac to most recent
-        if genomic_tx_data["alt_ac"].startswith("EN"):
-            order_by_cond = "ORDER BY alt_ac DESC;"
-        else:
-            order_by_cond = """
-            ORDER BY CAST(SUBSTR(alt_ac, position('.' in alt_ac) + 1,
-            LENGTH(alt_ac)) AS INT) DESC;
-            """
-        query = f"""
-            SELECT alt_ac
-            FROM {self.schema}.genomic
-            WHERE alt_ac LIKE '{genomic_tx_data['alt_ac'].split('.')[0]}%'
-            {order_by_cond}
-            """  # noqa: S608
-        nc_acs = await self.execute_query(query)
-        genomic_tx_data["alt_ac"] = nc_acs[0][0]
-
-    def get_liftover(
-        self, chromosome: str, pos: int, liftover_to_assembly: Assembly
-    ) -> tuple[str, int] | None:
-        """Get new genome assembly data for a position on a chromosome.
-
-        :param chromosome: The chromosome number. Must be prefixed with ``chr``
-        :param pos: Position on the chromosome
-        :param liftover_to_assembly: Assembly to liftover to
-        :return: Target chromosome and target position for assembly
-        """
-        if not chromosome.startswith("chr"):
-            logger.warning("`chromosome` must be prefixed with chr")
-            return None
-
-        if liftover_to_assembly == Assembly.GRCH38:
-            liftover = self.liftover_37_to_38.convert_coordinate(chromosome, pos)
-        elif liftover_to_assembly == Assembly.GRCH37:
-            liftover = self.liftover_38_to_37.convert_coordinate(chromosome, pos)
-        else:
-            logger.warning("%s assembly not supported", liftover_to_assembly)
-            liftover = None
-
-        if not liftover:
-            logger.warning("%s does not exist on %s", pos, chromosome)
-            return None
-        return liftover[0][:2]
-
-    def _set_liftover(
-        self,
-        genomic_tx_data: dict,
-        key: str,
-        chromosome: str,
-        liftover_to_assembly: Assembly,
-    ) -> None:
-        """Update genomic_tx_data to have coordinates for given assembly.
-
-        :param genomic_tx_data: Dictionary containing gene, nc_accession, alt_pos, and
-            strand
-        :param key: Key to access coordinate positions
-        :param chromosome: Chromosome, must be prefixed with ``chr``
-        :param liftover_to_assembly: Assembly to liftover to
-        """
-        liftover_start_i = self.get_liftover(
-            chromosome, genomic_tx_data[key][0], liftover_to_assembly
-        )
-        if liftover_start_i is None:
-            logger.warning(
-                "Unable to liftover position %s on %s",
-                genomic_tx_data[key][0],
-                chromosome,
-            )
-            return
-
-        liftover_end_i = self.get_liftover(
-            chromosome, genomic_tx_data[key][1], liftover_to_assembly
-        )
-        if liftover_end_i is None:
-            logger.warning(
-                "Unable to liftover position %s on %s",
-                genomic_tx_data[key][1],
-                chromosome,
-            )
-            return
-
-        genomic_tx_data[key] = liftover_start_i[1], liftover_end_i[1]
-
     async def p_to_c_ac(self, p_ac: str) -> list[str]:
         """Return cDNA reference sequence accession from protein reference sequence
         accession (i.e. ``p.`` to ``c.`` in HGVS syntax)
@@ -1121,7 +957,12 @@ class UtaDatabase:
 
     @staticmethod
     def get_secret() -> str:
-        """Get secrets for UTA DB instances. Used for deployment on AWS."""
+        """Get secrets for UTA DB instances. Used for deployment on AWS.
+
+        :raises ClientError: If unable to retrieve secret value due to decryption
+            decryption failure, internal service error, invalid parameter, invalid
+            request, or resource not found.
+        """
         secret_name = environ["UTA_DB_SECRET"]
         region_name = "us-east-2"
 
@@ -1132,27 +973,12 @@ class UtaDatabase:
         try:
             get_secret_value_response = client.get_secret_value(SecretId=secret_name)
         except ClientError as e:
-            logger.warning(e)
-            if e.response["Error"]["Code"] in {
-                # Secrets Manager can"t decrypt the protected secret text using the provided KMS key.
-                "DecryptionFailureException",
-                # An error occurred on the server side.
-                "InternalServiceErrorException",
-                # You provided an invalid value for a parameter.
-                "InvalidParameterException",
-                # You provided a parameter value that is not valid for the current state of the resource.
-                "InvalidRequestException",
-                # We can"t find the resource that you asked for.
-                "ResourceNotFoundException",
-            }:
-                raise e
+            # For a list of exceptions thrown, see
+            # https://docs.aws.amazon.com/secretsmanager/latest/apireference/API_GetSecretValue.html
+            _logger.error(e)
+            raise e
         else:
-            # Decrypts secret using the associated KMS CMK.
-            # Depending on whether the secret is a string or binary,
-            # one of these fields will be populated.
-            if "SecretString" in get_secret_value_response:
-                return get_secret_value_response["SecretString"]
-        return base64.b64decode(get_secret_value_response["SecretBinary"])
+            return get_secret_value_response["SecretString"]
 
 
 class ParseResult(UrlLibParseResult):

cool_seq_tool/utils.py

@@ -3,10 +3,12 @@
 import datetime
 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.version import __version__
 
-logger = logging.getLogger(__name__)
+_logger = logging.getLogger(__name__)
 
 
 def get_inter_residue_pos(
@@ -47,3 +49,41 @@ def service_meta() -> ServiceMeta:
         version=__version__,
         response_datetime=datetime.datetime.now(tz=datetime.timezone.utc),
     )
+
+
+def process_chromosome_input(chromosome: str, context: str = "") -> str:
+    """Perform processing on a chromosome arg.
+
+    E.g.
+
+    >>> from cool_seq_tool.utils import process_chromosome_input
+    >>> process_chromosome_input("7")
+    'chr7'
+    >>> process_chromosome_input("x")
+    'chrX'
+    >>> process_chromosome_input("chr7")
+    'chr7'
+
+    In the future, we could also use this method to be more opinionated about legal
+    chromosome values, or throw exceptions in the event of invalid or unrecognized
+    terms.
+
+    :param chromosome: user-provided chromosome input
+    :param context: calling context to provide in log
+    :return: processed chromosome value. Idempotent -- returns original value if no
+        changes needed.
+    """
+    original_chromosome_value = chromosome
+    if chromosome.lower().startswith("chr"):
+        chromosome = f"chr{chromosome[3:].upper()}"
+    else:
+        chromosome = chromosome.upper()
+    chromosome = chr22XY(chromosome)
+    if original_chromosome_value != chromosome:
+        _logger.warning(
+            "Transformed provided chromosome value from `%s` to `%s` in `%s`",
+            original_chromosome_value,
+            chromosome,
+            context if context else "cool_seq_tool",
+        )
+    return chromosome

{cool_seq_tool-0.4.1.dist-info → cool_seq_tool-0.5.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cool_seq_tool
-Version: 0.4.1
+Version: 0.5.1
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -31,7 +31,6 @@ Project-URL: Changelog, https://github.com/genomicmedlab/cool-seq-tool/releases
 Project-URL: Source, https://github.com/genomicmedlab/cool-seq-tool
 Project-URL: Bug Tracker, https://github.com/genomicmedlab/cool-seq-tool/issues
 Classifier: Development Status :: 3 - Alpha
-Classifier: Framework :: FastAPI
 Classifier: Framework :: Pydantic
 Classifier: Framework :: Pydantic :: 2
 Classifier: Intended Audience :: Science/Research
@@ -53,12 +52,11 @@ Requires-Dist: polars ~=1.0
 Requires-Dist: hgvs
 Requires-Dist: biocommons.seqrepo
 Requires-Dist: pydantic ==2.*
-Requires-Dist: uvicorn
-Requires-Dist: fastapi
 Requires-Dist: ga4gh.vrs
 Requires-Dist: wags-tails ~=0.1.3
+Requires-Dist: bioutils
 Provides-Extra: dev
-Requires-Dist: pre-commit ; extra == 'dev'
+Requires-Dist: pre-commit >=3.7.1 ; extra == 'dev'
 Requires-Dist: ipython ; extra == 'dev'
 Requires-Dist: ipykernel ; extra == 'dev'
 Requires-Dist: psycopg2-binary ; extra == 'dev'
@@ -71,11 +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-0.5.1.dist-info/RECORD

@@ -0,0 +1,24 @@
+cool_seq_tool/__init__.py,sha256=fJmjglvv3Ylm0khQSD-XTqdyUA5YzEiS3iB8FGTOhIs,247
+cool_seq_tool/app.py,sha256=DJFcPVHQ5Ar9xdmHwrFKFMqbjDtx3L9gn84_wP63ARY,4982
+cool_seq_tool/schemas.py,sha256=hZ4pStUHgCarXPFLkuGU26znC0dooVDvixO_7eO5eUQ,16301
+cool_seq_tool/utils.py,sha256=mq_eGgqiILDcrtb1trMwRdsTERixuj8kDxHfgwsWsko,2914
+cool_seq_tool/handlers/__init__.py,sha256=KalQ46vX1MO4SJz2SlspKoIRy1n3c3Vp1t4Y2pIfqow,78
+cool_seq_tool/handlers/seqrepo_access.py,sha256=jKUn9mdyK0rHJk9I274N9H_B-M1m4r-hmOX7VwfjRC0,9135
+cool_seq_tool/mappers/__init__.py,sha256=O0JRxNFk8nWxD4v5ij47xelhvfVLdEXS43l2tzRuiUE,305
+cool_seq_tool/mappers/alignment.py,sha256=6Vk4XEar54ivuH8N7oBqa9gUa8E5GjWCI9hC1HCkM18,9552
+cool_seq_tool/mappers/exon_genomic_coords.py,sha256=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/resources/__init__.py,sha256=VwUC8YaucTS6SmRirToulZTF6CuvuLQRSxFfSfAovCc,77
+cool_seq_tool/resources/data_files.py,sha256=3lhu28tzlSoTs4vHZNu-hhoAWRrPGuZj_oIjqk2sYQM,3837
+cool_seq_tool/resources/status.py,sha256=L0KM-VG3N4Yuaqh3AKZd_2KPDLR0Y7rvW_OD6x8mF7A,5717
+cool_seq_tool/resources/transcript_mapping.tsv,sha256=AO3luYQAbFiCoRgiiPXotakb5pAwx1jDCeXpvGdIuac,24138769
+cool_seq_tool/sources/__init__.py,sha256=51QiymeptF7AeVGgV-tW_9f4pIUr0xtYbyzpvHOCneM,304
+cool_seq_tool/sources/mane_transcript_mappings.py,sha256=IQtaRWrIi3f1k0WiDtlmlfOlQQB6bTKSEAh2PHk-Lsw,4079
+cool_seq_tool/sources/transcript_mappings.py,sha256=903RKTMBO2rbKh6iTQ1BEWnY4C7saBFMPw2_4ATuudg,10054
+cool_seq_tool/sources/uta_database.py,sha256=TKMx_yoqWe5QVnqkZe_10x-Lp4PtKvArbMg5ufba0_Q,38353
+cool_seq_tool-0.5.1.dist-info/LICENSE,sha256=IpqC9A-tZW7XXXvCS8c4AVINqkmpxiVA-34Qe3CZSjo,1072
+cool_seq_tool-0.5.1.dist-info/METADATA,sha256=9GLDkcYGYGfUmhlkJ8S1bfjgbzPE2adEKy4iEwsyRnU,6210
+cool_seq_tool-0.5.1.dist-info/WHEEL,sha256=Wyh-_nZ0DJYolHNn1_hMa4lM7uDedD_RGVwbmTjyItk,91
+cool_seq_tool-0.5.1.dist-info/top_level.txt,sha256=cGuxdN6p3y16jQf6hCwWhE4OptwUeZPm_PNJlPb3b0k,14
+cool_seq_tool-0.5.1.dist-info/RECORD,,

{cool_seq_tool-0.4.1.dist-info → cool_seq_tool-0.5.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (70.2.0)
+Generator: setuptools (71.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

cool_seq_tool/api.py

@@ -1,41 +0,0 @@
-"""Main application for FastAPI"""
-
-from fastapi import FastAPI
-from fastapi.openapi.utils import get_openapi
-
-from cool_seq_tool.routers import SERVICE_NAME, default, mane, mappings
-from cool_seq_tool.version import __version__
-
-app = FastAPI(
-    docs_url=f"/{SERVICE_NAME}",
-    openapi_url=f"/{SERVICE_NAME}/openapi.json",
-    swagger_ui_parameters={"tryItOutEnabled": True},
-)
-
-
-app.include_router(default.router)
-app.include_router(mane.router)
-app.include_router(mappings.router)
-
-
-def custom_openapi() -> dict:
-    """Generate custom fields for OpenAPI response."""
-    if app.openapi_schema:
-        return app.openapi_schema
-    openapi_schema = get_openapi(
-        title="The GenomicMedLab Cool-Seq-Tool",
-        version=__version__,
-        description="Common Operations On Lots of Sequences Tool.",
-        routes=app.routes,
-    )
-
-    openapi_schema["info"]["contact"] = {
-        "name": "Alex H. Wagner",
-        "email": "Alex.Wagner@nationwidechildrens.org",
-        "url": "https://www.nationwidechildrens.org/specialties/institute-for-genomic-medicine/research-labs/wagner-lab",
-    }
-    app.openapi_schema = openapi_schema
-    return app.openapi_schema
-
-
-app.openapi = custom_openapi

cool_seq_tool/routers/__init__.py

@@ -1,17 +0,0 @@
-"""Module for routers"""
-
-from enum import Enum
-
-from cool_seq_tool.app import CoolSeqTool
-
-cool_seq_tool = CoolSeqTool()
-SERVICE_NAME = "cool_seq_tool"
-RESP_DESCR = "A response to a validly-formed query."
-UNHANDLED_EXCEPTION_MSG = "Unhandled exception occurred. Check logs for more details."
-
-
-class Tags(str, Enum):
-    """Define tags for endpoints"""
-
-    MANE_TRANSCRIPT = "MANE Transcript"
-    ALIGNMENT_MAPPER = "Alignment Mapper"