cool-seq-tool 0.14.4__py3-none-any.whl → 0.15.0__py3-none-any.whl

cool_seq_tool/app.py

@@ -107,6 +107,7 @@ class CoolSeqTool:
         self.ex_g_coords_mapper = ExonGenomicCoordsMapper(
             self.seqrepo_access,
             self.uta_db,
+            self.mane_transcript,
             self.mane_transcript_mappings,
             self.liftover,
         )

cool_seq_tool/mappers/exon_genomic_coords.py

@@ -2,17 +2,21 @@
 
 import logging
 
+from ga4gh.core.models import Extension
 from ga4gh.vrs.models import SequenceLocation, SequenceReference
 from pydantic import ConfigDict, Field, StrictInt, StrictStr, model_validator
 
 from cool_seq_tool.handlers.seqrepo_access import SeqRepoAccess
 from cool_seq_tool.mappers.liftover import LiftOver
+from cool_seq_tool.mappers.mane_transcript import ManeTranscript
 from cool_seq_tool.schemas import (
+    AnnotationLayer,
     Assembly,
     BaseModelForbidExtra,
     CoordinateType,
     ServiceMeta,
     Strand,
+    TranscriptPriority,
 )
 from cool_seq_tool.sources.mane_transcript_mappings import ManeTranscriptMappings
 from cool_seq_tool.sources.uta_database import GenomicAlnData, UtaDatabase
@@ -65,9 +69,6 @@ class TxSegment(BaseModelForbidExtra):
     genomic_location: SequenceLocation = Field(
         ..., description="The genomic position of a transcript segment."
     )
-    is_exonic: bool = Field(
-        default=True, description="If the position occurs on an exon"
-    )
 
     @model_validator(mode="before")
     def check_seg_pos(cls, values: dict) -> dict:  # noqa: N805
@@ -99,8 +100,8 @@ class TxSegment(BaseModelForbidExtra):
                         "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                     },
                     "end": 154192135,
+                    "extensions": [{"name": "is_exonic", "value": True}],
                 },
-                "is_exonic": True,
             }
         }
     )
@@ -115,6 +116,9 @@ class GenomicTxSeg(BaseModelForbidExtra):
     )
     genomic_ac: StrictStr | None = Field(None, description="RefSeq genomic accession.")
     tx_ac: StrictStr | None = Field(None, description="RefSeq transcript accession.")
+    tx_status: TranscriptPriority | None = Field(
+        None, description="Transcript priority for RefSeq transcript accession"
+    )
     strand: Strand | None = Field(
         None, description="The strand that the transcript accession exists on."
     )
@@ -146,6 +150,7 @@ class GenomicTxSeg(BaseModelForbidExtra):
                 "gene": "TPM3",
                 "genomic_ac": "NC_000001.11",
                 "tx_ac": "NM_152263.3",
+                "tx_status": "longest_compatible_remaining",
                 "strand": -1,
                 "seg": {
                     "exon_ord": 0,
@@ -157,8 +162,8 @@ class GenomicTxSeg(BaseModelForbidExtra):
                             "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                         },
                         "end": 154192135,
+                        "extensions": [{"name": "is_exonic", "value": True}],
                     },
-                    "is_exonic": True,
                 },
                 "errors": [],
             }
@@ -174,6 +179,9 @@ class GenomicTxSegService(BaseModelForbidExtra):
     )
     genomic_ac: StrictStr | None = Field(None, description="RefSeq genomic accession.")
     tx_ac: StrictStr | None = Field(None, description="RefSeq transcript accession.")
+    tx_status: TranscriptPriority | None = Field(
+        None, description="Transcript priority for RefSeq transcript accession"
+    )
     strand: Strand | None = Field(
         None, description="The strand that the transcript exists on."
     )
@@ -213,6 +221,7 @@ class GenomicTxSegService(BaseModelForbidExtra):
                 "gene": "TPM3",
                 "genomic_ac": "NC_000001.11",
                 "tx_ac": "NM_152263.3",
+                "tx_status": "longest_compatible_remaining",
                 "strand": -1,
                 "seg_start": {
                     "exon_ord": 0,
@@ -224,8 +233,8 @@ class GenomicTxSegService(BaseModelForbidExtra):
                             "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                         },
                         "end": 154192135,
+                        "extensions": [{"name": "is_exonic", "value": True}],
                     },
-                    "is_exonic": True,
                 },
                 "seg_end": {
                     "exon_ord": 7,
@@ -237,8 +246,8 @@ class GenomicTxSegService(BaseModelForbidExtra):
                             "refgetAccession": "SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO",
                         },
                         "start": 154170399,
+                        "extensions": [{"name": "is_exonic", "value": True}],
                     },
-                    "is_exonic": True,
                 },
             }
         }
@@ -266,6 +275,7 @@ class ExonGenomicCoordsMapper:
         self,
         seqrepo_access: SeqRepoAccess,
         uta_db: UtaDatabase,
+        mane_transcript: ManeTranscript,
         mane_transcript_mappings: ManeTranscriptMappings,
         liftover: LiftOver,
     ) -> None:
@@ -290,11 +300,13 @@ class ExonGenomicCoordsMapper:
 
         :param seqrepo_access: SeqRepo instance to give access to query SeqRepo database
         :param uta_db: UtaDatabase instance to give access to query UTA database
+        :param mane_transcript: ManeTranscript instance to give access to ManeTranscript class
         :param mane_transcript_mappings: Instance to provide access to ManeTranscriptMappings class
         :param liftover: Instance to provide mapping between human genome assemblies
         """
         self.seqrepo_access = seqrepo_access
         self.uta_db = uta_db
+        self.mane_transcript = mane_transcript
         self.mane_transcript_mappings = mane_transcript_mappings
         self.liftover = liftover
 
@@ -433,6 +445,7 @@ class ExonGenomicCoordsMapper:
             gene=gene,
             genomic_ac=genomic_ac,
             tx_ac=transcript,
+            tx_status=self.mane_transcript_mappings.get_transcript_status(transcript),
             strand=strand,
             seg_start=seg_start,
             seg_end=seg_end,
@@ -524,6 +537,7 @@ class ExonGenomicCoordsMapper:
             params["gene"] = start_tx_seg_data.gene
             params["genomic_ac"] = start_tx_seg_data.genomic_ac
             params["tx_ac"] = start_tx_seg_data.tx_ac
+            params["tx_status"] = start_tx_seg_data.tx_status
             params["strand"] = start_tx_seg_data.strand
             params["seg_start"] = start_tx_seg_data.seg
         else:
@@ -559,6 +573,7 @@ class ExonGenomicCoordsMapper:
                 params["gene"] = end_tx_seg_data.gene
                 params["genomic_ac"] = end_tx_seg_data.genomic_ac
                 params["tx_ac"] = end_tx_seg_data.tx_ac
+                params["tx_status"] = end_tx_seg_data.tx_status
                 params["strand"] = end_tx_seg_data.strand
 
             params["seg_end"] = end_tx_seg_data.seg
@@ -730,7 +745,12 @@ class ExonGenomicCoordsMapper:
         ), None
 
     def _get_vrs_seq_loc(
-        self, genomic_ac: str, genomic_pos: int, is_seg_start: bool, strand: Strand
+        self,
+        genomic_ac: str,
+        genomic_pos: int,
+        is_seg_start: bool,
+        strand: Strand,
+        is_exonic: bool = True,
     ) -> tuple[SequenceLocation | None, str | None]:
         """Create VRS Sequence Location for genomic position where transcript segment
         occurs
@@ -740,6 +760,8 @@ class ExonGenomicCoordsMapper:
         :param is_seg_start: ``True`` if ``genomic_pos`` is where the transcript segment
             starts. ``False`` if ``genomic_pos`` is where the transcript segment ends.
         :param strand: Strand
+        :param is_exonic: A boolean indicating if the genomic breakpoint occurs
+            on an exon. By default, this is set to ``True``.
         :return: Tuple containing VRS location (if successful) and error message (if
             unable to get GA4GH identifier for ``genomic_ac``).
         """
@@ -759,6 +781,7 @@ class ExonGenomicCoordsMapper:
             ),
             start=genomic_pos if use_start else None,
             end=genomic_pos if not use_start else None,
+            extensions=[Extension(name="is_exonic", value=is_exonic)],
         ), None
 
     async def _genomic_to_tx_segment(
@@ -852,14 +875,18 @@ class ExonGenomicCoordsMapper:
             if mane_transcripts:
                 transcript = mane_transcripts[0]["RefSeq_nuc"]
             else:
-                # Attempt to find a coding transcript if a MANE transcript
+                # Attempt to find longest compatible transcript if a MANE transcript
                 # cannot be found
-                results = await self.uta_db.get_transcripts(
-                    gene=gene, alt_ac=genomic_ac
+                results = await self.mane_transcript.get_longest_compatible_transcript(
+                    start_pos=genomic_pos,
+                    end_pos=genomic_pos,
+                    gene=gene,
+                    alt_ac=genomic_ac,
+                    start_annotation_layer=AnnotationLayer.GENOMIC,
                 )
 
-                if not results.is_empty():
-                    transcript = results[0]["tx_ac"][0]
+                if results:
+                    transcript = results.refseq
                 else:
                     # Run if gene is for a noncoding transcript
                     query = f"""
@@ -947,7 +974,7 @@ class ExonGenomicCoordsMapper:
         )
 
         genomic_location, err_msg = self._get_vrs_seq_loc(
-            genomic_ac, genomic_pos, is_seg_start, strand
+            genomic_ac, genomic_pos, is_seg_start, strand, is_exonic
         )
         if err_msg:
             return GenomicTxSeg(errors=[err_msg])
@@ -956,12 +983,12 @@ class ExonGenomicCoordsMapper:
             gene=gene,
             genomic_ac=genomic_ac,
             tx_ac=transcript,
+            tx_status=self.mane_transcript_mappings.get_transcript_status(transcript),
             strand=strand,
             seg=TxSegment(
                 exon_ord=exon_num,
                 offset=offset,
                 genomic_location=genomic_location,
-                is_exonic=is_exonic,
             ),
         )
 

cool_seq_tool/resources/status.py

@@ -3,6 +3,7 @@
 import logging
 from collections import namedtuple
 from pathlib import Path
+from urllib.parse import urlparse
 
 from agct._core import ChainfileError
 from asyncpg import InvalidCatalogNameError, UndefinedTableError
@@ -11,7 +12,7 @@ from biocommons.seqrepo import SeqRepo
 from cool_seq_tool.handlers.seqrepo_access import SEQREPO_ROOT_DIR, SeqRepoAccess
 from cool_seq_tool.mappers.liftover import LiftOver
 from cool_seq_tool.resources.data_files import DataFile, get_data_file
-from cool_seq_tool.sources.uta_database import UTA_DB_URL, UtaDatabase
+from cool_seq_tool.sources.uta_database import UTA_DB_URL, ParseResult, UtaDatabase
 
 _logger = logging.getLogger(__name__)
 
@@ -119,14 +120,20 @@ async def check_status(
     else:
         status["liftover"] = True
 
+    parsed_result = ParseResult(urlparse(db_url))
+    sanitized_url = parsed_result.sanitized_url
     try:
         await UtaDatabase.create(db_url)
+    except ValueError:
+        _logger.exception("Database URL is not valid")
     except (OSError, InvalidCatalogNameError, UndefinedTableError):
-        _logger.exception("Encountered error instantiating UTA at URI %s", UTA_DB_URL)
+        _logger.exception(
+            "Encountered error instantiating UTA at URI %s", sanitized_url
+        )
     except Exception as e:
         _logger.critical(
             "Encountered unexpected error instantiating UTA from URI %s: %s",
-            UTA_DB_URL,
+            sanitized_url,
             e,
         )
     else:

cool_seq_tool/sources/mane_transcript_mappings.py

@@ -8,7 +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
+from cool_seq_tool.schemas import ManeGeneData, TranscriptPriority
 
 _logger = logging.getLogger(__name__)
 
@@ -85,6 +85,22 @@ class ManeTranscriptMappings:
             return []
         return mane_rows.to_dicts()
 
+    def get_transcript_status(self, tx_ac: str) -> TranscriptPriority:
+        """Get MANE status for a transcript
+
+        :param tx_ac: A RefSeq transcript accession
+        :return: A TranscriptPriority object
+        """
+        mane_info = self.get_mane_from_transcripts([tx_ac])
+        if not mane_info:
+            return TranscriptPriority.LONGEST_COMPATIBLE_REMAINING
+        mane_info = mane_info[0]["MANE_status"]
+        return (
+            TranscriptPriority.MANE_SELECT
+            if mane_info == "MANE Select"
+            else TranscriptPriority.MANE_PLUS_CLINICAL
+        )
+
     def get_mane_data_from_chr_pos(
         self, alt_ac: str, start: int, end: int
     ) -> list[dict]:

cool_seq_tool/sources/uta_database.py

@@ -5,7 +5,7 @@ import logging
 from os import environ
 from typing import Any, Literal, TypeVar
 from urllib.parse import ParseResult as UrlLibParseResult
-from urllib.parse import quote, unquote, urlparse
+from urllib.parse import unquote, urlparse, urlunparse
 
 import asyncpg
 import boto3
@@ -101,8 +101,7 @@ class UtaDatabase:
         """
         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.db_url = db_url
         self.args = self._get_conn_args()
 
     def _get_conn_args(self) -> DbConnectionArgs:
@@ -954,3 +953,28 @@ class ParseResult(UrlLibParseResult):
         """Create schema property."""
         path_elems = self.path.split("/")
         return path_elems[2] if len(path_elems) > 2 else None
+
+    @property
+    def sanitized_url(self) -> str:
+        """Sanitized DB URL with the password masked"""
+        netloc = ""
+        if self.username:
+            netloc += self.username
+            if self.password is not None and self.password != "":
+                netloc += ":***"
+            netloc += "@"
+        if self.hostname:
+            netloc += f"{self.hostname}"
+        if self.port:
+            netloc += f":{self.port}"
+
+        return urlunparse(
+            (
+                self.scheme,
+                netloc,
+                self.path,
+                self.params,
+                self.query,
+                self.fragment,
+            )
+        )

{cool_seq_tool-0.14.4.dist-info → cool_seq_tool-0.15.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cool_seq_tool
-Version: 0.14.4
+Version: 0.15.0
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -50,7 +50,7 @@ Requires-Dist: agct>=0.1.0-dev1
 Requires-Dist: polars~=1.0
 Requires-Dist: biocommons.seqrepo
 Requires-Dist: pydantic<3.0,>=2.0
-Requires-Dist: ga4gh.vrs<3.0,>=2.1.3
+Requires-Dist: ga4gh.vrs<3.0,>=2.1.4
 Requires-Dist: wags-tails~=0.4.0
 Requires-Dist: bioutils
 Provides-Extra: dev

{cool_seq_tool-0.14.4.dist-info → cool_seq_tool-0.15.0.dist-info}/RECORD

@@ -1,25 +1,25 @@
 cool_seq_tool/__init__.py,sha256=pJyVj7Z275BBAwpeFMm-WEn_tp-y1_ihRl1sLc4FFZY,400
-cool_seq_tool/app.py,sha256=vyqlQRffC8sWZXMm-f_f-8WuTTWo3oRNfPUa_qdPV2M,4944
+cool_seq_tool/app.py,sha256=ThdumeXtLNrrGkQW9wwLT3Zm_Fc1wzg88ZxLIwMzcJU,4978
 cool_seq_tool/schemas.py,sha256=6c87iuA6v7BX7a8nkWEqFbJTksFysuuIeuYxkNCrAsI,5356
 cool_seq_tool/utils.py,sha256=jra2ZHS7HUqXqabSvyqd5imf6kkhYL8nQd20BWNLpb8,2950
 cool_seq_tool/handlers/__init__.py,sha256=KalQ46vX1MO4SJz2SlspKoIRy1n3c3Vp1t4Y2pIfqow,78
 cool_seq_tool/handlers/seqrepo_access.py,sha256=lRzPc8V0eZJTlefbHuVKeZTEC8-KcyPzpqX7vx3amu8,9118
 cool_seq_tool/mappers/__init__.py,sha256=tavpwkNogg_nF1J_kb6Q9jk7ezqdRz063v7BMZ4koLM,390
 cool_seq_tool/mappers/alignment.py,sha256=kWgYssM8YL-Z13H9GdpL77P7simNcbxltAs9YDXHE54,9640
-cool_seq_tool/mappers/exon_genomic_coords.py,sha256=fV4LyrpHPLRrx6AtV15g93q5XCH3i-y3Wj9tl-Cg8mM,45845
+cool_seq_tool/mappers/exon_genomic_coords.py,sha256=I59vvswLbXk1fOWLNyNd8NTVT39f5yxTCv20utlTCpo,47361
 cool_seq_tool/mappers/feature_overlap.py,sha256=X5UFClaH6ixRsO2fDLxqjywp-Z0bvNx4uzgBICy394U,9758
 cool_seq_tool/mappers/liftover.py,sha256=lltx9zxfkrb5PHtJlKp3a39JCwPP4e0Zft-mQc1jXL8,3367
 cool_seq_tool/mappers/mane_transcript.py,sha256=IluiLBxPQoY-CxkpqpjEBcMlHvrNLa34wdKdQxtKgDY,54613
 cool_seq_tool/resources/__init__.py,sha256=VwUC8YaucTS6SmRirToulZTF6CuvuLQRSxFfSfAovCc,77
 cool_seq_tool/resources/data_files.py,sha256=6d1M5WjeFHdTQpzxqjQ78auQRZvIBVqH8QNCrmRRDXw,4205
-cool_seq_tool/resources/status.py,sha256=5UKx5FIQuyIY7FU4kSinDIM4MhLpr9_MiQDDBNt9kRo,5990
+cool_seq_tool/resources/status.py,sha256=iP-4NiSmqV-D--gypZyrSqVbOWQvyBZICKQb-VinTik,6241
 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=C5puIA1xuEzBaSvs8VtSxVb2OIDGUg5no8v6Ma2QSdw,6597
+cool_seq_tool/sources/mane_transcript_mappings.py,sha256=PLJymduwvG1pt9mravE58BfJsGXdAYXcZYZdHPy12z0,7211
 cool_seq_tool/sources/transcript_mappings.py,sha256=903RKTMBO2rbKh6iTQ1BEWnY4C7saBFMPw2_4ATuudg,10054
-cool_seq_tool/sources/uta_database.py,sha256=zzRzmYuybqzEg7zeuQjhK46SPK5GfbiWWNRGNJju8AI,36197
-cool_seq_tool-0.14.4.dist-info/licenses/LICENSE,sha256=IpqC9A-tZW7XXXvCS8c4AVINqkmpxiVA-34Qe3CZSjo,1072
-cool_seq_tool-0.14.4.dist-info/METADATA,sha256=gPz48irXCwNUecTcgpKrdrHiBhi8R_Is55S2UYs9Qtk,6535
-cool_seq_tool-0.14.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-cool_seq_tool-0.14.4.dist-info/top_level.txt,sha256=cGuxdN6p3y16jQf6hCwWhE4OptwUeZPm_PNJlPb3b0k,14
-cool_seq_tool-0.14.4.dist-info/RECORD,,
+cool_seq_tool/sources/uta_database.py,sha256=38CQ0QHHh0kA87tdgsJHJiHdJHQc06ylBYfemGFUlZc,36759
+cool_seq_tool-0.15.0.dist-info/licenses/LICENSE,sha256=IpqC9A-tZW7XXXvCS8c4AVINqkmpxiVA-34Qe3CZSjo,1072
+cool_seq_tool-0.15.0.dist-info/METADATA,sha256=MEcG0vc2k8F8lQljcFgkIrabFHJec_pE7Ib6DzLZR2M,6535
+cool_seq_tool-0.15.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+cool_seq_tool-0.15.0.dist-info/top_level.txt,sha256=cGuxdN6p3y16jQf6hCwWhE4OptwUeZPm_PNJlPb3b0k,14
+cool_seq_tool-0.15.0.dist-info/RECORD,,