rm gene-normalizer dep + get_mapped_mane_data

GenomicMedLab · Oct 6, 2023 · 036fdc1 · 036fdc1
1 parent 1894458
commit 036fdc1
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Showing 7 changed files with 4 additions and 268 deletions.
diff --git a/Pipfile b/Pipfile
@@ -14,7 +14,6 @@ hgvs = "*"
 pydantic = "*"
 fastapi = "*"
 uvicorn = "*"
-gene-normalizer = ">=0.1.40.dev1, != 0.2.0, != 0.2.1, != 0.2.2, != 0.2.3, != 0.2.4, != 0.2.5, != 0.2.6, != 0.2.7, != 0.2.8, != 0.2.9, != 0.2.10"
 "ga4gh.vrs" = "*"
 
 [dev-packages]

diff --git a/cool_seq_tool/app.py b/cool_seq_tool/app.py
@@ -4,8 +4,6 @@
 import logging
 
 from biocommons.seqrepo import SeqRepo
-from gene.query import QueryHandler as GeneQueryHandler
-from gene.database import create_db
 
 from cool_seq_tool.mappers import (
     MANETranscript, AlignmentMapper, ExonGenomicCoordsMapper
@@ -29,7 +27,7 @@ def __init__(
         transcript_file_path: Path = TRANSCRIPT_MAPPINGS_PATH,
         lrg_refseqgene_path: Path = LRG_REFSEQGENE_PATH,
         mane_data_path: Path = MANE_SUMMARY_PATH,
-        db_url: str = UTA_DB_URL, gene_query_handler: Optional[GeneQueryHandler] = None,
+        db_url: str = UTA_DB_URL,
         sr: Optional[SeqRepo] = None
     ) -> None:
         """Initialize CoolSeqTool class
@@ -39,9 +37,6 @@ def __init__(
         :param mane_data_path: Path to RefSeq MANE summary data
         :param db_url: PostgreSQL connection URL
             Format: `driver://user:password@host/database/schema`
-        :param gene_query_handler: Gene normalizer query handler instance. If this is
-            provided, will use a current instance. If this is not provided, will create
-            a new instance.
         :param sr: SeqRepo instance. If this is not provided, will create a new instance
         """
         if not sr:
@@ -53,13 +48,10 @@ def __init__(
         self.mane_transcript_mappings = MANETranscriptMappings(
             mane_data_path=mane_data_path)
         self.uta_db = UTADatabase(db_url=db_url)
-        if not gene_query_handler:
-            gene_query_handler = GeneQueryHandler(create_db())
-        self.gene_query_handler = gene_query_handler
         self.alignment_mapper = AlignmentMapper(
             self.seqrepo_access, self.transcript_mappings, self.uta_db)
         self.mane_transcript = MANETranscript(
             self.seqrepo_access, self.transcript_mappings,
-            self.mane_transcript_mappings, self.uta_db, self.gene_query_handler)
+            self.mane_transcript_mappings, self.uta_db)
         self.exon_genomic_coords_mapper = ExonGenomicCoordsMapper(self.uta_db,
                                                                   self.mane_transcript)
diff --git a/cool_seq_tool/mappers/mane_transcript.py b/cool_seq_tool/mappers/mane_transcript.py
@@ -12,7 +12,6 @@
 from typing import Optional, Set, Tuple, Dict, List, Union
 
 import pandas as pd
-from gene.query import QueryHandler as GeneQueryHandler
 
 from cool_seq_tool.schemas import (
     AnnotationLayer, Assembly, ResidueMode, TranscriptPriorityLabel
@@ -27,20 +26,13 @@
 logger = logging.getLogger(__name__)
 
 
-class MANETranscriptError(Exception):
-    """Custom exception for MANETranscript class"""
-
-    pass
-
-
 class MANETranscript:
     """Class for retrieving MANE transcripts."""
 
     def __init__(self, seqrepo_access: SeqRepoAccess,
                  transcript_mappings: TranscriptMappings,
                  mane_transcript_mappings: MANETranscriptMappings,
-                 uta_db: UTADatabase,
-                 gene_query_handler: GeneQueryHandler) -> None:
+                 uta_db: UTADatabase) -> None:
         """Initialize the MANETranscript class.
 
         :param seqrepo_access: Access to seqrepo queries
@@ -49,13 +41,11 @@ def __init__(self, seqrepo_access: SeqRepoAccess,
         :param mane_transcript_mappings: Access to MANE Transcript accession mapping
             data
         :param uta_db: UTADatabase instance to give access to query UTA database
-        :param gene_query_handler: Access to Gene Normalizer
         """
         self.seqrepo_access = seqrepo_access
         self.transcript_mappings = transcript_mappings
         self.mane_transcript_mappings = mane_transcript_mappings
         self.uta_db = uta_db
-        self.gene_query_handler = gene_query_handler
 
     @staticmethod
     def _get_reading_frame(pos: int) -> int:
@@ -869,126 +859,3 @@ async def g_to_mane_c(
                 refseq_c_ac=current_mane_data["RefSeq_nuc"],
                 ensembl_c_ac=current_mane_data["Ensembl_nuc"],
                 alt_ac=grch38["ac"] if grch38 else None)
-
-    # Will be added once Chromosome Locations are added back to VRS 2.0-alpha
-    # def _get_hgnc_data(self, gene: str) -> Dict:
-    #     """Return HGNC data for a given gene
-
-    #     :param gene: Gene query
-    #     :return: HGNC data
-    #     """
-    #     hgnc_data = {}
-    #     gene_resp = self.gene_query_handler.normalize_unmerged(gene)
-    #     hgnc_matches = gene_resp.source_matches.get(SourceName.HGNC)
-    #     if hgnc_matches and hgnc_matches.records:
-    #         hgnc_data = hgnc_matches.records[0].dict()
-    #     else:
-    #         logger.warning(f"Unable to get HGNC symbol for {gene}")
-    #     return hgnc_data
-
-    # async def get_mapped_mane_data(
-    #     self, gene: str, assembly: Assembly, genomic_position: int,
-    #     residue_mode: ResidueMode = ResidueMode.INTER_RESIDUE
-    # ) -> Optional[MappedManeData]:
-    #     """Get MANE data for gene, assembly, and position. If GRCh37 assembly is given,  # noqa: E501
-    #     will return mapped MANE data.
-
-    #     :param str gene: Gene symbol or identifier
-    #     :param Assembly assembly: Assembly for the provided genomic position
-    #     :param int genomic_position: Position on the genomic reference sequence to find  # noqa: E501
-    #         MANE data for
-    #     :param ResidueMode residue_mode: Starting residue mode for `start_pos`
-    #         and `end_pos`. Will always return coordinates in inter-residue
-    #     :return: Mapped MANE or Longest Compatible Remaining data if found/compatible.
-    #         MANETranscriptError will be raised if unable to get required data for
-    #         retrieving mapped MANE data.
-    #     """
-    #     hgnc_gene_data = self._get_hgnc_data(gene)
-    #     if not hgnc_gene_data:
-    #         raise MANETranscriptError(f"Unable to get HGNC data for gene: {gene}")
-
-    #     gene = hgnc_gene_data["symbol"]
-
-    #     mane_data = self.mane_transcript_mappings.get_gene_mane_data(gene)
-    #     if not mane_data:
-    #         raise MANETranscriptError(f"Unable to get MANE data for gene: {gene}")
-
-    #     mane_data_len = len(mane_data)
-
-    #     alt_ac = None
-    #     if hgnc_gene_data["locations"]:
-    #         chr = hgnc_gene_data["locations"][0].get("chr") or ""
-    #         alt_acs, _ = self.seqrepo_access.translate_identifier(
-    #             f"{assembly.value}:{chr}", "refseq"
-    #         )
-    #         if alt_acs:
-    #             alt_ac = alt_acs[0].split(":")[1]
-    #         else:
-    #             raise MANETranscriptError(f"Unable to translate identifier for: "
-    #                                       f"{assembly}:{chr}")
-    #     else:
-    #         raise MANETranscriptError("Unable to get HGNC gene location data")
-
-    #     inter_residue_pos, _ = get_inter_residue_pos(genomic_position, residue_mode)
-    #     g_pos = inter_residue_pos[0]
-
-    #     mane_transcripts = set()
-    #     for i in range(mane_data_len):
-    #         index = mane_data_len - i - 1
-    #         current_mane_data = mane_data[index]
-    #         mane_transcripts |= set((current_mane_data["RefSeq_nuc"],
-    #                                  current_mane_data["Ensembl_nuc"]))
-    #         mane_c_ac = current_mane_data["RefSeq_nuc"]
-
-    #         ac_query = mane_c_ac.split(".")[0]
-    #         tx_exon_aln_v_data = await self.uta_db.get_tx_exon_aln_v_data(
-    #             ac_query, g_pos, g_pos, alt_ac, False, True)
-
-    #         if not tx_exon_aln_v_data:
-    #             continue
-    #         else:
-    #             len_of_aligned_data = len(tx_exon_aln_v_data)
-    #             if len_of_aligned_data == 1:
-    #                 tx_exon_aln_v_data = tx_exon_aln_v_data[0]
-    #             else:
-    #                 logger.debug(f"Found {len_of_aligned_data} records for aligned "
-    #                              f"mapped MANE data for {ac_query}, {g_pos}, {alt_ac}")  # noqa: E501
-
-    #                 # Try checking for MANE match
-    #                 filter_data = list(filter(lambda x: x[1] == mane_c_ac,
-    #                                           tx_exon_aln_v_data))
-    #                 if filter_data:
-    #                     tx_exon_aln_v_data = filter_data[0]
-    #                 else:
-    #                     # Try checking for older versions of MANE
-    #                     filter_data = list(filter(lambda x: x[1].startswith(
-    #                         mane_c_ac.split(".")[0]), tx_exon_aln_v_data))
-    #                     if filter_data:
-    #                         filter_data.sort(key=lambda x: x[1], reverse=True)
-    #                         tx_exon_aln_v_data = filter_data[0]
-    #         return MappedManeData(
-    #             gene=gene,
-    #             refseq=current_mane_data["RefSeq_nuc"],
-    #             ensembl=current_mane_data["Ensembl_nuc"],
-    #             strand="-" if tx_exon_aln_v_data[7] == -1 else "+",
-    #             status="_".join(current_mane_data["MANE_status"].split()).lower(),
-    #             alt_ac=alt_ac,
-    #             assembly=assembly.value
-    #         )
-
-    #     lcr_data = await self.get_longest_compatible_transcript(
-    #         gene, g_pos, g_pos, AnnotationLayer.GENOMIC,
-    #         residue_mode=ResidueMode.INTER_RESIDUE, mane_transcripts=mane_transcripts,
-    #         alt_ac=alt_ac)
-    #     if lcr_data:
-    #         return MappedManeData(
-    #             gene=gene,
-    #             refseq=lcr_data["refseq"],
-    #             ensembl=lcr_data["ensembl"],
-    #             strand=lcr_data["strand"],
-    #             status=lcr_data["status"],
-    #             alt_ac=alt_ac,
-    #             assembly=assembly.value
-    #         )
-
-    #     return None
diff --git a/cool_seq_tool/routers/mane.py b/cool_seq_tool/routers/mane.py
@@ -76,53 +76,3 @@ async def get_mane_data(
         warnings=warnings,
         service_meta=cool_seq_tool.service_meta()
     )
-
-
-# @router.get(
-#     "/get_mapped_mane_data",
-#     summary="Retrieve MANE Transcript mapped to a given assembly",
-#     response_description=RESP_DESCR,
-#     description="Return mapped MANE Transcript data to a given assembly",
-#     response_model=MappedManeDataService,
-#     tags=[Tags.MANE_TRANSCRIPT]
-# )
-# async def get_mapped_mane_data(
-#     gene: str = Query(..., description="HGNC Symbol or Identifier"),
-#     assembly: Assembly = Query(..., description="Genomic assembly to use"),
-#     genomic_position: int = Query(..., description="Genomic position associated to the given gene and assembly"),  # noqa: E501
-#     residue_mode: ResidueMode = Query(ResidueMode.INTER_RESIDUE,
-#                                       description="Residue mode for `genomic_position`")  # noqa: E501
-# ) -> MappedManeDataService:
-#     """Get MANE data for gene, assembly, and position. If GRCh37 assembly is given,
-#     will return mapped MANE data.
-
-#     :param str gene: HGNC symbol or identifier
-#     :param Assembly assembly: Assembly for the provided genomic position
-#     :param int genomic_position: Position on the genomic reference sequence to find
-#         MANE data for
-#     :param ResidueMode residue_mode: Starting residue mode for `start_pos`
-#         and `end_pos`. Will always return coordinates in inter-residue
-#     :return: Mapped MANE or Longest Compatible Remaining data
-#     """
-#     warnings: List = list()
-#     mapped_mane_data = None
-#     try:
-#         mapped_mane_data = await cool_seq_tool.mane_transcript.get_mapped_mane_data(
-#             gene, assembly, genomic_position, residue_mode)
-#         if not mapped_mane_data:
-#             warnings.append(f"Unable to find mapped data for gene {gene} at position "
-#                             f"{genomic_position} ({residue_mode} coordinates) on "
-#                             f"assembly {assembly}")
-#     except MANETranscriptError as e:
-#         e = str(e)
-#         logger.exception(e)
-#         warnings.append(e)
-#     except Exception as e:
-#         logger.exception(f"get_mapped_mane_data unhandled exception {e}")
-#         warnings.append(UNHANDLED_EXCEPTION_MSG)
-
-#     return MappedManeDataService(
-#         mapped_mane_data=mapped_mane_data,
-#         warnings=warnings,
-#         service_meta=cool_seq_tool.service_meta()
-#     )
diff --git a/setup.cfg b/setup.cfg
@@ -23,7 +23,6 @@ install_requires =
     pydantic
     uvicorn
     fastapi
-    gene-normalizer >=0.1.40.dev1, != 0.2.0, != 0.2.1, != 0.2.2, != 0.2.3, != 0.2.4, != 0.2.5, != 0.2.6, != 0.2.7, != 0.2.8, != 0.2.9, != 0.2.10
     ga4gh.vrs
 
 [options.package_data]

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -42,9 +42,3 @@ def test_transcript_mappings(test_cool_seq_tool):
 def test_mane_transcript_mappings(test_cool_seq_tool):
     """Create MANE Transcript Mappings test fixture"""
     return test_cool_seq_tool.mane_transcript_mappings
-
-
-@pytest.fixture(scope="session")
-def test_gene_query_handler(test_cool_seq_tool):
-    """Create Gene Query Handler test fixture"""
-    return test_cool_seq_tool.gene_query_handler
diff --git a/tests/mappers/test_mane_transcript.py b/tests/mappers/test_mane_transcript.py
@@ -5,9 +5,8 @@
 from mock import patch
 import pandas as pd
 
-from cool_seq_tool.mappers.mane_transcript import MANETranscriptError
 from cool_seq_tool.handlers.seqrepo_access import SeqRepoAccess
-from cool_seq_tool.schemas import AnnotationLayer, Assembly, ResidueMode
+from cool_seq_tool.schemas import AnnotationLayer
 
 
 @pytest.fixture(scope="module")
@@ -565,70 +564,6 @@ async def test_g_to_mane_c(test_mane_transcript, egfr_l858r_mane_c,
     }
 
 
-@pytest.mark.skipif(True, reason="chromosome locations not supported in 2.0-alpha")
-@pytest.mark.asyncio
-async def test_get_mapped_mane_data(test_mane_transcript):
-    """Test that get_mapped_mane_data works correctly"""
-    resp = await test_mane_transcript.get_mapped_mane_data(
-        "braf", Assembly.GRCH38, 140785808, ResidueMode.INTER_RESIDUE)
-    assert resp.model_dump() == {
-        "gene": "BRAF",
-        "refseq": "NM_001374258.1",
-        "ensembl": "ENST00000644969.2",
-        "strand": "-",
-        "status": "mane_plus_clinical",
-        "alt_ac": "NC_000007.14",
-        "assembly": "GRCh38"
-    }
-
-    resp = await test_mane_transcript.get_mapped_mane_data(
-        "Braf", Assembly.GRCH37, 140485608, ResidueMode.INTER_RESIDUE)
-    assert resp.model_dump() == {
-        "gene": "BRAF",
-        "refseq": "NM_001374258.1",
-        "ensembl": "ENST00000644969.2",
-        "strand": "-",
-        "status": "mane_plus_clinical",
-        "alt_ac": "NC_000007.13",
-        "assembly": "GRCh37"
-    }
-
-    resp = await test_mane_transcript.get_mapped_mane_data(
-        "BRAF", Assembly.GRCH38, 140783157, ResidueMode.INTER_RESIDUE)
-    assert resp.model_dump() == {
-        "gene": "BRAF",
-        "refseq": "NM_004333.6",
-        "ensembl": "ENST00000646891.2",
-        "strand": "-",
-        "status": "mane_select",
-        "alt_ac": "NC_000007.14",
-        "assembly": "GRCh38"
-    }
-
-    resp = await test_mane_transcript.get_mapped_mane_data(
-        "BRAF", Assembly.GRCH37, 140482958, ResidueMode.RESIDUE)
-    assert resp.model_dump() == {
-        "gene": "BRAF",
-        "refseq": "NM_004333.6",
-        "ensembl": "ENST00000646891.2",
-        "strand": "-",
-        "status": "mane_select",
-        "alt_ac": "NC_000007.13",
-        "assembly": "GRCh37"
-    }
-
-    # Invalid coord given assembly, so no result should be found
-    resp = await test_mane_transcript.get_mapped_mane_data(
-        "BRAF", Assembly.GRCH38, 140482957, ResidueMode.INTER_RESIDUE)
-    assert resp is None
-
-    # Invalid gene
-    with pytest.raises(MANETranscriptError) as e:
-        await test_mane_transcript.get_mapped_mane_data(
-            "dummy", Assembly.GRCH37, 140482958, ResidueMode.RESIDUE)
-    assert str(e.value) == "Unable to get HGNC data for gene: dummy"
-
-
 @pytest.mark.asyncio
 async def test_valid(test_mane_transcript):
     """Test that valid queries do not raise any exceptions"""