fix!: Expect user to supply valid, case-sensitive HGNC symbol (#375)

closes #374
GenomicMedLab · Oct 29, 2024 · f1448f4 · f1448f4
1 parent e9a917e
commit f1448f4
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Showing 2 changed files with 14 additions and 22 deletions.
diff --git a/src/cool_seq_tool/mappers/exon_genomic_coords.py b/src/cool_seq_tool/mappers/exon_genomic_coords.py
@@ -87,7 +87,9 @@ class GenomicTxSeg(BaseModelForbidExtra):
     """Model for representing a boundary for a transcript segment."""
 
     seg: TxSegment | None = Field(None, description="Transcript segment.")
-    gene: StrictStr | None = Field(None, description="HGNC gene symbol.")
+    gene: StrictStr | None = Field(
+        None, description="Valid, case-sensitive HGNC gene symbol."
+    )
     genomic_ac: StrictStr | None = Field(None, description="RefSeq genomic accession.")
     tx_ac: StrictStr | None = Field(None, description="RefSeq transcript accession.")
     errors: list[StrictStr] = Field([], description="Error messages.")
@@ -139,7 +141,9 @@ def check_errors(cls, values: dict) -> dict:  # noqa: N805
 class GenomicTxSegService(BaseModelForbidExtra):
     """Service model for genomic and transcript data."""
 
-    gene: StrictStr | None = Field(None, description="HGNC gene symbol.")
+    gene: StrictStr | None = Field(
+        None, description="Valid, case-sensitive HGNC gene symbol."
+    )
     genomic_ac: StrictStr | None = Field(None, description="RefSeq genomic accession.")
     tx_ac: StrictStr | None = Field(None, description="RefSeq transcript accession.")
     seg_start: TxSegment | None = Field(None, description="Start transcript segment.")
@@ -292,7 +296,7 @@ async def tx_segment_to_genomic(
         ('NC_000001.11', 154192135, 154170399)
 
         :param transcript: RefSeq transcript accession
-        :param gene: HGNC gene symbol
+        :param gene: Valid, case-sensitive HGNC gene symbol
         :param exon_start: Starting transcript exon number (1-based). If not provided,
             must provide ``exon_end``
         :param exon_start_offset: Starting exon offset
@@ -335,9 +339,6 @@ async def tx_segment_to_genomic(
         if errors:
             return _return_service_errors(errors)
 
-        if gene:
-            gene = gene.upper()
-
         # Get aligned genomic data (hgnc gene, alt_ac, alt_start_i, alt_end_i, strand)
         # for exon(s)
         (
@@ -455,7 +456,7 @@ async def genomic_to_tx_segment(
             following the breakpoint for the 3' end. For the negative strand, adjacent
             is defined as the exon following the breakpoint for the 5' end and the exon
             preceding the breakpoint for the 3' end.
-        :param gene: gene name. Ideally, HGNC symbol. Must be given if no ``transcript``
+        :param gene: A valid, case-sensitive HGNC symbol. Must be given if no ``transcript``
             value is provided.
         :param coordinate_type: Coordinate type for ``seg_start_genomic`` and
             ``seg_end_genomic``
@@ -473,9 +474,6 @@ async def genomic_to_tx_segment(
         if errors:
             return _return_service_errors(errors)
 
-        if gene is not None:
-            gene = gene.upper()
-
         params = {}
 
         if seg_start_genomic:
@@ -630,7 +628,7 @@ async def _get_genomic_aln_coords(
             must provide ``tx_exon_end``
         :param tx_exon_end: Transcript's exon end coordinates. If not provided, must
             provide ``tx_exon_start``
-        :param gene: HGNC gene symbol
+        :param gene: A valid, case-sensitive HGNC gene symbol
         :return: Tuple containing aligned genomic data for start and end exon and
             warnings if found
         """
@@ -755,7 +753,7 @@ async def _genomic_to_tx_segment(
         :param transcript: The transcript to use. If this is not given, we will try the
             following transcripts: MANE Select, MANE Clinical Plus, Longest Remaining
             Compatible Transcript
-        :param gene: HGNC gene symbol
+        :param gene: Valid, case-sensitive HGNC gene symbol
         :param get_nearest_transcript_junction: If ``True``, this will return the
             adjacent exon if the position specified by``seg_start_genomic`` or
             ``seg_end_genomic`` does not occur on an exon. For the positive strand, adjacent
@@ -1062,7 +1060,7 @@ async def _get_tx_seg_genomic_metadata(
         :param genomic_ac: Genomic RefSeq accession
         :param genomic_pos: Genomic position where the transcript segment occurs
         :param is_seg_start: Whether or not ``genomic_pos`` represents the start position.
-        :param gene: HGNC gene symbol
+        :param gene: Valid, case-sensitive HGNC gene symbol
         :param tx_ac: Transcript RefSeq accession. If not provided, will use MANE
             transcript
         :return: Transcript segment data and associated genomic metadata

diff --git a/tests/mappers/test_exon_genomic_coords.py b/tests/mappers/test_exon_genomic_coords.py
@@ -1162,7 +1162,7 @@ async def test_wee1(test_egc_mapper, wee1_exon2_exon11, mane_wee1_exon2_exon11):
         "seg_start_genomic": 9597639,
         "seg_end_genomic": 9609996,
         "transcript": "NM_003390.3",
-        "gene": "wee1",
+        "gene": "WEE1",
     }
     g_to_t_resp = await test_egc_mapper.genomic_to_tx_segment(**inputs)
     genomic_tx_seg_service_checks(g_to_t_resp, wee1_exon2_exon11)
@@ -1177,7 +1177,7 @@ async def test_wee1(test_egc_mapper, wee1_exon2_exon11, mane_wee1_exon2_exon11):
         "genomic_ac": "NC_000011.9",
         "seg_start_genomic": 9597639,  # GRCh38 coords: 9576092
         "seg_end_genomic": 9609996,  # GRCh38 coords: 9588449
-        "gene": "wee1",
+        "gene": "WEE1",
     }
     g_to_t_resp = await test_egc_mapper.genomic_to_tx_segment(**inputs)
     genomic_tx_seg_service_checks(g_to_t_resp, mane_wee1_exon2_exon11)
@@ -1216,12 +1216,6 @@ async def test_transcript_to_genomic(
     expected.seg_end.genomic_location.start = 154170399
     genomic_tx_seg_service_checks(resp, expected)
 
-    resp = await test_egc_mapper.tx_segment_to_genomic(
-        exon_start=None, exon_end=8, gene="tpm3", transcript="NM_152263.3"
-    )
-    expected.seg_end.genomic_location.start = 154170399
-    genomic_tx_seg_service_checks(resp, expected)
-
     expected = tpm3_exon1_exon8.model_copy(deep=True)
     resp = await test_egc_mapper.tx_segment_to_genomic(
         exon_start=1, exon_end=8, exon_end_offset=-5, transcript="NM_152263.3"
@@ -1371,7 +1365,7 @@ async def test_invalid(test_egc_mapper):
         gene="dummy gene",
     )
     genomic_tx_seg_service_checks(resp, is_valid=False)
-    assert resp.errors == ["Expected gene, DUMMY GENE, but found TPM3"]
+    assert resp.errors == ["Expected gene, dummy gene, but found TPM3"]
 
     # Invalid accession
     resp = await test_egc_mapper.genomic_to_tx_segment(