rename 'GenomicSequence' to NucleotideSequence' for specificity

Author: jennifer-bowser

src/anyvlm/functions/get_caf.py

@@ -5,8 +5,8 @@
 from anyvlm.anyvar.base_client import BaseAnyVarClient
 from anyvlm.utils.types import (
     ChromosomeName,
-    GenomicSequence,
     GrcAssemblyId,
+    NucleotideSequence,
     UcscAssemblyBuild,
 )
 
@@ -16,8 +16,8 @@ def get_caf(
     assembly_id: GrcAssemblyId | UcscAssemblyBuild,
     reference_name: ChromosomeName,
     start: int,
-    reference_bases: GenomicSequence,
-    alternate_bases: GenomicSequence,
+    reference_bases: NucleotideSequence,
+    alternate_bases: NucleotideSequence,
 ) -> list[CohortAlleleFrequencyStudyResult]:
     """Retrieve Cohort Allele Frequency data for all known variants matching provided search params
 

src/anyvlm/restapi/vlm.py

@@ -12,8 +12,8 @@
 from anyvlm.utils.types import (
     ChromosomeName,
     EndpointTag,
-    GenomicSequence,
     GrcAssemblyId,
+    NucleotideSequence,
     UcscAssemblyBuild,
 )
 
@@ -44,10 +44,10 @@ def variant_counts(
     ],
     start: Annotated[int, Query(..., description="Variant position")],
     referenceBases: Annotated[
-        GenomicSequence, Query(..., description="Genomic bases ('T', 'AC', etc.)")
+        NucleotideSequence, Query(..., description="Genomic bases ('T', 'AC', etc.)")
     ],
     alternateBases: Annotated[
-        GenomicSequence, Query(..., description="Genomic bases ('T', 'AC', etc.)")
+        NucleotideSequence, Query(..., description="Genomic bases ('T', 'AC', etc.)")
     ],
 ) -> VlmResponse:
     anyvar_client: BaseAnyVarClient = request.app.state.anyvar_client

src/anyvlm/utils/types.py

@@ -27,7 +27,7 @@ class UcscAssemblyBuild(StrEnum):
     HG19 = "hg19"
 
 
-GenomicSequence = Annotated[
+NucleotideSequence = Annotated[
     str,
     BeforeValidator(str.upper),
     StringConstraints(pattern=r"^[ACGTURYKMSWBDHVN]*$"),