cleanup

Author: korikuzma

src/anyvlm/anyvar/base_client.py

@@ -62,10 +62,8 @@ def search_by_interval(
         """Get all variation IDs located within the specified range
 
         :param accession: sequence accession
-        :param start: Inclusive, inter-residue genomic start position of the interval
-            to search
-        :param end: Inclusive, inter-residue genomic end position of the interval to
-            search
+        :param start: start position for genomic region
+        :param end: end position for genomic region
         :return: list of matching variant objects
         :raise AnyVarClientConnectionError: if connection is unsuccessful during search query
         """

src/anyvlm/anyvar/http_client.py

@@ -152,10 +152,8 @@ def search_by_interval(
         """Get all variation IDs located within the specified range
 
         :param accession: sequence accession
-        :param start: Inclusive, inter-residue genomic start position of the interval
-            to search
-        :param end: Inclusive, inter-residue genomic end position of the interval to
-            search
+        :param start: start position for genomic region
+        :param end: end position for genomic region
         :return: list of matching variant objects
         :raise AnyVarClientError: if connection is unsuccessful during search query
         """

src/anyvlm/anyvar/python_client.py

@@ -69,11 +69,9 @@ def get_registered_allele_expression(
         :return: VRS Allele if translation succeeds and VRS Allele has already been registered, else `None`
         """
         translated_variation = self._translate_allele_expression(expression, assembly)
-        if translated_variation and translated_variation.id:
+        if translated_variation:
             try:
-                vrs_variation = self.av.get_object(translated_variation.id, Allele)
-                if isinstance(vrs_variation, Allele):
-                    return vrs_variation
+                return self.av.get_object(translated_variation.id, Allele)  # type: ignore
             except KeyError:
                 _logger.exception(
                     "VRS Allele with ID %s not found", translated_variation.id
@@ -114,10 +112,8 @@ def search_by_interval(
         """Get all variation IDs located within the specified range
 
         :param accession: sequence accession
-        :param start: Inclusive, inter-residue genomic start position of the interval
-            to search
-        :param end: Inclusive, inter-residue genomic end position of the interval to
-            search
+        :param start: start position for genomic region
+        :param end: end position for genomic region
         :return: list of matching variant objects
         """
         try:

src/anyvlm/functions/get_caf.py

@@ -36,14 +36,15 @@ def get_caf(
     :param reference_bases: Genomic bases ('T', 'AC', etc.)
     :param alternate_bases: Genomic bases ('T', 'AC', etc.)
     :raises ValueError: if unsupported assembly ID is provided
-    :return: list of CAFs contained in search interval
+    :return: list of CohortAlleleFrequencyStudyResult objects for the provided variant
     """
     gnomad_vcf: str = f"{reference_name}-{start}-{reference_bases}-{alternate_bases}"
     try:
         assembly = ASSEMBLY_MAP[assembly_id]
     except KeyError as e:
         msg = "Unsupported assembly ID: {assembly_id}"
         raise ValueError(msg) from e
+
     vrs_variation = anyvar_client.get_registered_allele_expression(gnomad_vcf, assembly)
     if not vrs_variation:
         return []

src/anyvlm/storage/mappers.py

@@ -47,16 +47,16 @@ def from_db_entity(
         an = db_entity.an
 
         if filter_ := db_entity.filter:
-            filter_ = QualityMeasures(qcFilters=db_entity.filter).model_dump()
+            quality_measures = QualityMeasures(qcFilters=filter_).model_dump()
         else:
-            filter_ = None
+            quality_measures = None
 
         return CohortAlleleFrequencyStudyResult(
             focusAllele=iriReference(db_entity.vrs_id),
             focusAlleleCount=ac,
             locusAlleleCount=an,
             focusAlleleFrequency=round(ac / an, 9),
-            qualityMeasures=filter_,
+            qualityMeasures=quality_measures,
             ancillaryResults=AncillaryResults(
                 homozygotes=homozygotes,
                 heterozygotes=heterozygotes,
@@ -80,7 +80,7 @@ def to_db_entity(
             raise ValueError("Invalid ancillaryResults data") from e
 
         try:
-            filter_ = QualityMeasures(**va_model.qualityMeasures or {})
+            quality_measures = QualityMeasures(**va_model.qualityMeasures or {})
         except ValidationError as e:
             raise ValueError("Invalid qualityMeasures data") from e
 
@@ -98,6 +98,6 @@ def to_db_entity(
             ac_het=ancillary_results.heterozygotes,
             ac_hom=ancillary_results.homozygotes,
             ac_hemi=ancillary_results.hemizygotes,
-            filter=filter_.qcFilters,
+            filter=quality_measures.qcFilters,
             cohort=va_model.cohort.name,
         )