cool-seq-tool 0.6.0__py3-none-any.whl → 0.7.1__py3-none-any.whl

cool_seq_tool/mappers/mane_transcript.py

@@ -25,8 +25,9 @@ from cool_seq_tool.mappers.liftover import LiftOver
 from cool_seq_tool.schemas import (
     AnnotationLayer,
     Assembly,
+    CoordinateType,
+    GenomicTxMetadata,
     ManeGeneData,
-    ResidueMode,
     Strand,
     TranscriptPriority,
 )
@@ -101,7 +102,7 @@ class ManeTranscript:
         A handful of resources are required for initialization, so when defaults are
         enough, it's easiest to let the core CoolSeqTool class handle it for you:
 
-        >>> from cool_seq_tool.app import CoolSeqTool
+        >>> from cool_seq_tool import CoolSeqTool
         >>> mane_mapper = CoolSeqTool().mane_transcript
 
         Note that most methods are defined as Python coroutines, so they must be called
@@ -182,13 +183,12 @@ class ManeTranscript:
         pos = self._p_to_c_pos(start_pos, end_pos)
         return ac, pos
 
-    async def _c_to_g(self, ac: str, pos: tuple[int, int]) -> dict | None:
+    async def _c_to_g(self, ac: str, pos: tuple[int, int]) -> GenomicTxMetadata | None:
         """Get g. annotation from c. annotation.
 
         :param ac: cDNA accession
         :param pos: [cDNA pos start, cDNA pos end]
-        :return: Gene, Transcript accession and position change,
-            Altered transcript accession and position change, Strand
+        :return: Metadata for genomic and transcript accessions
         """
         # UTA does not store ENST versions
         # So we want to make sure version is valid
@@ -220,13 +220,13 @@ class ManeTranscript:
             ac, pos, AnnotationLayer.CDNA, coding_start_site=coding_start_site
         )
 
-    async def _liftover_to_38(self, genomic_tx_data: dict) -> None:
+    async def _liftover_to_38(self, genomic_tx_data: GenomicTxMetadata) -> None:
         """Liftover genomic_tx_data to hg38 assembly.
 
-        :param genomic_tx_data: Dictionary containing gene, nc_accession, alt_pos, and
-            strand. This will be mutated in-place if not GRCh38 assembly.
+        :param genomic_tx_data: Metadata for genomic and transcript accessions. This
+            will be mutated in-place if not GRCh38 assembly.
         """
-        descr = await self.uta_db.get_chr_assembly(genomic_tx_data["alt_ac"])
+        descr = await self.uta_db.get_chr_assembly(genomic_tx_data.alt_ac)
         if descr is None:
             # already grch38
             return
@@ -235,14 +235,14 @@ class ManeTranscript:
         query = f"""
             SELECT DISTINCT alt_ac
             FROM {self.uta_db.schema}.tx_exon_aln_v
-            WHERE tx_ac = '{genomic_tx_data['tx_ac']}';
+            WHERE tx_ac = '{genomic_tx_data.tx_ac}';
             """  # noqa: S608
         nc_acs = await self.uta_db.execute_query(query)
         nc_acs = [nc_ac[0] for nc_ac in nc_acs]
-        if nc_acs == [genomic_tx_data["alt_ac"]]:
+        if nc_acs == [genomic_tx_data.alt_ac]:
             _logger.warning(
                 "UTA does not have GRCh38 assembly for %s",
-                genomic_tx_data["alt_ac"].split(".")[0],
+                genomic_tx_data.alt_ac.split(".")[0],
             )
             return
 
@@ -258,7 +258,7 @@ class ManeTranscript:
         )
 
         # Change alt_ac to most recent
-        if genomic_tx_data["alt_ac"].startswith("EN"):
+        if genomic_tx_data.alt_ac.startswith("EN"):
             order_by_cond = "ORDER BY alt_ac DESC;"
         else:
             order_by_cond = """
@@ -268,50 +268,49 @@ class ManeTranscript:
         query = f"""
             SELECT alt_ac
             FROM {self.uta_db.schema}.genomic
-            WHERE alt_ac LIKE '{genomic_tx_data['alt_ac'].split('.')[0]}%'
+            WHERE alt_ac LIKE '{genomic_tx_data.alt_ac.split('.')[0]}%'
             {order_by_cond}
             """  # noqa: S608
         nc_acs = await self.uta_db.execute_query(query)
-        genomic_tx_data["alt_ac"] = nc_acs[0][0]
+        genomic_tx_data.alt_ac = nc_acs[0][0]
 
     def _set_liftover(
         self,
-        genomic_tx_data: dict,
+        genomic_tx_data: GenomicTxMetadata,
         key: str,
         chromosome: str,
         liftover_to_assembly: Assembly,
     ) -> None:
         """Update genomic_tx_data to have coordinates for given assembly.
 
-        :param genomic_tx_data: Dictionary containing gene, nc_accession, alt_pos, and
-            strand
+        :param genomic_tx_data: Metadata for genomic and transcript accessions
         :param key: Key to access coordinate positions
         :param chromosome: Chromosome, must be prefixed with ``chr``
         :param liftover_to_assembly: Assembly to liftover to
         """
+        coords = getattr(genomic_tx_data, key)
         liftover_start_i = self.liftover.get_liftover(
-            chromosome, genomic_tx_data[key][0], liftover_to_assembly
+            chromosome, coords[0], liftover_to_assembly
         )
         if liftover_start_i is None:
             _logger.warning(
                 "Unable to liftover position %s on %s",
-                genomic_tx_data[key][0],
+                coords[0],
                 chromosome,
             )
             return
 
         liftover_end_i = self.liftover.get_liftover(
-            chromosome, genomic_tx_data[key][1], liftover_to_assembly
+            chromosome, coords[1], liftover_to_assembly
         )
         if liftover_end_i is None:
             _logger.warning(
                 "Unable to liftover position %s on %s",
-                genomic_tx_data[key][1],
+                coords[1],
                 chromosome,
             )
             return
-
-        genomic_tx_data[key] = liftover_start_i[1], liftover_end_i[1]
+        setattr(genomic_tx_data, key, (liftover_start_i[1], liftover_end_i[1]))
 
     async def _get_and_validate_genomic_tx_data(
         self,
@@ -321,7 +320,7 @@ class ManeTranscript:
         | Literal[AnnotationLayer.GENOMIC] = AnnotationLayer.CDNA,
         coding_start_site: int | None = None,
         alt_ac: str | None = None,
-    ) -> dict | None:
+    ) -> GenomicTxMetadata | None:
         """Get and validate genomic_tx_data
 
         :param tx_ac: Accession on c. coordinate
@@ -329,7 +328,8 @@ class ManeTranscript:
         :param annotation_layer: Annotation layer for ``ac`` and ``pos``
         :param coding_start_site: Coding start site
         :param alt_ac: Accession on g. coordinate
-        :return: genomic_tx_data if found and validated, else None
+        :return: Metadata for genomic and transcript accessions if found and validated,
+            else None
         """
         genomic_tx_data = await self.uta_db.get_genomic_tx_data(
             tx_ac, pos, annotation_layer, alt_ac=alt_ac
@@ -342,14 +342,14 @@ class ManeTranscript:
                 annotation_layer,
             )
             return None
-        genomic_tx_data["coding_start_site"] = coding_start_site
+        genomic_tx_data.coding_start_site = coding_start_site
 
         if not alt_ac:
             # Only want to liftover if alt_ac not provided. If alt_ac is provided,
             # it means user wants to stick with the queried assembly
-            og_alt_exon_id = genomic_tx_data["alt_exon_id"]
+            og_alt_exon_id = genomic_tx_data.alt_exon_id
             await self._liftover_to_38(genomic_tx_data)
-            liftover_alt_exon_id = genomic_tx_data["alt_exon_id"]
+            liftover_alt_exon_id = genomic_tx_data.alt_exon_id
 
             # Validation check: Exon structure
             if og_alt_exon_id != liftover_alt_exon_id:
@@ -467,14 +467,14 @@ class ManeTranscript:
         :return: Transcript data
         """
         if found_result:
-            tx_g_pos = g["alt_pos_range"]
-            tx_pos_range = g["tx_pos_range"]
+            tx_g_pos = g.alt_pos_range
+            tx_pos_range = g.tx_pos_range
         else:
             result = await self.uta_db.get_tx_exon_aln_v_data(
                 refseq_c_ac,
-                g["alt_pos_change_range"][0],
-                g["alt_pos_change_range"][1],
-                alt_ac=alt_ac if alt_ac else g["alt_ac"],
+                g.alt_pos_change_range[0],
+                g.alt_pos_change_range[1],
+                alt_ac=alt_ac if alt_ac else g.alt_ac,
                 use_tx_pos=False,
             )
 
@@ -484,18 +484,18 @@ class ManeTranscript:
                 )
                 return None
             result = result[-1]
-            tx_g_pos = result[5], result[6]  # alt_start_i, alt_end_i
-            tx_pos_range = result[2], result[3]  # tx_start_i, tx_end_i
+            tx_g_pos = result.alt_start_i, result.alt_end_i
+            tx_pos_range = result.tx_start_i, result.tx_end_i
 
         cds_start_end = await self.uta_db.get_cds_start_end(refseq_c_ac)
         if not cds_start_end:
             return None
         coding_start_site = cds_start_end[0]
 
-        g_pos = g["alt_pos_change_range"]  # start/end genomic change
+        g_pos = g.alt_pos_change_range  # start/end genomic change
         g_pos_change = g_pos[0] - tx_g_pos[0], tx_g_pos[1] - g_pos[1]
 
-        if g["strand"] == Strand.NEGATIVE:
+        if g.strand == Strand.NEGATIVE:
             g_pos_change = (tx_g_pos[1] - g_pos[0], g_pos[1] - tx_g_pos[0])
 
         c_pos_change = (
@@ -507,10 +507,10 @@ class ManeTranscript:
             c_pos_change = c_pos_change[1], c_pos_change[0]
 
         return self._get_c_data(
-            gene=g["gene"],
+            gene=g.gene,
             cds_start_end=cds_start_end,
             c_pos_change=c_pos_change,
-            strand=g["strand"],
+            strand=g.strand,
             alt_ac=alt_ac,
             status=status,
             refseq_c_ac=refseq_c_ac,
@@ -562,7 +562,7 @@ class ManeTranscript:
         | GenomicRepresentation,
         expected_ref: str,
         anno: AnnotationLayer,
-        residue_mode: ResidueMode,
+        coordinate_type: CoordinateType,
     ) -> bool:
         """Return whether or not reference changes are the same.
 
@@ -574,7 +574,7 @@ class ManeTranscript:
             position change
         :param expected_ref: Reference at position given during input
         :param anno: Annotation layer we are starting from
-        :param residue_mode: Residue mode for ``start_pos`` and ``end_pos``
+        :param coordinate_type: Coordinate type for ``start_pos`` and ``end_pos``
         :return: ``True`` if reference check passes. ``False`` otherwise.
         """
         if anno == AnnotationLayer.CDNA:
@@ -582,7 +582,7 @@ class ManeTranscript:
             end_pos += coding_start_site
 
         ref, _ = self.seqrepo_access.get_reference_sequence(
-            ac, start=start_pos, end=end_pos, residue_mode=residue_mode
+            ac, start=start_pos, end=end_pos, coordinate_type=coordinate_type
         )
         if ref is None:
             return False
@@ -598,7 +598,7 @@ class ManeTranscript:
                 mane_transcript.refseq,
                 start=mane_start_pos,
                 end=mane_end_pos if mane_start_pos != mane_end_pos else None,
-                residue_mode=residue_mode,
+                coordinate_type=coordinate_type,
             )
             if not mane_ref:
                 _logger.info("Unable to validate reference for MANE Transcript")
@@ -633,7 +633,10 @@ class ManeTranscript:
         end_pos = pos[1] + coding_start_site
         return bool(
             self.seqrepo_access.get_reference_sequence(
-                ac, start=start_pos, end=end_pos, residue_mode=ResidueMode.INTER_RESIDUE
+                ac,
+                start=start_pos,
+                end=end_pos,
+                coordinate_type=CoordinateType.INTER_RESIDUE,
             )[0]
         )
 
@@ -690,7 +693,7 @@ class ManeTranscript:
         start_annotation_layer: AnnotationLayer,
         gene: str | None = None,
         ref: str | None = None,
-        residue_mode: ResidueMode = ResidueMode.RESIDUE,
+        coordinate_type: CoordinateType = CoordinateType.RESIDUE,
         mane_transcripts: set | None = None,
         alt_ac: str | None = None,
         end_annotation_layer: EndAnnotationLayer | None = None,
@@ -700,8 +703,8 @@ class ManeTranscript:
         information.
 
         >>> import asyncio
-        >>> from cool_seq_tool.app import CoolSeqTool
-        >>> from cool_seq_tool.schemas import AnnotationLayer, ResidueMode
+        >>> from cool_seq_tool import CoolSeqTool
+        >>> from cool_seq_tool.schemas import AnnotationLayer, CoordinateType
         >>> mane_mapper = CoolSeqTool().mane_transcript
         >>> mane_transcripts = {
         ...     "ENST00000646891.2",
@@ -715,7 +718,7 @@ class ManeTranscript:
         ...         599,
         ...         gene="BRAF",
         ...         start_annotation_layer=AnnotationLayer.PROTEIN,
-        ...         residue_mode=ResidueMode.INTER_RESIDUE,
+        ...         coordinate_type=CoordinateType.INTER_RESIDUE,
         ...         mane_transcripts=mane_transcripts,
         ...     )
         ... )
@@ -732,7 +735,7 @@ class ManeTranscript:
         :param start_annotation_layer: Starting annotation layer
         :param gene: HGNC gene symbol
         :param ref: Reference at position given during input
-        :param residue_mode: Residue mode for ``start_pos`` and ``end_pos``
+        :param coordinate_type: Coordinate type for ``start_pos`` and ``end_pos``
         :param mane_transcripts: Attempted mane transcripts that were not compatible
         :param alt_ac: Genomic accession
         :param end_annotation_layer: The end annotation layer. If not provided, will be
@@ -768,8 +771,8 @@ class ManeTranscript:
             )
 
         lcr_result = None
-        start_pos, end_pos = get_inter_residue_pos(start_pos, end_pos, residue_mode)
-        residue_mode = ResidueMode.INTER_RESIDUE
+        start_pos, end_pos = get_inter_residue_pos(start_pos, end_pos, coordinate_type)
+        coordinate_type = CoordinateType.INTER_RESIDUE
 
         is_p_or_c_start_anno = True
         if start_annotation_layer == AnnotationLayer.PROTEIN:
@@ -857,7 +860,7 @@ class ManeTranscript:
                         {},
                         ref,
                         AnnotationLayer.PROTEIN,
-                        residue_mode,
+                        coordinate_type,
                     )
                 elif start_annotation_layer == AnnotationLayer.CDNA:
                     valid_references = self._validate_references(
@@ -868,7 +871,7 @@ class ManeTranscript:
                         {},
                         ref,
                         AnnotationLayer.CDNA,
-                        residue_mode,
+                        coordinate_type,
                     )
                 else:
                     valid_references = self._validate_references(
@@ -879,7 +882,7 @@ class ManeTranscript:
                         {},
                         ref,
                         AnnotationLayer.GENOMIC,
-                        residue_mode,
+                        coordinate_type,
                     )
 
                 if not valid_references:
@@ -903,7 +906,7 @@ class ManeTranscript:
                         gene,
                         row["pro_ac"],
                         lcr_c_data.pos,
-                        g["strand"],
+                        g.strand,
                         lcr_c_data.status,
                     )
                     coding_start_site = 0
@@ -925,7 +928,7 @@ class ManeTranscript:
                     gene,
                     row["pro_ac"],
                     lcr_c_data.pos,
-                    g["strand"],
+                    g.strand,
                     lcr_c_data.status,
                 ),
                 cdna=lcr_c_data,
@@ -960,8 +963,8 @@ class ManeTranscript:
         gene: str | None = None,
         ref: str | None = None,
         try_longest_compatible: bool = False,
-        residue_mode: Literal[ResidueMode.RESIDUE]
-        | Literal[ResidueMode.INTER_RESIDUE] = ResidueMode.RESIDUE,
+        coordinate_type: Literal[CoordinateType.RESIDUE]
+        | Literal[CoordinateType.INTER_RESIDUE] = CoordinateType.RESIDUE,
     ) -> DataRepresentation | CdnaRepresentation | None:
         """Return MANE representation
 
@@ -974,8 +977,8 @@ class ManeTranscript:
             ``AnnotationLayer.GENOMIC`` GRCh38 representation if ``gene`` is NOT
             provided.
 
-        >>> from cool_seq_tool.app import CoolSeqTool
-        >>> from cool_seq_tool.schemas import AnnotationLayer, ResidueMode
+        >>> from cool_seq_tool import CoolSeqTool
+        >>> from cool_seq_tool.schemas import AnnotationLayer, CoordinateType
         >>> import asyncio
         >>> mane_mapper = CoolSeqTool().mane_transcript
         >>> result = asyncio.run(
@@ -983,7 +986,7 @@ class ManeTranscript:
         ...         "NP_004324.2",
         ...         599,
         ...         AnnotationLayer.PROTEIN,
-        ...         residue_mode=ResidueMode.INTER_RESIDUE,
+        ...         coordinate_type=CoordinateType.INTER_RESIDUE,
         ...     )
         ... )
         >>> result.gene, result.refseq, result.status
@@ -1001,13 +1004,13 @@ class ManeTranscript:
         :param ref: Reference at position given during input
         :param try_longest_compatible: ``True`` if should try longest compatible remaining
             if mane transcript was not compatible. ``False`` otherwise.
-        :param ResidueMode residue_mode: Starting residue mode for ``start_pos`` and
-            ``end_pos``. Will always return coordinates in inter-residue
+        :param CoordinateType coordinate_type: Starting Coordinate type for
+            ``start_pos`` and ``end_pos``. Will always return inter-residue coordinates
         :return: MANE data or longest transcript compatible data if validation
             checks are correct. Will return inter-residue coordinates. Else, ``None``.
         """
-        start_pos, end_pos = get_inter_residue_pos(start_pos, end_pos, residue_mode)
-        residue_mode = ResidueMode.INTER_RESIDUE
+        start_pos, end_pos = get_inter_residue_pos(start_pos, end_pos, coordinate_type)
+        coordinate_type = CoordinateType.INTER_RESIDUE
         if ref:
             ref = ref[: end_pos - start_pos]
 
@@ -1026,7 +1029,7 @@ class ManeTranscript:
             if g is None:
                 return None
             # Get mane data for gene
-            mane_data = self.mane_transcript_mappings.get_gene_mane_data(g["gene"])
+            mane_data = self.mane_transcript_mappings.get_gene_mane_data(g.gene)
             if not mane_data:
                 return None
 
@@ -1053,10 +1056,8 @@ class ManeTranscript:
                 if not mane:
                     continue
 
-                if not mane.alt_ac:
-                    g_alt_ac = g.get("alt_ac")
-                    if g_alt_ac:
-                        mane.alt_ac = g_alt_ac
+                if not mane.alt_ac and g.alt_ac:
+                    mane.alt_ac = g.alt_ac
 
                 valid_reading_frame = self._validate_reading_frames(
                     c_ac, c_pos[0], c_pos[1], mane
@@ -1072,13 +1073,13 @@ class ManeTranscript:
                 if ref:
                     valid_references = self._validate_references(
                         ac,
-                        g["coding_start_site"],
+                        g.coding_start_site,
                         start_pos,
                         end_pos,
                         mane,
                         ref,
                         start_annotation_layer,
-                        residue_mode,
+                        coordinate_type,
                     )
                     if not valid_references:
                         continue
@@ -1092,8 +1093,8 @@ class ManeTranscript:
                         end_pos,
                         AnnotationLayer.PROTEIN,
                         ref=ref,
-                        gene=g["gene"],
-                        residue_mode=residue_mode,
+                        gene=g.gene,
+                        coordinate_type=coordinate_type,
                         mane_transcripts=mane_transcripts,
                     )
                 return await self.get_longest_compatible_transcript(
@@ -1102,7 +1103,7 @@ class ManeTranscript:
                     AnnotationLayer.CDNA,
                     ref=ref,
                     gene=g["gene"],
-                    residue_mode=residue_mode,
+                    coordinate_type=coordinate_type,
                     mane_transcripts=mane_transcripts,
                 )
             return None
@@ -1113,11 +1114,11 @@ class ManeTranscript:
                     start_pos,
                     end_pos,
                     get_mane_genes=True,
-                    residue_mode=residue_mode,
+                    coordinate_type=coordinate_type,
                 )
 
             return await self.g_to_mane_c(
-                ac, start_pos, end_pos, gene, residue_mode=residue_mode
+                ac, start_pos, end_pos, gene, coordinate_type=coordinate_type
             )
         _logger.warning("Annotation layer not supported: %s", start_annotation_layer)
         return None
@@ -1128,7 +1129,7 @@ class ManeTranscript:
         start_pos: int,
         end_pos: int,
         get_mane_genes: bool = False,
-        residue_mode: ResidueMode = ResidueMode.RESIDUE,
+        coordinate_type: CoordinateType = CoordinateType.RESIDUE,
     ) -> GenomicRepresentation | None:
         """Return genomic coordinate on GRCh38 when not given gene context.
 
@@ -1137,11 +1138,11 @@ class ManeTranscript:
         :param end_pos: Genomic end position
         :param get_mane_genes: ``True`` if mane genes for genomic position should be
             included in response. ``False``, otherwise.
-        :param residue_mode: Residue mode for ``start_pos`` and ``end_pos``
+        :param coordinate_type: Coordinate type for ``start_pos`` and ``end_pos``
         :return: GRCh38 genomic representation (accession and start/end inter-residue
             position)
         """
-        start_pos, end_pos = get_inter_residue_pos(start_pos, end_pos, residue_mode)
+        start_pos, end_pos = get_inter_residue_pos(start_pos, end_pos, coordinate_type)
 
         # Checking to see what chromosome and assembly we're on
         descr = await self.uta_db.get_chr_assembly(ac)
@@ -1200,7 +1201,7 @@ class ManeTranscript:
 
     @staticmethod
     def get_mane_c_pos_change(
-        mane_tx_genomic_data: dict, coding_start_site: int
+        mane_tx_genomic_data: GenomicTxMetadata, coding_start_site: int
     ) -> tuple[int, int]:
         """Get mane c position change
 
@@ -1208,12 +1209,12 @@ class ManeTranscript:
         :param coding_start_site: Coding start site
         :return: cDNA pos start, cDNA pos end
         """
-        tx_pos_range = mane_tx_genomic_data["tx_pos_range"]
-        alt_pos_change = mane_tx_genomic_data["alt_pos_change"]
+        tx_pos_range = mane_tx_genomic_data.tx_pos_range
+        pos_change = mane_tx_genomic_data.pos_change
 
         mane_c_pos_change = (
-            tx_pos_range[0] + alt_pos_change[0] - coding_start_site,
-            tx_pos_range[1] - alt_pos_change[1] - coding_start_site,
+            tx_pos_range[0] + pos_change[0] - coding_start_site,
+            tx_pos_range[1] - pos_change[1] - coding_start_site,
         )
 
         if mane_c_pos_change[0] > mane_c_pos_change[1]:
@@ -1226,12 +1227,12 @@ class ManeTranscript:
         start_pos: int,
         end_pos: int,
         gene: str,
-        residue_mode: ResidueMode = ResidueMode.RESIDUE,
+        coordinate_type: CoordinateType = CoordinateType.RESIDUE,
     ) -> CdnaRepresentation | None:
         """Return MANE Transcript on the c. coordinate.
 
         >>> import asyncio
-        >>> from cool_seq_tool.app import CoolSeqTool
+        >>> from cool_seq_tool import CoolSeqTool
         >>> cst = CoolSeqTool()
         >>> result = asyncio.run(
         ...     cst.mane_transcript.g_to_mane_c(
@@ -1248,12 +1249,12 @@ class ManeTranscript:
         :param start_pos: genomic start position
         :param end_pos: genomic end position
         :param gene: HGNC gene symbol
-        :param residue_mode: Starting residue mode for ``start_pos`` and ``end_pos``.
-            Will always return coordinates in inter-residue.
+        :param coordinate_type: Starting Coordinate type for ``start_pos`` and
+            ``end_pos``. Will always return inter-residue coordinates.
         :return: MANE Transcripts with cDNA change on c. coordinate
         """
-        start_pos, end_pos = get_inter_residue_pos(start_pos, end_pos, residue_mode)
-        residue_mode = ResidueMode.INTER_RESIDUE
+        start_pos, end_pos = get_inter_residue_pos(start_pos, end_pos, coordinate_type)
+        coordinate_type = CoordinateType.INTER_RESIDUE
 
         if not await self.uta_db.validate_genomic_ac(ac):
             _logger.warning("Genomic accession does not exist: %s", ac)
@@ -1268,7 +1269,11 @@ class ManeTranscript:
 
             # Liftover to GRCh38
             grch38 = await self.g_to_grch38(
-                ac, start_pos, end_pos, get_mane_genes=False, residue_mode=residue_mode
+                ac,
+                start_pos,
+                end_pos,
+                get_mane_genes=False,
+                coordinate_type=coordinate_type,
             )
             mane_tx_genomic_data = None
             if grch38:
@@ -1286,8 +1291,8 @@ class ManeTranscript:
                     continue
                 _logger.info("Not using most recent assembly")
 
-            coding_start_site = mane_tx_genomic_data["coding_start_site"]
-            coding_end_site = mane_tx_genomic_data["coding_end_site"]
+            coding_start_site = mane_tx_genomic_data.coding_start_site
+            coding_end_site = mane_tx_genomic_data.coding_end_site
             mane_c_pos_change = self.get_mane_c_pos_change(
                 mane_tx_genomic_data, coding_start_site
             )
@@ -1323,7 +1328,7 @@ class ManeTranscript:
         start_pos: int,
         end_pos: int,
         gene: str | None = None,
-        residue_mode: ResidueMode = ResidueMode.RESIDUE,
+        coordinate_type: CoordinateType = CoordinateType.RESIDUE,
         try_longest_compatible: bool = False,
     ) -> dict | None:
         """Given GRCh38 genomic representation, return protein representation.
@@ -1336,8 +1341,8 @@ class ManeTranscript:
         :param start_pos: Start position
         :param end_pos: End position
         :param gene: HGNC gene symbol
-        :param residue_mode: Starting residue mode for ``start_pos`` and ``end_pos``. Will
-            always return coordinates as inter-residue.
+        :param coordinate_type: Starting Coordinate type for ``start_pos`` and
+            ``end_pos``. Will always return inter-residue coordinates.
         :param try_longest_compatible: ``True`` if should try longest compatible remaining
             if mane transcript(s) not compatible. ``False`` otherwise.
         :return: If successful, return MANE data or longest compatible remaining (if
@@ -1356,8 +1361,8 @@ class ManeTranscript:
             return None
 
         # Step 2: Get inter-residue position
-        start_pos, end_pos = get_inter_residue_pos(start_pos, end_pos, residue_mode)
-        residue_mode = ResidueMode.INTER_RESIDUE
+        start_pos, end_pos = get_inter_residue_pos(start_pos, end_pos, coordinate_type)
+        coordinate_type = CoordinateType.INTER_RESIDUE
 
         # Step 3: Try getting MANE protein representation
         mane_transcripts = set()  # Used if getting longest compatible remaining
@@ -1373,8 +1378,8 @@ class ManeTranscript:
                 continue
 
             # Get MANE C positions
-            coding_start_site = mane_tx_genomic_data["coding_start_site"]
-            coding_end_site = mane_tx_genomic_data["coding_end_site"]
+            coding_start_site = mane_tx_genomic_data.coding_start_site
+            coding_end_site = mane_tx_genomic_data.coding_end_site
             mane_c_pos_change = self.get_mane_c_pos_change(
                 mane_tx_genomic_data, coding_start_site
             )
@@ -1394,7 +1399,7 @@ class ManeTranscript:
                 cdna=self._get_c_data(
                     (coding_start_site, coding_end_site),
                     mane_c_pos_change,
-                    mane_tx_genomic_data["strand"],
+                    mane_tx_genomic_data.strand,
                     TranscriptPriority(
                         "_".join(current_mane_data["MANE_status"].split()).lower()
                     ),
@@ -1410,7 +1415,7 @@ class ManeTranscript:
                 start_pos,
                 end_pos,
                 AnnotationLayer.GENOMIC,
-                residue_mode=residue_mode,
+                coordinate_type=coordinate_type,
                 alt_ac=alt_ac,
                 end_annotation_layer=EndAnnotationLayer.PROTEIN_AND_CDNA,
                 mane_transcripts=mane_transcripts,