build: pin cool-seq-tool version ~=0.9.1 (#589)

close #588

pyproject.toml

@@ -31,7 +31,7 @@ dependencies = [
     "ga4gh.vrs[extras] ==2.0.0a13",
     "gene-normalizer ~=0.6.0",
     "boto3",
-    "cool-seq-tool ~=0.6.0",
+    "cool-seq-tool ~=0.9.1",
     "bioutils"
 ]
 dynamic = ["version"]

src/variation/hgvs_dup_del_mode.py

@@ -1,7 +1,7 @@
 """Module for hgvs_dup_del_mode in normalize endpoint."""
 
 from cool_seq_tool.handlers import SeqRepoAccess
-from cool_seq_tool.schemas import ResidueMode
+from cool_seq_tool.schemas import CoordinateType
 from ga4gh.core import ga4gh_identify
 from ga4gh.core.models import (
     Extension,
@@ -179,7 +179,7 @@ def allele_mode(
                 vrs_seq_loc_ac,
                 start=location["start"],
                 end=location["end"],
-                residue_mode=ResidueMode.INTER_RESIDUE,
+                coordinate_type=CoordinateType.INTER_RESIDUE,
             )
 
             if ref:

src/variation/main.py

@@ -10,7 +10,7 @@
 
 import pkg_resources
 from bioutils.exceptions import BioutilsError
-from cool_seq_tool.schemas import Assembly, ResidueMode
+from cool_seq_tool.schemas import Assembly, CoordinateType
 from fastapi import FastAPI, Query
 from ga4gh.vrs import models
 from ga4gh.vrs.dataproxy import DataProxyValidationError
@@ -678,8 +678,8 @@ async def p_to_c(
     p_ac: str = Query(..., description="Protein RefSeq accession"),
     p_start_pos: int = Query(..., description="Protein start position"),
     p_end_pos: int = Query(..., description="Protein end position"),
-    residue_mode: ResidueMode = Query(
-        ResidueMode.RESIDUE,
+    residue_mode: CoordinateType = Query(
+        CoordinateType.RESIDUE,
         description="Residue mode for `p_start_pos` and `p_end_pos`",
     ),
 ) -> ToCdnaService:
@@ -688,7 +688,7 @@ async def p_to_c(
     :param str p_ac: Protein RefSeq accession
     :param int p_start_pos: Protein start position
     :param int p_end_pos: Protein end position
-    :param ResidueMode residue_mode: Residue mode for `p_start_pos` and `p_end_pos`.
+    :param CoordinateType residue_mode: Residue mode for `p_start_pos` and `p_end_pos`.
     :return: ToCdnaService containing cDNA representation, warnings, and
         service meta
     """
@@ -727,8 +727,8 @@ async def c_to_g(
     cds_start: int | None = Query(
         None, description="CDS start site. If not provided, this will be computed."
     ),
-    residue_mode: ResidueMode = Query(
-        ResidueMode.RESIDUE,
+    residue_mode: CoordinateType = Query(
+        CoordinateType.RESIDUE,
         description="Residue mode for `c_start_pos` and `c_end_pos`",
     ),
     target_genome_assembly: Assembly = Query(
@@ -742,7 +742,7 @@ async def c_to_g(
     :param int c_end_pos: cDNA end position for codon
     :param Optional[int] cds_start: CDS start site. If not provided, this will be
         computed.
-    :param ResidueMode residue_mode: Residue mode for `c_start_pos` and `c_end_pos`.
+    :param CoordinateType residue_mode: Residue mode for `c_start_pos` and `c_end_pos`.
     :param Assembly target_genome_assembly: Genome assembly to get genomic data for
     :return: ToGenomicService containing genomic representation, warnings, and
         service meta
@@ -753,7 +753,7 @@ async def c_to_g(
             c_start_pos,
             c_end_pos,
             cds_start=cds_start,
-            residue_mode=residue_mode,
+            coordinate_type=residue_mode,
             target_genome_assembly=target_genome_assembly,
         )
     except Exception as e:
@@ -784,8 +784,8 @@ async def p_to_g(
     p_ac: str = Query(..., description="Protein RefSeq accession"),
     p_start_pos: int = Query(..., description="Protein start position"),
     p_end_pos: int = Query(..., description="Protein end position"),
-    residue_mode: ResidueMode = Query(
-        ResidueMode.RESIDUE,
+    residue_mode: CoordinateType = Query(
+        CoordinateType.RESIDUE,
         description="Residue mode for `p_start_pos` and `p_end_pos`",
     ),
     target_genome_assembly: Assembly = Query(
@@ -797,7 +797,7 @@ async def p_to_g(
     :param str p_ac: Protein RefSeq accession
     :param int p_start_pos: Protein start position
     :param int p_end_pos: Protein end position
-    :param ResidueMode residue_mode: Residue mode for `p_start_pos` and `p_end_pos`.
+    :param CoordinateType residue_mode: Residue mode for `p_start_pos` and `p_end_pos`.
     :param Assembly target_genome_assembly: Genome assembly to get genomic data for
     :return: ToGenomicService containing genomic representation, warnings, and
         service meta
@@ -807,7 +807,7 @@ async def p_to_g(
             p_ac,
             p_start_pos,
             p_end_pos,
-            residue_mode=residue_mode,
+            coordinate_type=residue_mode,
             target_genome_assembly=target_genome_assembly,
         )
     except Exception as e:

src/variation/schemas/service_schema.py

@@ -3,7 +3,7 @@
 from enum import Enum
 from typing import Literal
 
-from cool_seq_tool.schemas import ResidueMode
+from cool_seq_tool.schemas import CoordinateType
 from pydantic import BaseModel, ConfigDict, StrictInt, StrictStr
 
 from variation import __version__
@@ -28,7 +28,7 @@ class CdnaRepresentation(BaseModel, extra="forbid"):
     c_start_pos: StrictInt
     c_end_pos: StrictInt
     cds_start: StrictInt
-    residue_mode: Literal["inter-residue"] = ResidueMode.INTER_RESIDUE.value
+    residue_mode: Literal["inter-residue"] = CoordinateType.INTER_RESIDUE.value
 
     model_config = ConfigDict(
         json_schema_extra={
@@ -37,7 +37,7 @@ class CdnaRepresentation(BaseModel, extra="forbid"):
                 "c_start_pos": 1797,
                 "c_end_pos": 1800,
                 "cds_start": 226,
-                "residue_mode": ResidueMode.INTER_RESIDUE.value,
+                "residue_mode": CoordinateType.INTER_RESIDUE.value,
             }
         }
     )
@@ -78,15 +78,15 @@ class GenomicRepresentation(BaseModel, extra="forbid"):
     g_ac: StrictStr
     g_start_pos: StrictInt
     g_end_pos: StrictInt
-    residue_mode: Literal["inter-residue"] = ResidueMode.INTER_RESIDUE.value
+    residue_mode: Literal["inter-residue"] = CoordinateType.INTER_RESIDUE.value
 
     model_config = ConfigDict(
         json_schema_extra={
             "example": {
                 "g_ac": "NC_000007.13",
                 "g_start_pos": 140453134,
                 "g_end_pos": 140453137,
-                "residue_mode": ResidueMode.INTER_RESIDUE.value,
+                "residue_mode": CoordinateType.INTER_RESIDUE.value,
             }
         }
     )

src/variation/translators/genomic_del_dup_base.py

@@ -2,7 +2,7 @@
 
 from typing import NamedTuple
 
-from cool_seq_tool.schemas import ManeGeneData, ResidueMode
+from cool_seq_tool.schemas import CoordinateType, ManeGeneData
 from ga4gh.vrs import models
 from pydantic import StrictInt, StrictStr, ValidationError
 
@@ -116,7 +116,7 @@ async def translate(
         grch38_data = None
         vrs_variation = None
         vrs_seq_loc_ac_status = VrsSeqLocAcStatus.NA
-        residue_mode = ResidueMode.RESIDUE
+        residue_mode = CoordinateType.RESIDUE
         mane_genes = None
 
         if do_liftover or endpoint_name == Endpoint.NORMALIZE:
@@ -141,7 +141,7 @@ async def translate(
                     pos1 = grch38_data.pos0
                 else:
                     pos1 = grch38_data.pos1
-                residue_mode = ResidueMode.INTER_RESIDUE
+                residue_mode = CoordinateType.INTER_RESIDUE
                 ac = grch38_data.ac
 
                 if (
@@ -154,7 +154,7 @@ async def translate(
                         pos0,
                         pos0 + (len(ref) - 1),
                         ref,
-                        residue_mode=residue_mode,
+                        coordinate_type=residue_mode,
                     )
                     if invalid_ref_msg:
                         warnings.append(invalid_ref_msg)
@@ -198,7 +198,7 @@ async def translate(
             pos0 = grch38_data.pos0 - 1
             pos1 = grch38_data.pos0 if grch38_data.pos1 is None else grch38_data.pos1
             mane_genes = grch38_data.mane_genes
-            residue_mode = ResidueMode.INTER_RESIDUE
+            residue_mode = CoordinateType.INTER_RESIDUE
             self.is_valid(classification.gene_token, ac, pos0, pos1, errors)
 
             if errors:
@@ -211,7 +211,7 @@ async def translate(
                 pos1,
                 "g",
                 try_longest_compatible=True,
-                residue_mode=residue_mode,
+                coordinate_type=residue_mode,
                 gene=classification.gene_token.token
                 if classification.gene_token
                 else None,
@@ -223,7 +223,7 @@ async def translate(
                 vrs_seq_loc_ac_status = mane.status
                 pos0 = mane.pos[0] + mane.coding_start_site
                 pos1 = mane.pos[1] + mane.coding_start_site
-                residue_mode = ResidueMode.INTER_RESIDUE
+                residue_mode = CoordinateType.INTER_RESIDUE
             else:
                 return None
 
@@ -239,7 +239,7 @@ async def translate(
         if alt_type == AltType.INSERTION:
             alt = classification.inserted_sequence
 
-        start = pos0 if residue_mode == ResidueMode.INTER_RESIDUE else pos0 - 1
+        start = pos0 if residue_mode == CoordinateType.INTER_RESIDUE else pos0 - 1
         end = pos1 if pos1 else pos0
 
         refget_accession = get_refget_accession(self.seqrepo_access, ac, warnings)

src/variation/translators/genomic_delins.py

@@ -1,6 +1,6 @@
 """Module for Genomic DelIns Translation."""
 
-from cool_seq_tool.schemas import AnnotationLayer, ResidueMode
+from cool_seq_tool.schemas import AnnotationLayer, CoordinateType
 from ga4gh.vrs import models
 
 from variation.schemas.app_schemas import Endpoint
@@ -70,7 +70,7 @@ async def translate(
                 else classification.pos0,
                 AnnotationLayer.GENOMIC,
                 try_longest_compatible=True,
-                residue_mode=ResidueMode.RESIDUE,
+                coordinate_type=CoordinateType.RESIDUE,
                 gene=gene,
             )
 
@@ -103,7 +103,7 @@ async def translate(
                     warnings,
                     alt=classification.inserted_sequence,
                     cds_start=mane.coding_start_site if gene else None,
-                    residue_mode=ResidueMode.INTER_RESIDUE,
+                    residue_mode=CoordinateType.INTER_RESIDUE,
                     extensions=extensions,
                 )
         else:
@@ -116,7 +116,7 @@ async def translate(
                 AltType.DELINS,
                 warnings,
                 alt=classification.inserted_sequence,
-                residue_mode=ResidueMode.RESIDUE,
+                residue_mode=CoordinateType.RESIDUE,
             )
 
         if vrs_allele and vrs_seq_loc_ac:

src/variation/translators/genomic_insertion.py

@@ -1,6 +1,6 @@
 """Module for Genomic Insertion Translation."""
 
-from cool_seq_tool.schemas import AnnotationLayer, ResidueMode
+from cool_seq_tool.schemas import AnnotationLayer, CoordinateType
 from ga4gh.vrs import models
 
 from variation.schemas.app_schemas import Endpoint
@@ -71,7 +71,7 @@ async def translate(
                 classification.pos1,
                 AnnotationLayer.GENOMIC,
                 try_longest_compatible=True,
-                residue_mode=ResidueMode.RESIDUE,
+                coordinate_type=CoordinateType.RESIDUE,
                 gene=gene,
             )
 
@@ -104,7 +104,7 @@ async def translate(
                     warnings,
                     alt=classification.inserted_sequence,
                     cds_start=mane.coding_start_site if gene else None,
-                    residue_mode=ResidueMode.INTER_RESIDUE,
+                    residue_mode=CoordinateType.INTER_RESIDUE,
                     extensions=extensions,
                 )
         else:
@@ -117,7 +117,7 @@ async def translate(
                 AltType.INSERTION,
                 warnings,
                 alt=classification.inserted_sequence,
-                residue_mode=ResidueMode.RESIDUE,
+                residue_mode=CoordinateType.RESIDUE,
             )
 
         if vrs_allele and vrs_seq_loc_ac:

src/variation/translators/genomic_reference_agree.py

@@ -1,6 +1,6 @@
 """Module for Genomic Reference Agree Translation."""
 
-from cool_seq_tool.schemas import AnnotationLayer, ResidueMode
+from cool_seq_tool.schemas import AnnotationLayer, CoordinateType
 from ga4gh.vrs import models
 
 from variation.schemas.app_schemas import Endpoint
@@ -70,7 +70,7 @@ async def translate(
                 classification.pos,
                 AnnotationLayer.GENOMIC,
                 try_longest_compatible=True,
-                residue_mode=ResidueMode.RESIDUE,
+                coordinate_type=CoordinateType.RESIDUE,
                 gene=gene,
             )
 
@@ -101,7 +101,7 @@ async def translate(
                     AltType.REFERENCE_AGREE,
                     warnings,
                     cds_start=mane.coding_start_site if gene else None,
-                    residue_mode=ResidueMode.INTER_RESIDUE,
+                    residue_mode=CoordinateType.INTER_RESIDUE,
                     extensions=extensions,
                 )
         else:
@@ -113,7 +113,7 @@ async def translate(
                 AnnotationLayer.GENOMIC,
                 AltType.REFERENCE_AGREE,
                 warnings,
-                residue_mode=ResidueMode.RESIDUE,
+                residue_mode=CoordinateType.RESIDUE,
             )
 
         if vrs_allele and vrs_seq_loc_ac:

src/variation/translators/genomic_substitution.py

@@ -1,6 +1,6 @@
 """Module for Genomic Substitution Translation."""
 
-from cool_seq_tool.schemas import AnnotationLayer, ResidueMode, Strand
+from cool_seq_tool.schemas import AnnotationLayer, CoordinateType, Strand
 from ga4gh.vrs import models
 
 from variation.schemas.app_schemas import Endpoint
@@ -73,7 +73,7 @@ async def translate(
                 classification.pos,
                 AnnotationLayer.GENOMIC,
                 try_longest_compatible=True,
-                residue_mode=ResidueMode.RESIDUE,
+                coordinate_type=CoordinateType.RESIDUE,
                 gene=gene,
             )
 
@@ -124,7 +124,7 @@ async def translate(
                     errors,
                     alt=classification.alt,
                     cds_start=mane.coding_start_site if gene else None,
-                    residue_mode=ResidueMode.INTER_RESIDUE,
+                    residue_mode=CoordinateType.INTER_RESIDUE,
                     extensions=extensions,
                 )
         else:
@@ -137,7 +137,7 @@ async def translate(
                 AltType.SUBSTITUTION,
                 errors,
                 alt=classification.alt,
-                residue_mode=ResidueMode.RESIDUE,
+                residue_mode=CoordinateType.RESIDUE,
             )
 
         if vrs_allele and vrs_seq_loc_ac: