build: pin cool-seq-tool~=0.6.0

Pipfile

@@ -22,5 +22,5 @@ pydantic = "==2.*"
 "ga4gh.vrs" = {version = "~=2.0.0a10", extras = ["extras"]}
 gene-normalizer = "~=0.4.0"
 boto3 = "*"
-cool-seq-tool = "~=0.5.0"
+cool-seq-tool = "~=0.6.0"
 bioutils = "*"

pyproject.toml

@@ -31,7 +31,7 @@ dependencies = [
  "ga4gh.vrs[extras] ~= 2.0.0a10",
  "gene-normalizer ~=0.4.0",
  "boto3",
- "cool-seq-tool ~=0.5.0",
+ "cool-seq-tool ~=0.6.0",
  "bioutils"
 ]
 dynamic = ["version"]

src/variation/gnomad_vcf_to_protein_variation.py

@@ -272,8 +272,8 @@ def _get_genomic_pos_range(
  for the original position change
  """
  # Get cDNA reading frame
- start_reading_frame = self.mane_transcript._get_reading_frame(c_start_pos + 1) # noqa: SLF001
- end_reading_frame = self.mane_transcript._get_reading_frame(c_end_pos) # noqa: SLF001
+ start_reading_frame = self.mane_transcript.get_reading_frame(c_start_pos + 1)
+ end_reading_frame = self.mane_transcript.get_reading_frame(c_end_pos)
 
  # Get genomic position range change
  # This ensures that there 3 nucleotides needed for codon

src/variation/schemas/service_schema.py

@@ -1,10 +1,10 @@
 """Module containing schemas for services"""
 
 from enum import Enum
+from typing import Literal
 
-from cool_seq_tool.schemas import ToCdnaService as ToCdna
-from cool_seq_tool.schemas import ToGenomicService as ToGenomic
-from pydantic import ConfigDict
+from cool_seq_tool.schemas import ResidueMode
+from pydantic import BaseModel, ConfigDict, StrictInt, StrictStr
 
 from variation import __version__
 from variation.schemas.normalize_response_schema import ServiceMeta
@@ -21,9 +21,33 @@ class ClinVarAssembly(str, Enum):
  HG18 = "hg18"
 
 
-class ToCdnaService(ToCdna):
+class CdnaRepresentation(BaseModel, extra="forbid"):
+ """Model response for cDNA representation"""
+
+ c_ac: StrictStr
+ c_start_pos: StrictInt
+ c_end_pos: StrictInt
+ cds_start: StrictInt
+ residue_mode: Literal["inter-residue"] = ResidueMode.INTER_RESIDUE.value
+
+ model_config = ConfigDict(
+ json_schema_extra={
+ "example": {
+ "c_ac": "NM_004333.6",
+ "c_start_pos": 1797,
+ "c_end_pos": 1800,
+ "cds_start": 226,
+ "residue_mode": ResidueMode.INTER_RESIDUE.value,
+ }
+ }
+ )
+
+
+class ToCdnaService(BaseModel, extra="forbid"):
  """Service model response for protein -> cDNA"""
 
+ c_data: CdnaRepresentation | None = None
+ warnings: list[StrictStr] = []
  service_meta: ServiceMeta
 
  model_config = ConfigDict(
@@ -48,9 +72,31 @@ class ToCdnaService(ToCdna):
  )
 
 
-class ToGenomicService(ToGenomic):
+class GenomicRepresentation(BaseModel, extra="forbid"):
  """Model response for genomic representation"""
 
+ g_ac: StrictStr
+ g_start_pos: StrictInt
+ g_end_pos: StrictInt
+ residue_mode: Literal["inter-residue"] = ResidueMode.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,
+ }
+ }
+ )
+
+
+class ToGenomicService(BaseModel, extra="forbid"):
+ """Service model response for cDNA -> genomic"""
+
+ g_data: GenomicRepresentation | None = None
+ warnings: list[StrictStr] = []
  service_meta: ServiceMeta
 
  model_config = ConfigDict(

src/variation/translators/ambiguous_translator_base.py

@@ -52,20 +52,24 @@ async def get_grch38_data_ambiguous(
  """
  pos0, pos1, pos2, pos3, new_ac = None, None, None, None, None
  if classification.ambiguous_type == AmbiguousType.AMBIGUOUS_1:
+ # `g_to_grch38` return inter-residue, but we want residue here
+ # so we increment start by 1
  grch38_pos0_pos1 = await self.mane_transcript.g_to_grch38(
- ac, classification.pos0, classification.pos1
+ ac, classification.pos0 + 1, classification.pos1
  )
  if grch38_pos0_pos1:
- pos0, pos1 = grch38_pos0_pos1["pos"]
- ac_pos0_pos1 = grch38_pos0_pos1["ac"]
+ pos0, pos1 = grch38_pos0_pos1.pos
+ ac_pos0_pos1 = grch38_pos0_pos1.ac
 
+ # `g_to_grch38` return inter-residue, but we want residue here
+ # so we increment start by 1
  grch38_pos2_pos3 = await self.mane_transcript.g_to_grch38(
- ac, classification.pos2, classification.pos3
+ ac, classification.pos2 + 1, classification.pos3
  )
 
  if grch38_pos2_pos3:
- pos2, pos3 = grch38_pos2_pos3["pos"]
- ac_pos2_pos3 = grch38_pos2_pos3["ac"]
+ pos2, pos3 = grch38_pos2_pos3.pos
+ ac_pos2_pos3 = grch38_pos2_pos3.ac
 
  if ac_pos0_pos1 != ac_pos2_pos3:
  errors.append(
@@ -78,22 +82,26 @@ async def get_grch38_data_ambiguous(
  AmbiguousType.AMBIGUOUS_2,
  AmbiguousType.AMBIGUOUS_5,
  }:
+ # `g_to_grch38` return inter-residue, but we want residue here
+ # so we increment start by 1
  grch38 = await self.mane_transcript.g_to_grch38(
- ac, classification.pos1, classification.pos2
+ ac, classification.pos1 + 1, classification.pos2
  )
  if grch38:
- pos1, pos2 = grch38["pos"]
- new_ac = grch38["ac"]
+ pos1, pos2 = grch38.pos
+ new_ac = grch38.ac
  elif classification.ambiguous_type == AmbiguousType.AMBIGUOUS_7:
+ # `g_to_grch38` return inter-residue, but we want residue here
+ # so we increment start by 1
  grch38 = await self.mane_transcript.g_to_grch38(
- ac, classification.pos0, classification.pos2
+ ac, classification.pos0 + 1, classification.pos2
  )
  if grch38:
  (
  pos0,
  pos2,
- ) = grch38["pos"]
- new_ac = grch38["ac"]
+ ) = grch38.pos
+ new_ac = grch38.ac
 
  if not new_ac:
  errors.append(f"Unable to find a GRCh38 accession for: {ac}")

src/variation/translators/genomic_del_dup_base.py

@@ -54,19 +54,23 @@ async def get_grch38_data(
  pos0, pos1, new_ac = None, None, None
 
  if classification.pos1:
+ # `g_to_grch38` return inter-residue, but we want residue here
+ # so we increment start by 1
  grch38_pos = await self.mane_transcript.g_to_grch38(
- ac, classification.pos0, classification.pos1
+ ac, classification.pos0 + 1, classification.pos1
  )
  if grch38_pos:
- pos0, pos1 = grch38_pos["pos"]
- new_ac = grch38_pos["ac"]
+ pos0, pos1 = grch38_pos.pos
+ new_ac = grch38_pos.ac
  else:
+ # `g_to_grch38` return inter-residue, but we want residue here
+ # so we increment start by 1
  grch38_pos = await self.mane_transcript.g_to_grch38(
- ac, classification.pos0, classification.pos0
+ ac, classification.pos0 + 1, classification.pos0
  )
  if grch38_pos:
- pos0, _ = grch38_pos["pos"]
- new_ac = grch38_pos["ac"]
+ pos0, _ = grch38_pos.pos
+ new_ac = grch38_pos.ac
 
  if not new_ac:
  errors.append(f"Unable to find a GRCh38 accession for: {ac}")

src/variation/translators/genomic_delins.py

@@ -89,7 +89,7 @@ async def translate(
  coord_type = AnnotationLayer.CDNA
  validation_result.classification = classification
  else:
- vrs_seq_loc_ac = mane.alt_ac
+ vrs_seq_loc_ac = mane.ac
  coord_type = AnnotationLayer.GENOMIC
 
  vrs_allele = self.vrs.to_vrs_allele(

src/variation/translators/genomic_insertion.py

@@ -90,7 +90,7 @@ async def translate(
  coord_type = AnnotationLayer.CDNA
  validation_result.classification = classification
  else:
- vrs_seq_loc_ac = mane.alt_ac
+ vrs_seq_loc_ac = mane.ac
  coord_type = AnnotationLayer.GENOMIC
 
  vrs_allele = self.vrs.to_vrs_allele(

src/variation/translators/genomic_reference_agree.py

@@ -88,7 +88,7 @@ async def translate(
  coord_type = AnnotationLayer.CDNA
  validation_result.classification = classification
  else:
- vrs_seq_loc_ac = mane.alt_ac
+ vrs_seq_loc_ac = mane.ac
  coord_type = AnnotationLayer.GENOMIC
 
  vrs_allele = self.vrs.to_vrs_allele(

src/variation/translators/genomic_substitution.py

@@ -110,7 +110,7 @@ async def translate(
  coord_type = AnnotationLayer.CDNA
  validation_result.classification = classification
  else:
- vrs_seq_loc_ac = mane.alt_ac
+ vrs_seq_loc_ac = mane.ac
  coord_type = AnnotationLayer.GENOMIC
 
  vrs_allele = self.vrs.to_vrs_allele(