Add variants related models

docs/CHANGELOG.rst

@@ -16,6 +16,7 @@ Changed
 Added
 -----
 - Add ``restart`` method to the ``Data`` resource
+- Add variants related models
 
 Fixed
 -----

src/resdk/resolwe.py

@@ -47,6 +47,9 @@
  Relation,
  Sample,
  User,
+ Variant,
+ VariantCall,
+ VariantExperiment,
 )
 from .resources.base import BaseResource
 from .resources.kb import Feature, Mapping
@@ -114,6 +117,9 @@ class Resolwe:
  resource_query_mapping = {
  AnnotationField: "annotation_field",
  AnnotationValue: "annotation_value",
+ Variant: "variant",
+ VariantExperiment: "variant_experiment",
+ VariantCall: "variant_calls",
  Data: "data",
  Collection: "collection",
  Sample: "sample",

src/resdk/resources/__init__.py

@@ -54,6 +54,10 @@
  :members:
  :inherited-members:
 
+.. autoclass:: resdk.resources.Variants
+ :members:
+ :inherited-members:
+
 .. autoclass:: resdk.resources.User
  :members:
  :inherited-members:
@@ -102,6 +106,7 @@
 from .relation import Relation
 from .sample import Sample
 from .user import Group, User
+from .variants import Variant, VariantCall, VariantExperiment
 
 __all__ = (
  "AnnotationField",
@@ -117,4 +122,7 @@
  "Process",
  "Relation",
  "User",
+ "Variant",
+ "VariantCall",
+ "VariantExperiment",
 )

src/resdk/resources/variants.py

@@ -0,0 +1,101 @@
+"""Variant resources."""
+
+from .base import BaseResource
+
+
+class Variant(BaseResource):
+ """ResolweBio Variant resource."""
+
+ endpoint = "variant"
+
+ READ_ONLY_FIELDS = BaseResource.READ_ONLY_FIELDS + (
+ "species",
+ "genome_assembly",
+ "chromosome",
+ "position",
+ "reference",
+ "alternative",
+ )
+
+ def __repr__(self) -> str:
+ """Return string representation."""
+ return (
+ f"Variant <chr: {self.chromosome}, pos: {self.position}, "
+ f"ref: {self.reference}, alt: {self.alternative}>"
+ )
+
+
+class VariantAnnotation(BaseResource):
+ """VariantAnnotation resource."""
+
+ endpoint = "variant_annotation"
+
+ READ_ONLY_FIELDS = BaseResource.READ_ONLY_FIELDS + (
+ "variant",
+ "type",
+ "clinical_diagnosis",
+ "clinical_significance",
+ "dbsnp_id",
+ "clinvar_id",
+ "data",
+ )
+
+ def __repr__(self) -> str:
+ """Return string representation."""
+ return f"VariantAnnotation <variant: {self.variant}>"
+
+
+class VariantAnnotationTranscript(BaseResource):
+ """VariantAnnotationTranscript resource."""
+
+ endpoint = "variant_annotation_transcript"
+
+ READ_ONLY_FIELDS = BaseResource.READ_ONLY_FIELDS + (
+ "variant_annotation",
+ "annotation",
+ "annotation_impact",
+ "gene",
+ "protein_impact",
+ "transcript_ids",
+ "cananical",
+ )
+
+ def __repr__(self) -> str:
+ """Return string representation."""
+ return f"VariantAnnotationTrascript <variant annotation: {self.variant_annotation}>"
+
+
+class VariantExperiment(BaseResource):
+ """Variant experiment resource."""
+
+ endpoint = "variant_experiment"
+
+ READ_ONLY_FIELDS = BaseResource.READ_ONLY_FIELDS + (
+ "variant_data_source",
+ "timestamp",
+ "contributor",
+ )
+
+
+class VariantCall(BaseResource):
+ """VariantCall resource."""
+
+ endpoint = "variant_calls"
+
+ READ_ONLY_FIELDS = BaseResource.READ_ONLY_FIELDS + (
+ "sample",
+ "variant",
+ "experiment",
+ "quality",
+ "depth_norm_quality",
+ "unfiltered_allele_depth",
+ "depth",
+ "genotype",
+ "genotype_quality",
+ "filter",
+ "data",
+ )
+
+ def __repr__(self) -> str:
+ """Return string representation."""
+ return f"VariantCall <pk: {self.id}>"