Add variants related models

docs/CHANGELOG.rst

@@ -12,6 +12,7 @@ Unreleased
 Added
 -----
 - Add ``restart`` method to the ``Data`` resource
+- Add variants related models
 
 
 ===================

src/resdk/resources/variants.py

@@ -0,0 +1,80 @@
+"""Variant resources."""
+
+import logging
+from typing import TYPE_CHECKING, Optional, Union
+
+from ..utils.decorators import assert_object_exists
+from .base import BaseResource
+from .sample import Sample
+from .utils import parse_resolwe_datetime
+
+if TYPE_CHECKING:
+    from resdk.resolwe import Resolwe
+
+
+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",
+        "annotation",
+        "annotation_impact",
+        "gene",
+        "protein_impact",
+        "feature_id",
+        "clinical_diagnosis",
+        "clinical_significance",
+        "dbsnp_id",
+        "clinical_var_id",
+        "data",
+    )
+
+    def __repr__(self) -> str:
+        """Return string representation."""
+        return f"VariantAnnotation <variant: {self.variant}>"
+
+
+class VariantCall(BaseResource):
+    """VariantCall resource."""
+
+    endpoint = "variant_call"
+
+    READ_ONLY_FIELDS = BaseResource.READ_ONLY_FIELDS + (
+        "sample",
+        "variant",
+        "experiment",
+        "quality",
+        "depth",
+        "filter",
+        "genotype",
+        "data",
+    )
+
+    def __repr__(self) -> str:
+        """Return string representation."""
+        return f"VariantCall <path: {self.field.group.name}.{self.field.name}, value: '{self.value}'>"