From e7b24c200d528b6976e50fbbe33d250e8faf7ad1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gregor=20Jer=C5=A1e?= <gregor.jerse@genialis.com>
Date: Mon, 18 Mar 2024 10:40:17 +0100
Subject: [PATCH] Add variants related models

---
 docs/CHANGELOG.rst              |  1 +
 src/resdk/resources/variants.py | 71 +++++++++++++++++++++++++++++++++
 2 files changed, 72 insertions(+)
 create mode 100644 src/resdk/resources/variants.py

diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst
index 70dd46b6..1112eb4b 100644
--- a/docs/CHANGELOG.rst
+++ b/docs/CHANGELOG.rst
@@ -12,6 +12,7 @@ Unreleased
 Added
 -----
 - Add ``restart`` method to the ``Data`` resource
+- Add variants related models
 
 
 ===================
diff --git a/src/resdk/resources/variants.py b/src/resdk/resources/variants.py
new file mode 100644
index 00000000..9585a0fa
--- /dev/null
+++ b/src/resdk/resources/variants.py
@@ -0,0 +1,71 @@
+"""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",
+        "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 <pk: {self.id}>"