Add variant 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/query.py

@@ -175,7 +175,9 @@ def _add_filter(self, filter_):
  """Add filtering parameters."""
  for key, value in filter_.items():
  # 'sample' is called 'entity' in the backend.
- key = key.replace("sample", "entity")
+ if not key.startswith("variant_calls__"):
+ key = key.replace("sample", "entity")
+ print("Adding filter", key, value)
  value = self._dehydrate_resources(value)
  if self._non_string_iterable(value):
  value = ",".join(map(str, value))

src/resdk/resolwe.py

@@ -47,6 +47,10 @@
  Relation,
  Sample,
  User,
+ Variant,
+ VariantAnnotation,
+ VariantCall,
+ VariantExperiment,
 )
 from .resources.base import BaseResource
 from .resources.kb import Feature, Mapping
@@ -114,6 +118,10 @@ class Resolwe:
  resource_query_mapping = {
  AnnotationField: "annotation_field",
  AnnotationValue: "annotation_value",
+ Variant: "variant",
+ VariantAnnotation: "variant_annotation",
+ VariantExperiment: "variant_experiment",
+ VariantCall: "variant_calls",
  Data: "data",
  Collection: "collection",
  Sample: "sample",
@@ -126,6 +134,7 @@ class Resolwe:
  Mapping: "mapping",
  Geneset: "geneset",
  Metadata: "metadata",
+ Variant: "variant",
  }
  # Map ResolweQuery name to it's slug_field
  slug_field_mapping = {

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, VariantAnnotation, VariantCall, VariantExperiment
 
 __all__ = (
  "AnnotationField",
@@ -117,4 +122,8 @@
  "Process",
  "Relation",
  "User",
+ "Variant",
+ "VariantAnnotation",
+ "VariantCall",
+ "VariantExperiment",
 )

src/resdk/resources/sample.py

@@ -1,14 +1,15 @@
 """Sample resource."""
 
 import logging
-from typing import TYPE_CHECKING, Any, Dict, Optional
+from typing import TYPE_CHECKING, Any, Dict, List, Optional
 
 from resdk.exceptions import ResolweServerError
 from resdk.shortcuts.sample import SampleUtilsMixin
 
 from ..utils.decorators import assert_object_exists
 from .background_task import BackgroundTask
 from .collection import BaseCollection, Collection
+from .variants import Variant
 
 if TYPE_CHECKING:
  from .annotations import AnnotationValue
@@ -39,6 +40,8 @@ def __init__(self, resolwe, **model_data):
  self._background = None
  #: is this sample background to any other sample?
  self._is_background = None
+ #: list of ``Variant`` objects attached to the sample
+ self._variants = None
 
  super().__init__(resolwe, **model_data)
 
@@ -60,6 +63,19 @@ def data(self):
 
  return self._data
 
+ @property
+ def variants(self):
+ """Get variants."""
+ if self._variants is None:
+ self._variants = self.resolwe.variant.filter(variant_calls__sample=self.id)
+ return self._variants
+
+ def variants_by_experiment(self, experiment):
+ """Get variants for sample detected by the given experiment."""
+ return self.resolwe.variant.filter(
+ variant_calls__sample=self.id, variant_calls__experiment=experiment.id
+ )
+
  @property
  def collection(self):
  """Get collection."""

src/resdk/resources/variants.py

@@ -0,0 +1,154 @@
+"""Variant resources."""
+
+from typing import Any
+
+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 __init__(self, resolwe, **model_data):
+ """Initialize object."""
+ super().__init__(resolwe, **model_data)
+ self._annotations = None
+ self._samples = None
+ self._calls = None
+
+ @property
+ def annotations(self):
+ """Get the annotations for this variant."""
+ if self._annotations is None:
+ self._annotations = self.resolwe.variant_annotation.filter(variant=self.id)
+ return self._annotations
+
+ @property
+ def samples(self):
+ """Get samples."""
+ if self._samples is None:
+ self._samples = self.resolwe.sample.filter(variant_calls__variant=self.id)
+ return self._samples
+
+ @property
+ def calls(self):
+ """Get variant calls associated with this variant."""
+ if self._calls is None:
+ self._calls = self.resolwe.variant_calls.filter(variant=self.id)
+ return self._calls
+
+ 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_annotations"
+
+ READ_ONLY_FIELDS = BaseResource.READ_ONLY_FIELDS + (
+ "variant_id",
+ "type",
+ "clinical_diagnosis",
+ "clinical_significance",
+ "dbsnp_id",
+ "clinvar_id",
+ "data",
+ "transcripts",
+ )
+
+ def __repr__(self) -> str:
+ """Return string representation."""
+ return f"VariantAnnotation <variant: {self.variant_id}>"
+
+
+class VariantExperiment(BaseResource):
+ """Variant experiment resource."""
+
+ endpoint = "variant_experiment"
+
+ READ_ONLY_FIELDS = BaseResource.READ_ONLY_FIELDS + (
+ "variant_data_source",
+ "timestamp",
+ "contributor",
+ )
+
+ def __repr__(self) -> str:
+ """Return string representation."""
+ return f"VariantExperiment <pk: {self.id}>"
+
+
+class VariantCall(BaseResource):
+ """VariantCall resource."""
+
+ endpoint = "variant_calls"
+
+ READ_ONLY_FIELDS = BaseResource.READ_ONLY_FIELDS + (
+ "sample_id",
+ "variant_id",
+ "quality",
+ "depth_norm_quality",
+ "alternative_allele_depth",
+ "depth",
+ "genotype",
+ "genotype_quality",
+ "filter",
+ "data_id",
+ "experiment_id",
+ )
+
+ def __init__(self, resolwe, **model_data: Any):
+ """Initialize object."""
+ super().__init__(resolwe, **model_data)
+ self._data = None
+ self._sample = None
+ self._experiment = None
+ self._variant = None
+
+ @property
+ def data(self):
+ """Get the data object for this variant call."""
+ if self._data is None:
+ self._data = self.resolwe.data.get(self.data_id)
+ return self._data
+
+ @property
+ def sample(self):
+ """Get the sample object for this variant call."""
+ if self._sample is None:
+ self._sample = self.resolwe.sample.get(self.sample_id)
+ return self._sample
+
+ @property
+ def experiment(self):
+ """Get the experiment object for this variant call."""
+ if self._experiment is None:
+ self._experiment = self.resolwe.variant_experiment.get(
+ id=self.experiment_id
+ )
+ return self._experiment
+
+ @property
+ def variant(self):
+ """Get the variant object for this variant call."""
+ if self._variant is None:
+ self._variant = self.resolwe.variant.get(id=self.variant_id)
+ return self._variant
+
+ def __repr__(self) -> str:
+ """Return string representation."""
+ return f"VariantCall <pk: {self.id}>"