wip

src/resdk/resources/sample.py

@@ -69,6 +69,9 @@ def variants(self):
  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):
+ self.resolwe.variant.filter(variant_calls__sample=self.id, variant_calls__experiment=experiment)
 
  @property
  def collection(self):

src/resdk/resources/variants.py

@@ -1,5 +1,7 @@
 """Variant resources."""
 
+from typing import Any
+
 from .base import BaseResource
 
 
@@ -21,14 +23,30 @@ 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(id=self.id)
+ 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 (
@@ -69,26 +87,68 @@ class VariantExperiment(BaseResource):
  "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",
- "variant",
- "experiment",
+ "sample_id",
+ "variant_id",
  "quality",
  "depth_norm_quality",
  "alternative_allele_depth",
  "depth",
  "genotype",
  "genotype_quality",
  "filter",
- "data",
+ "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}>"