def test_create_call_set(self):
call_set = VariantCallSet.create_and_save(
name="call_set",
sample_id="C00123",
variant_sets=self.variant_sets)
cs = VariantCallSet.objects.get(name="call_set")
assert call_set == cs
assert cs.name == "call_set"
assert cs.variant_sets[0].reference_set.name == "ref_set"
def test_create_call_set(self):
call_set = VariantCallSet.create_and_save(
name="call_set",
sample_id="C00123",
variant_sets=self.variant_sets)
cs = VariantCallSet.objects.get(name="call_set")
assert call_set == cs
assert cs.name == "call_set"
assert cs.variant_sets[0].reference_set.name == "ref_set"
def _create_call_sets(self):
for sample in self.vcf_reader.samples:
try:
cs = VariantCallSet.create_and_save(
name="_".join([sample, self.method]),
variant_sets=self.variant_sets,
sample_id=sample,
info={"variant_caller": self.method})
except NotUniqueError:
raise ValueError(
"There is already a call set for sample %s with method %s "
% (sample, self.method))
else:
self.call_sets[sample] = cs
def _create_call_sets(self):
try:
self.call_set = VariantCallSet.create_and_save(
name=self.call_set_name,
variant_sets=[self.global_variant_set],
sample_id=self.sample,
info={"variant_caller": self.method})
except NotUniqueError:
if self.force:
# logger.info("There is already a call set for sample %s with method %s but add has been called with --force so this callset is being removed from the DB" %
# (self.sample, self.method))
cs = VariantCallSet.objects.get(
name="_".join([self.sample, self.method]))
VariantCall.objects(call_set=cs).delete()
cs.delete()
self._create_call_sets()
else:
raise ValueError(
"There is already a call set for sample %s with method %s "
% (self.sample, self.method))