def get_variants_from_variant_tuples(project, variant_tuples):
datastore = get_datastore(project)
population_slugs = project.get_reference_population_slugs()
variant_tuples_by_family_id = {}
for xpos, ref, alt, family_id in variant_tuples:
if family_id not in variant_tuples_by_family_id:
variant_tuples_by_family_id[family_id] = []
variant_tuples_by_family_id[family_id].append((xpos, ref, alt))
variants = []
for family_id, variant_tuples in variant_tuples_by_family_id.items():
variants_for_family = datastore.get_multiple_variants(
project.project_id, family_id, variant_tuples)
for (xpos, ref, alt), variant in zip(variant_tuples,
variants_for_family):
if not variant:
variant = Variant(xpos, ref, alt)
get_annotator().annotate_variant(variant, population_slugs)
variant.set_extra('family_id', family_id)
variant.set_extra('project_id', project.project_id)
variants.append(variant)
return variants
def get_variants_from_variant_tuples(project, variant_tuples):
variants = []
for t in variant_tuples:
variant = get_datastore(project.project_id).get_single_variant(
project.project_id, t[3], t[0], t[1], t[2])
if not variant:
variant = Variant(t[0], t[1], t[2])
get_annotator().annotate_variant(
variant, project.get_reference_population_slugs())
variant.set_extra('family_id', t[3])
variant.set_extra('project_id', project.project_id)
variants.append(variant)
return variants
def get_variants_from_note_tuples(project, note_tuples):
variants = []
for note_t in note_tuples:
variant = get_datastore(project.project_id).get_single_variant(
project.project_id, note_t[3], note_t[0], note_t[1], note_t[2]
)
if not variant:
variant = Variant(note_t[0], note_t[1], note_t[2])
get_annotator().annotate_variant(variant, project.get_reference_population_slugs())
# variant.annotation = get_annotator().get_variant(note_t[0], note_t[1], note_t[2])
variant.set_extra("family_id", note_t[3])
variant.set_extra("project_id", project.project_id)
variants.append(variant)
return variants
def get_variants_from_variant_tuples(project, variant_tuples):
variants = []
for t in variant_tuples:
variant = get_datastore(project.project_id).get_single_variant(
project.project_id,
t[3],
t[0],
t[1],
t[2]
)
if not variant:
variant = Variant(t[0], t[1], t[2])
get_annotator().annotate_variant(variant, project.get_reference_population_slugs())
variant.set_extra('family_id', t[3])
variant.set_extra('project_id', project.project_id)
variants.append(variant)
return variants
def get_variants_from_variant_tuples(project, variant_tuples, user=None):
datastore = get_datastore(project)
population_slugs = project.get_reference_population_slugs()
variant_tuples_by_family_id = {}
for xpos, ref, alt, family_id in variant_tuples:
if family_id not in variant_tuples_by_family_id:
variant_tuples_by_family_id[family_id] = []
variant_tuples_by_family_id[family_id].append((xpos, ref, alt))
variants = []
for family_id, variant_tuples in variant_tuples_by_family_id.items():
variants_for_family = datastore.get_multiple_variants(
project.project_id,
family_id,
variant_tuples,
user=user
)
for (xpos, ref, alt), variant in zip(variant_tuples, variants_for_family):
if not variant:
variant = Variant(xpos, ref, alt)
get_annotator().annotate_variant(variant, population_slugs)
variant.set_extra('created_variant', True)
variant.set_extra('family_id', family_id)
variant.set_extra('project_id', project.project_id)
variants.append(variant)
return variants
