def get(self, request, *args, **kwargs):
genome_build_name = self.kwargs['genome_build_name']
variant_string = self.kwargs['variant_string']
genome_build = GenomeBuild.get_name_or_alias(genome_build_name)
variant = Variant.get_from_string(variant_string, genome_build)
if variant is None:
raise Http404(variant_string)
vav = VariantAnnotationVersion.latest(genome_build)
va = variant.variantannotation_set.get(version=vav)
serializer = VariantAnnotationSerializer(va)
return Response(serializer.data)
def create_analysis_from_template(request, genome_build_name):
data = request.POST.dict()
tag_uuid = data.pop("tag_uuid")
analysis_template_key = f"{tag_uuid}-analysis_template"
analysis_template_name = data.pop(analysis_template_key)
analysis_template = AnalysisTemplate.get_for_user(request.user,
analysis_template_name)
genome_build = GenomeBuild.get_name_or_alias(genome_build_name)
template_run = AnalysisTemplateRun.create(analysis_template,
genome_build,
user=request.user)
template_run.populate_arguments(data)
populate_analysis_from_template_run(template_run)
return view_active_node(template_run.analysis, None)
def handle(self, *args, **options):
f = sys.stdout
genome_build = GenomeBuild.get_name_or_alias("GRCh37")
header_lines = get_vcf_header_from_contigs(genome_build, {})
for line in header_lines:
f.write(line + '\n')
num_variants = options["num_variants"]
rows = []
for _ in range(num_variants):
ref = random_base()
alt = random_base(not_base=ref)
chrom = random_contig()
pos = randrange(MAX_SIZE)
rows.append([chrom, pos, '.', ref, alt, '.', '.', '.'])
rows = sorted(rows, key=lambda x: (x[0], int(x[1])))
for data in rows:
line = '\t'.join(map(str, data))
f.write(line + '\n')
def setUpClass(cls):
super().setUpClass()
user = User.objects.get_or_create(username='******')[0]
cls.grch37 = GenomeBuild.get_name_or_alias("GRCh37")
cls.annotation_version_grch37 = get_fake_annotation_version(cls.grch37)
gene_annotation_release = cls.annotation_version_grch37.gene_annotation_version.gene_annotation_release
cls.transcript_version = create_fake_transcript_version(cls.grch37,
release=gene_annotation_release)
cls.gene_symbol = cls.transcript_version.gene_version.gene_symbol
cls.trio = create_fake_trio(user, cls.grch37)
cls.analysis = Analysis(genome_build=cls.grch37)
cls.analysis.set_defaults_and_save(user)
cls.sample = cls.trio.get_samples()[0]
# Gene List
cls.gene_list = GeneList.objects.get_or_create(name="fake list",
user=cls.analysis.user,
import_status=ImportStatus.SUCCESS)[0]
GeneListGeneSymbol.objects.get_or_create(gene_list=cls.gene_list, gene_symbol=cls.gene_symbol)
# Need some overlapping variants so gene list will work
create_fake_variants(cls.grch37)
# Note: Variant probably doesn't overlap with gene, just want a random one
variant = Variant.objects.filter(Variant.get_no_reference_q()).first()
annotation_run = AnnotationRun.objects.create()
VariantGeneOverlap.objects.create(version=cls.annotation_version_grch37.variant_annotation_version,
annotation_run=annotation_run,
gene=cls.transcript_version.gene,
variant=variant)
# Tag that variant
cls.tag = Tag.objects.get_or_create(pk="foo")[0]
VariantTag.objects.create(genome_build=cls.grch37, analysis=cls.analysis,
variant=variant, tag=cls.tag, user=user)
def create_manual_variant_entry_from_text(request, genome_build_name,
variants_text):
genome_build = GenomeBuild.get_name_or_alias(genome_build_name)
create_manual_variants(request.user, genome_build, variants_text)
return redirect('manual_variant_entry')
variant_tag, created = VariantTag.objects.get_or_create(
variant_id=variant_id,
tag=tag,
genome_build=genome_build,
location=location,
analysis=analysis,
user=request.user)
if node_id:
variant_tag.node_id = node_id
variant_tag.save()
else:
if genome_build_name is None:
raise ValueError(
"Adding requires either 'analysis_id' or 'genome_build_name'"
)
genome_build = GenomeBuild.get_name_or_alias(genome_build_name)
variant_tag, created = VariantTag.objects.get_or_create(
variant_id=variant_id,
tag=tag,
analysis=None,
location=location,
user=request.user,
defaults={"genome_build": genome_build})
if created: # Only return new if anything created
ret = VariantTagSerializer(variant_tag,
context={
"request": request
}).data
elif op == 'del':
# Deletion of tags is for analysis (all users)