def test_variant_identity2(self):
""" Will test that the reference is not removed """
stringvar = 'NM_015120.4:c.34C='
var = self.hp.parse_hgvs_variant(stringvar)
output = utils.valstr(var)
self.assertEqual(var.posedit.edit.type, 'identity')
self.assertEqual(output, 'NM_015120.4:c.34C=')
def test_variant_sub(self):
""" Will test that reference isn't removed """
stringvar = 'NM_015120.4:c.34C>T'
var = self.hp.parse_hgvs_variant(stringvar)
output = utils.valstr(var)
self.assertEqual(var.posedit.edit.type, 'sub')
self.assertEqual(output, stringvar)
def get_ucsc_link(validator, output):
try:
if output['genome'] == 'GRCh37':
ucsc_assembly = 'hg19'
else:
ucsc_assembly = 'hg38'
hgvs_genomic = validator.hp.parse_hgvs_variant(
output['results'][0]['primary_assembly_loci'][ucsc_assembly]['hgvs_genomic_description'])
chromosome = to_chr_num_ucsc(hgvs_genomic.ac, ucsc_assembly)
vcf_varsome = output['results'][0]['primary_assembly_loci'][ucsc_assembly]['vcfstr_alt']
if chromosome is not None:
vcf_components = output['genomes'][ucsc_assembly].split('-')
vcf_components[0] = chromosome
vcf_varsome = '-'.join(vcf_components)
browser_start = str(hgvs_genomic.posedit.pos.start.base - 11)
browser_end = str(hgvs_genomic.posedit.pos.end.base + 11)
ucsc_browser_position = '%s:%s-%s' % (chromosome, browser_start, browser_end)
coding = output['results'][0]['hgvs_transcript_variant']
current_site = Site.objects.get_current()
ucsc_link = 'http://genome.ucsc.edu/cgi-bin/hgTracks?' \
'db=%s&position=%s&hgt.customText=http://%s/bed/?variant=%s|%s|%s|%s|%s' % \
(
ucsc_assembly,
ucsc_browser_position,
current_site.domain,
coding,
hgvs_genomic.ac,
output['genome'],
valstr(hgvs_genomic),
vcf_varsome
)
return ucsc_link
except Exception:
# This exception picks up variants with no primary assembly for the selected genome e.g. HLA-DRB4
pass
def test_string(self):
var = ''
with self.assertRaises(AttributeError):
utils.valstr(var)
