def test_get_metrics(self):
# Create a variant object
new_variant = Variant(chr=self.chromo,
pos=1,
ref="jon",
alt="ba",
md5="kid",
type=self.varianttype,)
new_variant.save()
response = self.client.get('/api/variants/{0}/assessment-metrics/'.
format(new_variant.id),
HTTP_ACCEPT='application/json')
# Should be ok
self.assertEqual(response.status_code, codes.ok)
def test_get_all(self):
count_before = Variant.objects.count()
new_variant = Variant(chr=self.chromo,
pos=1,
ref="jon",
alt="ba",
md5="kid",
type=self.varianttype,)
new_variant.save()
count_after = Variant.objects.count()
# Now try making a get request with the objects id
response = self.client.get('/api/variants/{0}/'.format(new_variant.id),
HTTP_ACCEPT='application/json')
# Request should be good and the count should have changed
self.assertEqual(response.status_code, codes.ok)
self.assertEqual(count_after, count_before+1)
def get_variant(self, record):
"Get or create a variant."
chrom, pos, ref, alt = record.CHROM, record.POS, record.REF, '/'.join([str(x) for x in record.ALT])
# Calculate MD5 and attempt to fetch the primary key from
# the local cache, otherwise use it when inserting.
md5 = calculate_md5(chrom, pos, ref, alt)
# Ensure the cache is valid for the chromosome
self.check_cache(chrom)
variant_id = self.variant_cache.get(md5, None)
# Just make a faux instance
if variant_id:
variant = Variant(pk=variant_id)
# Create if it does not exist
else:
variant = Variant(pos=pos, ref=ref, alt=alt, md5=md5)
# Update foreign key references
variant.chr = self.get_chromosome(chrom)
variant.type = self.get_variant_type(record.var_type.upper())
# Periods are useless..
variant.rsid = record.ID == '.' and None or record.ID
variant.save()
self.file_variants += 1
# Update cache
self.variant_cache[md5] = variant.pk
# Process SNPEff data if this is the first time this variant
# has been seen.
if 'EFF' in record.INFO:
effs = record.INFO['EFF'].split(',')
self.load_effects(effs, variant)
return variant
def get_variant(self, record):
"Get or create a variant."
chrom, pos, ref, alt = record.CHROM, record.POS, record.REF, '/'.join(
[str(x) for x in record.ALT])
# Calculate MD5 and attempt to fetch the primary key from
# the local cache, otherwise use it when inserting.
md5 = calculate_md5(chrom, pos, ref, alt)
# Ensure the cache is valid for the chromosome
self.check_cache(chrom)
variant_id = self.variant_cache.get(md5, None)
# Just make a faux instance
if variant_id:
variant = Variant(pk=variant_id)
# Create if it does not exist
else:
variant = Variant(pos=pos, ref=ref, alt=alt, md5=md5)
# Update foreign key references
variant.chr = self.get_chromosome(chrom)
variant.type = self.get_variant_type(record.var_type.upper())
# Periods are useless..
variant.rsid = record.ID == '.' and None or record.ID
variant.save()
self.file_variants += 1
# Update cache
self.variant_cache[md5] = variant.pk
# Process SNPEff data if this is the first time this variant
# has been seen.
if 'EFF' in record.INFO:
effs = record.INFO['EFF'].split(',')
self.load_effects(effs, variant)
return variant
def load_hgmd_snp(self, cursor, using=None):
cursor.execute('''
select distinct
cl.acc_num as hgmd_id,
c.value as chr,
c.id as chr_id,
v.id as variant_id,
trim(both from cl.disease) as phenotype,
ph.id as phenotype_id,
cl.gene as gene,
g.id as gene_id,
cl.pmid as pubmed,
pm.pmid as pubmed_id
from (
select m.acc_num, m.disease, m.gene, m.pmid, c.chromosome, c."coordSTART" as pos
from raw.hgmd_mutation m inner join raw.hgmd_hg19_coords c on (m.acc_num = c.acc_num)
) cl
left outer join chromosome c on (cl.chromosome = c.value)
left outer join variant v on (c.id = v.chr_id and cl.pos = v.pos)
left outer join variant_type vt on (v.type_id = vt.id)
left outer join phenotype ph on (lower(trim(both from regexp_replace(cl.disease, '\s*\?$', ''))) = lower(ph.term))
left outer join pubmed pm on (cl.pmid::varchar = pm.pmid::varchar)
left outer join gene g on (cl.gene::text = g.symbol::text)
left outer join variant_phenotype vp on (vp.variant_id = v.id)
where vt.value = 'SNP'
and cl.disease not like '%%?'
and v.id is not null and g.id is not null
order by c.id
''')
keys = ['hgmd_id', 'chr', 'chr_id', 'variant_id',
'phenotype', 'phenotype_id', 'gene', 'gene_id',
'pubmed', 'pubmed_id']
count = 0
new_pubmed_map = {}
new_phenotype_map = {}
chrs = dict(Chromosome.objects.values_list('value', 'id'))
while True:
rows = cursor.fetchmany(100)
if not rows:
break
for row in rows:
record = dict(zip(keys, row))
# Get or create a pubmed record
if record['pubmed_id']:
pubmed = PubMed(pmid=record['pubmed_id'])
pubmed._state.db = using
# Some records have a bogus PMID. Only proces the valid ones.
elif type(record['pubmed']) is int or record['pubmed'].isdigit():
pmid = int(record['pubmed'])
if pmid in new_pubmed_map:
pubmed = new_pubmed_map[pmid]
else:
pubmed = PubMed(pmid=pmid)
pubmed.save()
new_pubmed_map[pmid] = pubmed
else:
pubmed = None
# Get or create a the phenotype, associate the HGMD id with
if record['phenotype_id']:
phenotype = Phenotype(pk=record['phenotype_id'])
phenotype._state.db = using
else:
term = record['phenotype']
# Check newly added objects
if term in new_phenotype_map:
phenotype = new_phenotype_map[term]
else:
phenotype = Phenotype(term=record['phenotype'])
phenotype.save()
new_phenotype_map[term] = phenotype
_chr = Chromosome(pk=chrs[record['chr']])
_chr._state.db = using
if record['gene_id']:
gene = Gene(pk=record['gene_id'])
gene._state.db = using
try:
gp = GenePhenotype.objects.get(gene=gene, phenotype=phenotype)
except GenePhenotype.DoesNotExist:
gp = GenePhenotype(gene=gene, phenotype=phenotype)
gp.hgmd_id = record['hgmd_id']
gp.save()
else:
gene = None
if record['variant_id']:
variant = Variant(pk=record['variant_id'])
variant._state.db = using
try:
vp = VariantPhenotype.objects.get(variant=variant, phenotype=phenotype)
except VariantPhenotype.DoesNotExist:
vp = VariantPhenotype(variant=variant, phenotype=phenotype)
vp.hgmd_id = record['hgmd_id']
vp.save()
else:
variant = None
if pubmed:
phenotype.articles.add(pubmed)
if variant:
variant.articles.add(pubmed)
if gene:
gene.articles.add(pubmed)
count += 1
sys.stdout.write('{0}\r'.format(count))
sys.stdout.flush()
return count
