def test_clinvitae():
c = Clinvitae()
res = c.query_gene('brca1')
entry1 = res[0]
entry1.keys()
assert entry1['accessionId'] == 'SCV000039520'
assert entry1['lastEvaluated'] # not a stable test # == '2013-04-03'
assert entry1['source'] == 'ClinVar'
res = c.query_gene(
'NM_198578.3:c.1847A>G') # returns all entries in LRRK2 gene
entry1 = res[0]
assert entry1['accessionId'] == 'SCV000056058'
assert entry1['lastEvaluated'] == u'2012-09-13'
assert entry1['source'] == 'ClinVar'
res = c.all_variants(
'MUTYH') # returns all reported variants in MUTYH gene
assert len(res) > 0
pathogenic = c.get_pathogenic(
'brca1') # returns pathogenic or likely pathogenic
assert len(pathogenic) > 100
benign = c.get_benign('brca1') # returns benign or likely benign
assert len(benign) > 100
vus = c.get_VUS('brca1')
assert len(vus) > 100
def test_clinvitae():
c = Clinvitae()
res = c.query_gene('brca1')
entry1 = res[0]
print(entry1.keys()) # display fields for first entry
print(entry1['accessionId']) # accession id for first
print(entry1['lastEvaluated']) # date first variant
print(entry1['source']) # source of first
#hgvs = ''
#res = c.query_hgvs(hgvs):
res = c.all_variants('brca1')
def test_clinvitae():
c = Clinvitae()
res = c.query_gene('brca1')
entry1 = res[0]
print(entry1.keys()) # display fields for first entry
print(entry1['accessionId']) # accession id for first
print(entry1['lastEvaluated']) # date first variant
print(entry1['source']) # source of first
#hgvs = ''
#res = c.query_hgvs(hgvs):
res = c.all_variants('brca1')
def test_clinvitae():
c = Clinvitae()
res = c.query_gene('brca1')
entry1 = res[0]
entry1.keys()
assert entry1['accessionId'] # Not stable == 'SCV000039520'
assert entry1['lastEvaluated'] # not a stable test # == '2013-04-03'
assert entry1['source'] # not stable == 'ClinVar'
res = c.query_gene('NM_198578.3:c.1847A>G') # returns all entries in LRRK2 gene
entry1 = res[0]
assert entry1['accessionId'] # == 'SCV000056058'
assert entry1['lastEvaluated'] # == u'2012-09-13'
assert entry1['source'] # == 'ClinVar'
res = c.all_variants('MUTYH') # returns all reported variants in MUTYH gene
assert len(res)>0
pathogenic = c.get_pathogenic('brca1') # returns pathogenic or likely pathogenic
assert len(pathogenic) > 100
benign = c.get_benign('brca1') # returns benign or likely benign
assert len(benign) > 100
vus = c.get_VUS('brca1')
assert len(vus) > 100