def test_gene_loading():
g = session.query(KnownGene).limit(1).first()
print g
assert g
c = session.query(CcdsGene).limit(1).first()
print c
assert c
r = session.query(RefGene).limit(1).first()
print r
assert r
def test_gene_loading():
g = session.query(KnownGene).limit(1).first()
print g
assert g
c = session.query(CcdsGene).limit(1).first()
print c
assert c
r = session.query(RefGene).limit(1).first()
print r
assert r
def test_chainself():
link = session.query(ChainSelfLink).first()
print link
print link.chain
testint = config.genome.interval(10905, 11067, chrom='chr1')
print ChainSelf.for_interval(testint)
for link in ChainSelfLink.for_interval(testint):
print link
print link.source.sequence, link.source
print link.dest.sequence, link.dest
def test_chainself():
link = session.query(ChainSelfLink).first()
print link
print link.chain
testint = config.genome.interval(10905, 11067, chrom='chr1')
print ChainSelf.for_interval(testint)
for link in ChainSelfLink.for_interval(testint):
print link
print link.source.sequence, link.source
print link.dest.sequence, link.dest
def get_snp(name):
return session.query(CommonSnp).filter(CommonSnp.name == name).first()
def test_snp_loading():
g = session.query(KnownGene).limit(1).first()
assert len(Snp.for_interval(g.transcript))
def get_snp(name):return session.query(CommonSnp).filter(CommonSnp.name==name).first()
#### normal snp in + orientation
snp = get_snp('rs117577454')
def test_snp_loading():
g = session.query(KnownGene).limit(1).first()
assert len(Snp.for_interval(g.transcript))