def test_intersecting_genes(self):
'''Test retrieving genes intersecting a base-pair position segment.'''
# print repr(User.__table__) #@UndefinedVariable
Session = sessionmaker(bind=self.engine)
session = Session()
# I believe all of the following are equivalent statements and all are prepared statements
chrom = 1
(start, end) = (62151773, 62516683)
expected = [('NM_032027', 'TM2D1'), ('NM_176877', 'INADL')]
assert_equal([(gene.name, gene.name2) for gene in session.query(Gene).
filter(and_(Gene.chrom == 'chr%s' % (chrom,),
greatest(Gene.txStart, start) <=
least(Gene.txEnd, end))).
order_by(Gene.txStart)], expected)
assert_equal([(gene.name, gene.name2) for gene in session.query(Gene).
filter('chrom = :chrom and greatest(txStart, :start) <= least(txEnd, :end)').
params(chrom='chr%s' % (chrom,), start=start, end=end).
order_by(Gene.txStart)], expected)
assert_equal([(gene.name, gene.name2) for gene in
self.dao.intersecting_genes(chrom, start, end)], expected)
session.close()
def test_intersecting_genes(self):
'''Test retrieving genes intersecting a base-pair position segment.'''
# print repr(User.__table__) #@UndefinedVariable
Session = sessionmaker(bind=self.engine)
session = Session()
# I believe all of the following are equivalent statements and all are prepared statements
chrom = 1
(start, end) = (62151773, 62516683)
expected = [('NM_032027', 'TM2D1'), ('NM_176877', 'INADL')]
assert_equal(
[(gene.name, gene.name2) for gene in session.query(Gene).filter(
and_(Gene.chrom == 'chr%s' % (chrom, ),
greatest(Gene.txStart, start) <= least(Gene.txEnd, end))).
order_by(Gene.txStart)], expected)
assert_equal([(
gene.name, gene.name2
) for gene in session.query(Gene).filter(
'chrom = :chrom and greatest(txStart, :start) <= least(txEnd, :end)'
).params(chrom='chr%s' %
(chrom, ), start=start, end=end).order_by(Gene.txStart)],
expected)
assert_equal(
[(gene.name, gene.name2)
for gene in self.dao.intersecting_genes(chrom, start, end)],
expected)
session.close()
def intersecting_genes(self, chrom, start, end):
'''Return a collection of Gene entities that overlap the base-pair [start,end] on chromosome
chrom.'''
# print 'intersecting_genes', chrom, start, end
session = self.Session()
result = list(session.query(Gene).filter(and_(Gene.chrom == 'chr%s' % (chrom,),
greatest(Gene.txStart, start) <= least(Gene.txEnd, end))).\
order_by(Gene.txStart))
session.close()
return result
def intersecting_genes(self, chrom, start, end):
'''Return a collection of Gene entities that overlap the base-pair [start,end] on chromosome
chrom.'''
# print 'intersecting_genes', chrom, start, end
session = self.Session()
result = list(session.query(Gene).filter(and_(Gene.chrom == 'chr%s' % (chrom,),
greatest(Gene.txStart, start) <= least(Gene.txEnd, end))).\
order_by(Gene.txStart))
session.close()
return result
