def test_bed_gene_pred(self):
g = Genome('hg19', host="localhost", user="******")
from sqlalchemy import and_
from cStringIO import StringIO
query = g.knownGene.filter(and_(g.table('knownGene').c.txStart > 10000, g.table('knownGene').c.txEnd < 20000))
c = StringIO()
Genome.save_bed(query, c)
c.seek(0)
rows = c.readlines()
for toks in (row.split("\t") for row in rows):
self.assert_(len(toks) == 12)
self.assert_(int(toks[1]) > 10000)
self.assert_(int(toks[2]) < 20000)
def test_bed_gene_pred(self):
g = Genome('hg19')
from sqlalchemy import and_
from cStringIO import StringIO
query = g.knownGene.filter(
and_(
g.table('knownGene').c.txStart > 10000,
g.table('knownGene').c.txEnd < 20000))
c = StringIO()
Genome.save_bed(query, c)
c.seek(0)
rows = c.readlines()
for toks in (row.split("\t") for row in rows):
self.assert_(len(toks) == 12)
self.assert_(int(toks[1]) > 10000)
self.assert_(int(toks[2]) < 20000)
