class Test_pileup(unittest.TestCase):
"""Unittest for pileup_bdg() in cPileup.pyx.
"""
def setUp(self):
self.chrom = "chr1"
self.plus_pos = ( 0, 1, 3, 4, 5 )
self.minus_pos = ( 5, 6, 8, 9, 10 )
self.d = 5
self.expect = [ ( 0, 1, 2.0 ),
( 1, 3, 4.0 ),
( 3, 4, 6.0 ),
( 4, 6, 8.0 ),
( 6, 8, 6.0 ),
( 8, 9, 4.0 ),
( 9, 10, 2.0 )
]
def test_pileup(self):
# build FWTrackII
self.fwtrack2 = FWTrackII()
for i in self.plus_pos:
self.fwtrack2.add_loc(self.chrom, i, 0)
for i in self.minus_pos:
self.fwtrack2.add_loc(self.chrom, i, 1)
self.pileup = pileup_bdg(self.fwtrack2, self.d, halfextension=False)
self.result = []
chrs = self.pileup.get_chr_names()
for chrom in chrs:
(p,v) = self.pileup.get_data_by_chr(chrom)
pnext = iter(p).next
vnext = iter(v).next
pre = 0
for i in xrange(len(p)):
pos = pnext()
value = vnext()
self.result.append( (pre,pos,value) )
pre = pos
# check result
self.assertEqual(self.result, self.expect)
def test_pileup(self):
# build FWTrackII
self.fwtrack2 = FWTrackII()
for i in self.plus_pos:
self.fwtrack2.add_loc(self.chrom, i, 0)
for i in self.minus_pos:
self.fwtrack2.add_loc(self.chrom, i, 1)
self.pileup = pileup_bdg(self.fwtrack2, self.d, halfextension=False)
self.result = []
chrs = self.pileup.get_chr_names()
for chrom in chrs:
(p,v) = self.pileup.get_data_by_chr(chrom)
pnext = iter(p).next
vnext = iter(v).next
pre = 0
for i in xrange(len(p)):
pos = pnext()
value = vnext()
self.result.append( (pre,pos,value) )
pre = pos
# check result
self.assertEqual(self.result, self.expect)