def test_read_sequence(self):
expected_length = 2099
# make sure the randomized sequence does not lose any elements
seq, maps = rs.read_sequence(self.seq_fname)
self.assertEqual(expected_length, len(seq))
# relative to absolute map
self.assertEqual(expected_length, len(maps[0].keys()))
# absolute to relative map
self.assertEqual(expected_length, len(maps[1].keys()))
def test_no_masking(self):
seq, maps = rs.read_sequence(self.seq_fname)
rsr = rs.shuffle_sequence(seq, maps, n=100, mask=None)
similarity_count = 0
for idx, s in enumerate(rsr.seq):
if seq[idx] == s:
similarity_count += 1
print "similarity count : ", similarity_count
self.assertLess(similarity_count, len(seq))
def test_masking_first_bp(self):
mask = {"HSE1" : [(31795202, 31795202)]}
seq, maps = rs.read_sequence(self.seq_fname)
abs_rel_map = maps[1]
expected_seq = ''.join([seq[abs_rel_map[s]] for s in range(31795202, 31795202+1)])
print(expected_seq)
rsr = rs.shuffle_sequence(seq, maps, n=100, mask=("HSE1", mask["HSE1"]))
region_seq = ''.join([rsr.seq[abs_rel_map[s]] for s in range(31795202, 31795202+1)])
print(region_seq)
self.assertEqual(expected_seq, region_seq)
def test_masking_snp(self):
"""
HSE1: 31795312-31795325
HSE2: 31795405-31795418
TATA: 31795486-31795491
TSS: 31795512-31795512
TRIM28: 31795571-31795578
PB1: 31795743-31795749
PB2: 31796358-31796364
"""
mask = {"snp": [(31795512, 31795512)]}
seq, maps = rs.read_sequence(self.seq_fname)
abs_rel_map = maps[1]
snp = abs_rel_map[31795512]
print seq[snp]
rsr = rs.shuffle_sequence(seq, maps, n=100, mask=("snp", mask["snp"]))
print rsr.seq[snp]
self.assertEqual(seq[snp], rsr.seq[snp])
def test_masking_region(self):
"""
HSE1: 31795312-31795325
HSE2: 31795405-31795418
TATA: 31795486-31795491
TSS: 31795512-31795512
TRIM28: 31795571-31795578
PB1: 31795743-31795749
PB2: 31796358-31796364
"""
mask={"HSE1":[(31795312,31795325)]}
seq, maps = rs.read_sequence(self.seq_fname)
abs_rel_map = maps[1]
expected_seq = ''.join([seq[abs_rel_map[s]] for s in range(31795312,31795325+1)])
rsr = rs.shuffle_sequence(seq, maps, n=100, mask=("HSE1", mask["HSE1"])
)
region_seq = ''.join([rsr.seq[abs_rel_map[s]] for s in range(31795312,31795325+1)])
self.assertEqual(expected_seq, region_seq)