def test_pm_status_gt_order(self):
"""Status should have a right order when doing gt-comparison"""
r = Y() > Conserved(aa_pm=0) > Conserved(nt_pm=8, aa_pm=0) \
> PM(aa_pm=0) > PM(aa_pm=5, nt_pm=10) > NA() > NA(gaps=1)
self.assertTrue(r)
self.assertTrue(NA(aa_pm=9999999) > NA(aa_pm=None))
def test_convert_pm_status_to_string(self):
"""Convert status object to string"""
input_pairs = ((Y(), 'Y'), (Conserved(aa_pm=0), 'Conserved'),
(PM(), 'PM'), (NA(), 'NA'))
for status, str_status in input_pairs:
self.assertEqual(str(status), str_status)
def test_analyze_with_PM(self):
"""pm.analyze should give the expection value"""
seq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAACCT'
stdseq = 'ATGTCGTTCTGCAGCTTCTTCGGGGGCGAGGTTTTCCAGAATCACTTTGAAACT'
status = analyze(seq, stdseq)
self.assertEqual(status, PM(nt_pm=1, aa_pm=1, stdseq=stdseq))
self.assertEqual(status.seq, seq)
self.assertEqual(status.stdseq, stdseq)
self.assertEqual(status.gaps, 0)
self.assertEqual(status.length, len(seq))
self.assertEqual(status.nt_pm, 1)
self.assertEqual(status.aa_pm, 1)
self.assertIsInstance(status.pattern, TranslatedPattern)
def test_raise_TypeError1(self):
"""status should raise TypeError when comparing between status operand with incosistent stdseq"""
with self.assertRaises(TypeError):
Y(stdseq='atg') > Conserved(stdseq='tga', aa_pm=0) \
> PM(stdseq='aaa') > NA(stdseq='tgg')
def test_pm_status_orderablity(self):
"""pm.status should be orderable with gaps-removed but still consistent stdseq"""
self.assertTrue(
PM(stdseq='ATGATT', nt_pm=1) > NA(
stdseq='ATG-ATT', gaps=1, nt_pm=1))
def test_pm_status_ne_order(self):
"""Status should give right value when doing ne-comparison"""
r = NA() != PM() != Conserved(aa_pm=0) != Y()
self.assertTrue(r)
def test_pm_status_eq_order(self):
"""Status should give right value when doing eq-comparison"""
r = (Y() == Y()) and (Conserved(aa_pm=0) == Conserved(aa_pm=0)) \
and (PM() == PM()) and (NA() == NA())
self.assertTrue(r)
def test_pm_status_lt_order(self):
"""Status should have a right order when doing lt-comparison"""
r = NA() < PM() < Conserved(aa_pm=0) < Y()
self.assertTrue(r)