def lol_sequence(self):
""" Returns sequence as a list of lists, without the '+' separator.
Example:
['d1', 'd2', '+', 'd3'] ==> [['d1', 'd2'], ['d3']]
"""
return make_lol_sequence(self._sequence)
def size(self):
"""Size of the complex is the number of strands."""
if not self._strand_lengths :
if not self._lol_sequence:
self._lol_sequence = make_lol_sequence(self._sequence)
self._strand_lengths = list(map(len, self._lol_sequence))
return len(self._strand_lengths)
def canonical_form(self):
""" Sort Sequences in a unique way for each complex.
"""
if not self._canonical_form:
all_variants = dict()
if not self._lol_sequence:
self._lol_sequence = make_lol_sequence(self._sequence)
for e in range(0, self.size):
canon = tuple(map(lambda x: tuple(map(str, x)),
self._lol_sequence[e:] + self._lol_sequence[:e]))
if canon not in all_variants:
all_variants[canon] = e
if self._memorycheck:
self.do_memorycheck(canon, e)
self._canonical_form = sorted(all_variants)[0]
self._rotations = abs(all_variants[self._canonical_form] - self.size)
return self._canonical_form
def test_split_complex(self):
se = list('CCCTTTGGG')
ss = list('(((...)))')
ps = utils.make_lol_sequence(se)
pt = utils.make_pair_table(ss)
exp = [(se, ss)]
self.assertEqual(utils.split_complex(ps, pt), exp)
se = list('CCCT+TTGGG')
ss = list('(((.+..)))')
ps = utils.make_lol_sequence(se)
self.assertEqual(ps, [['C', 'C', 'C', 'T'], ['T', 'T', 'G', 'G', 'G']])
pt = utils.make_pair_table(ss)
exp = [(se, ss)]
self.assertEqual(utils.split_complex(ps, pt), exp)
se = list('CCCT+AAA+TTGGG')
ss = list('(((.+...+..)))')
ps = utils.make_lol_sequence(se)
self.assertEqual(
ps,
[['C', 'C', 'C', 'T'], ['A', 'A', 'A'], ['T', 'T', 'G', 'G', 'G']])
pt = utils.make_pair_table(ss)
exp = [(list('CCCT+TTGGG'), list('(((.+..)))')),
(list('AAA'), list('...'))]
self.assertEqual(sorted(utils.split_complex(ps, pt)), sorted(exp))
se = list('CCCT+AAA+TTTT+TTGGG')
ss = list('(((.+...+....+..)))')
ps = utils.make_lol_sequence(se)
pt = utils.make_pair_table(ss)
exp = [(list('CCCT+TTGGG'), list('(((.+..)))')),
(list('AAA'), list('...')), (list('TTTT'), list('....'))]
self.assertEqual(sorted(utils.split_complex(ps, pt)), sorted(exp))
se = list('CCCT+AAA+GCGC+TTTT+TTGGG')
ss = list('(((.+...+)()(+....+..)))')
ps = utils.make_lol_sequence(se)
pt = utils.make_pair_table(ss)
exp = [(list('CCCT+GCGC+TTGGG'), list('(((.+)()(+..)))')),
(list('AAA'), list('...')), (list('TTTT'), list('....'))]
self.assertEqual(sorted(utils.split_complex(ps, pt)), sorted(exp))
se = list('CCCT+AAA+GCGC+TTTT+TTGGG')
ss = list('(((.+.(.+)()(+.)..+..)))')
ps = utils.make_lol_sequence(se)
pt = utils.make_pair_table(ss)
exp = [(list('CCCT+TTGGG'), list('(((.+..)))')),
(list('AAA+GCGC+TTTT'), list('.(.+)()(+.)..'))]
self.assertEqual(sorted(utils.split_complex(ps, pt)), sorted(exp))
def get_domain(self, loc):
if not self._lol_sequence:
self._lol_sequence = make_lol_sequence(self._sequence)
return self._lol_sequence[loc[0]][loc[1]]
def strand_length(self, pos):
if not self._strand_lengths :
if not self._lol_sequence:
self._lol_sequence = make_lol_sequence(self._sequence)
self._strand_lengths = list(map(len, self._lol_sequence))
return self._strand_lengths[pos]