def test_strand_tables(self):
se = 'CCCTTTGGG'
assert make_strand_table(se) == [list(se)]
assert strand_table_to_sequence(make_strand_table(se), join=True) == se
se = 'CCCT+TTGGG'
assert make_strand_table(se) == [list('CCCT'), list('TTGGG')]
assert strand_table_to_sequence(make_strand_table(se), join=True) == se
se = 'CCCT+TTGGG'
assert make_strand_table(se) == [list('CCCT'), list('TTGGG')]
assert strand_table_to_sequence(make_strand_table(se), join=True) == se
se = 'CCCT+AAA+TTGGG'
assert make_strand_table(se) == [
list('CCCT'), list('AAA'),
list('TTGGG')
]
assert strand_table_to_sequence(make_strand_table(se), join=True) == se
se = list('CCCT+AAA+TTGGG')
assert make_strand_table(se) == [
list('CCCT'), list('AAA'),
list('TTGGG')
]
assert strand_table_to_sequence(make_strand_table(se),
join=False) == se
def test_split_complex_01(self):
se = 'CCCT+AAA+TTGGG'
ss = '(((.+...+..)))'
ps = make_strand_table(se)
pt = make_pair_table(ss)
out = list(split_complex_pt(ps, pt))
assert len(out) == 2
outdb = list(split_complex_db(se, ss, join=True))
assert ('CCCT+TTGGG', '(((.+..)))') in outdb
assert ('AAA', '...') in outdb
se = 'CCCT+AAA+TTTT+TTGGG'
ss = '(((.+...+....+..)))'
ps = make_strand_table(se)
pt = make_pair_table(ss)
out = list(split_complex_pt(ps, pt))
assert len(out) == 3
outdb = list(split_complex_db(se, ss, join=True))
assert ('CCCT+TTGGG', '(((.+..)))') in outdb
assert ('AAA', '...') in outdb
assert ('TTTT', '....') in outdb
def test_split_complex_02(self):
se = 'CCCT+AAA+GCGC+TTTT+TTGGG'
ss = '(((.+.(.+)()(+.)..+..)))'
ps = make_strand_table(se)
pt = make_pair_table(ss)
bs, bt = ps[:], pt[:]
out = list(split_complex_pt(ps, pt))
assert len(out) == 2
assert bs == ps
assert bt == pt
outdb = list(split_complex_db(se, ss, join=True))
assert len(outdb) == 2
assert ('CCCT+TTGGG', '(((.+..)))') in outdb
assert ('AAA+GCGC+TTTT', '.(.+)()(+.)..') in outdb
def test_split_complex_00(self):
se = list('CCCTTTGGG')
ss = list('(((...)))')
ps = make_strand_table(se)
pt = make_pair_table(ss)
out = list(split_complex_pt(ps, pt))
assert len(out) == 1
c1 = ([['C', 'C', 'C', 'T', 'T', 'T', 'G', 'G',
'G']], [[(0, 8), (0, 7), (0, 6), None, None, None, (0, 2),
(0, 1), (0, 0)]])
assert c1 in out
outdb = list(split_complex_db(se, ss))
assert (se, ss) in outdb
se = list('CCCT+TTGGG')
ss = list('(((.+..)))')
ps = make_strand_table(se)
pt = make_pair_table(ss)
out = list(split_complex_pt(ps, pt))
assert len(out) == 1
outdb = list(split_complex_db(se, ss))
assert (se, ss) in outdb
def test_split_complex_03(self):
se = 'CCCT+TC+GT+TG+C+GG'
ss = '(((.+.(+).+.)+.+))'
ps = make_strand_table(se)
pt = make_pair_table(ss)
out = list(split_complex_pt(ps, pt))
assert len(out) == 3
c1 = ([['T', 'C'], ['G', 'T']], [[None, (1, 0)], [(0, 1), None]])
c2 = ([['C']], [[None]])
c3 = ([['C', 'C', 'C', 'T'], ['T', 'G'], ['G', 'G']], [[(2, 1), (2, 0),
(1, 1), None],
[None, (0, 2)],
[(0, 1),
(0, 0)]])
assert c1 in out
assert c2 in out
assert c3 in out
outdb = list(split_complex_db(se, ss, join=True))
assert ('TC+GT', '.(+).') in outdb
assert ('C', '.') in outdb
assert ('CCCT+TG+GG', '(((.+.)+))') in outdb