def _suffix_circular():
sequence = linear_path()
sequence += sequence[:ksize - 1]
consume_collector(sequence)
check_fp_collector(
(lambda G: count_decision_nodes(sequence, G, ksize), {}))
return sequence
def _tandem_repeats_gt_ksize():
repeat = _get_random_sequence(ksize * 2)
tandem_repeats = repeat * request.param
consume_collector(tandem_repeats)
check_fp_collector(
(lambda G: count_decision_nodes(tandem_repeats, G, ksize), {}))
return (repeat, tandem_repeats), request.param
def _linear_path():
try:
sequence = sequence_generator.random_unitig(length)
except ValueError:
pytest.xfail('Greedy dead-end in sequence generation.')
consume_collector(sequence)
check_fp_collector(
(lambda G: count_decision_nodes(sequence, G, ksize), {}))
return sequence
def _right_sea():
root = sequence_generator.random_seed()
seqs = tuple(
sequence_generator.random_branches(root,
n_branches=n_branches,
n_tail_kmers=tip_length))
consume_collector(*seqs)
check_fp_collector(*((lambda G: count_decision_nodes(s, G, ksize), {
(0, n_branches): 1
}) for s in seqs))
return seqs
def _right_fork():
(core_sequence, tip), pivot = right_tip()
branch_sequence = random_sequence()
branch_sequence = tip + random_sequence()[:length - pivot - ksize]
consume_collector(core_sequence, branch_sequence)
check_fp_collector(
(lambda G: count_decision_nodes(core_sequence, G, ksize), {
(1, 2): 1
}),
(lambda G: count_decision_nodes(branch_sequence, G, ksize), {}))
return (core_sequence, branch_sequence), pivot
def _right_tip():
sequence = random_sequence()
pivot = internal_pivot
if pivot < 1:
raise ValueError("ksize too large for length")
# the branch kmer
tip = mutate_position(sequence[pivot + 1:pivot + 1 + ksize], -1)
consume_collector(sequence, tip)
check_fp_collector(
(lambda G: count_decision_nodes(sequence, G, ksize), {
(1, 2): 1
}), (lambda G: count_decision_nodes(tip, G, ksize), {}))
return (sequence, tip), pivot
def _tandem_quad_forks():
core = linear_path()
S_l = (len(core) // 2) - ksize
S_r = S_l + 1
left_branches = [kmer + random_sequence(exclude=kmer) \
for kmer in right_kmers(core[S_l:S_l+ksize]) \
if kmer not in core]
right_branches = [kmer + random_sequence(exclude=kmer) \
for kmer in right_kmers(core[S_r:S_r+ksize]) \
if kmer not in core]
consume_collector(core, *left_branches, *right_branches)
check_fp_collector((lambda G: count_decision_nodes(core, G, ksize), {(1,4): 2}),
*[(lambda G: count_decision_nodes(branch, G, ksize), {}) \
for branch in left_branches + right_branches])
return (core, left_branches, right_branches), S_l, S_r
def _left_hairpin():
core = linear_path()
pos = len(core) // 2
if core[pos - 1] == core[-1]:
core = mutate_position(core, -1)
hdn = core[pos:pos + ksize]
result = core + hdn
_collector = consume_collector()
_collector.pop()
consume_collector(result)
_check_fp_collector = check_fp_collector()
_check_fp_collector.pop()
check_fp_collector((lambda G: count_decision_nodes(result, G, ksize), {
(2, 1): 2
}))
return result, pos
def _bowtie_tangle():
top = linear_path()
decision_segment = top[middle_pivot:middle_pivot + ksize + 2]
decision_segment = mutate_position(decision_segment, 0)
decision_segment = mutate_position(decision_segment, -1)
bottom = random_sequence(exclude=decision_segment)[:middle_pivot] \
+ decision_segment
bottom += random_sequence(exclude=bottom)[:length - middle_pivot -
len(decision_segment)]
consume_collector(top, bottom)
check_fp_collector((lambda G: count_decision_nodes(top, G, ksize), {
(2, 2): 1
}), (lambda G: count_decision_nodes(bottom, G, ksize), {
(2, 2): 1
}))
return (top, bottom), middle_pivot
def _right_triple_fork():
(core_sequence, top_branch), pivot = right_fork()
bottom_branch = random_sequence()[:length - pivot - ksize]
# the branch sequence, mutated at position S+1
# choose a base not already represented at that position
bases = {'A', 'C', 'G', 'T'}
used = {core_sequence[pivot + ksize], top_branch[ksize - 1]}
mutated = random.choice(list(bases - used))
bottom_branch = top_branch[:ksize - 1] + mutated + bottom_branch
consume_collector(core_sequence, bottom_branch, top_branch)
check_fp_collector(
(lambda G: count_decision_nodes(core_sequence, G, ksize), {
(1, 3): 1
}), (lambda G: count_decision_nodes(bottom_branch, G, ksize), {}))
return (core_sequence, top_branch, bottom_branch), pivot
def _full_decision():
root = sequence_generator.random_seed()
lseqs = tuple(
sequence_generator.random_branches(root,
n_branches=n_branches,
fw=False,
n_tail_kmers=tip_length))
rseqs = tuple(
sequence_generator.random_branches(root,
n_branches=n_branches,
n_tail_kmers=tip_length))
consume_collector(*lseqs, *rseqs)
core = lseqs[0] + rseqs[0][ksize:]
lseqs = [seq[:-1] for seq in lseqs[1:]]
rseqs = [seq[1:] for seq in rseqs[1:]]
return core, (lseqs, rseqs)
def _left_fork():
(core_sequence, branch), pivot = right_fork()
core_sequence = revcomp(core_sequence)
branch = revcomp(branch)
pivot = length - pivot - ksize
_collector = consume_collector()
_collector.pop(
) # remove previous two fixtures that compose right_fork
_collector.pop()
consume_collector(core_sequence, branch)
_collector = check_fp_collector()
_collector.pop()
_collector.pop()
check_fp_collector(
(lambda G: count_decision_nodes(core_sequence, G, ksize), {
(2, 1): 1
}), (lambda G: count_decision_nodes(branch, G, ksize), {}))
return (core_sequence, branch), pivot
def _snp_bubble():
wildtype_sequence = linear_path()
decision_L = middle_pivot
decision_R = decision_L + ksize + 1
if decision_L < 1:
raise ValueError("ksize too long for length")
snp_sequence = mutate_position(wildtype_sequence, decision_L + ksize)
consume_collector(wildtype_sequence, snp_sequence)
check_fp_collector(
(lambda G: count_decision_nodes(wildtype_sequence, G, ksize), {
(1, 2): 1,
(2, 1): 1
}), (lambda G: count_decision_nodes(snp_sequence, G, ksize), {
(1, 2): 1,
(2, 1): 1
}))
return (wildtype_sequence, snp_sequence), decision_L, decision_R
def _circular_key():
loop = linear_path()
loop = loop + loop[:ksize - 1]
if pivot in (length - ksize, length - ksize - 1):
_pivot = pivot + ksize - 1
else:
_pivot = pivot
loop_kmers = list(kmers(loop, ksize))
tail_kmers = [
loop_kmers[i % len(loop_kmers)]
for i in range(_pivot + 1, _pivot + 1 + ksize)
]
tail = ''.join((kmer[0] for kmer in tail_kmers))
tail = mutate_position(tail, -1)
consume_collector(loop, tail)
check_fp_collector((lambda G: count_decision_nodes(loop, G, ksize), {
(1, 2): 1
}))
return (loop, tail), _pivot
def _suffix_circular_tangle():
base = suffix_circular()
L = middle_pivot
decision_segment = base[L:L + ksize + 1]
decision_segment = mutate_position(decision_segment, 0)
decision_segment = mutate_position(decision_segment, -1)
inducer = random_sequence(exclude=decision_segment)[:L] \
+ decision_segment
inducer += random_sequence(exclude=inducer)[:length - L -
len(decision_segment)]
consume_collector(base, inducer)
check_fp_collector((lambda G: count_decision_nodes(base, G, ksize), {
(1, 2): 1,
(2, 1): 1
}), (lambda G: count_decision_nodes(inducer, G, ksize), {
(1, 2): 1,
(2, 1): 1
}))
return (base, inducer), L
def _hourglass_tangle():
top = linear_path()
L = middle_pivot
decision_segment = top[L:L + ksize + 1]
decision_segment = mutate_position(decision_segment, 0)
decision_segment = mutate_position(decision_segment, -1)
bottom = random_sequence(exclude=decision_segment)[:L] \
+ decision_segment
bottom += random_sequence(exclude=bottom)[:length - L -
len(decision_segment)]
consume_collector(top, bottom)
check_fp_collector((lambda G: count_decision_nodes(top, G, ksize), {
(1, 2): 1,
(2, 1): 1
}), (lambda G: count_decision_nodes(bottom, G, ksize), {
(1, 2): 1,
(2, 1): 1
}))
return (top, bottom), L