def test_left_of_branch_to_beginning_revcomp(self, right_tip_structure):
# start from revcomp of HDN (left of branch)
graph, contig, L, HDN, R, tip = right_tip_structure
asm = khmer.LinearAssembler(graph)
path = asm.assemble(revcomp(L))
assert len(path) == HDN.pos + K
assert utils._equals_rc(path, contig[: len(path)])
def test_left_of_branch_to_beginning_revcomp(self, right_tip_structure):
# start from revcomp of HDN (left of branch)
graph, contig, L, HDN, R, tip = right_tip_structure
asm = khmer.LinearAssembler(graph)
path = asm.assemble(revcomp(L))
assert len(path) == HDN.pos + K
assert utils._equals_rc(path, contig[:len(path)])
def test_beginning_to_branch_revcomp(self, right_tip_structure):
# assemble from beginning of contig, up until branch point
# starting from rev comp
graph, contig, L, HDN, R, tip = right_tip_structure
asm = khmer.LinearAssembler(graph)
path = asm.assemble(revcomp(contig[0:K]))
assert len(path) == HDN.pos + K
assert utils._equals_rc(path, contig[:len(path)])
def test_beginning_to_branch_revcomp(self, right_tip_structure):
# assemble from beginning of contig, up until branch point
# starting from rev comp
graph, contig, L, HDN, R, tip = right_tip_structure
asm = khmer.LinearAssembler(graph)
path = asm.assemble(revcomp(contig[0:K]))
assert len(path) == HDN.pos + K
assert utils._equals_rc(path, contig[: len(path)])
def test_from_branch_to_ends_with_stopbf_revcomp(self, left_tip_structure):
# block the tip with the stop_bf. should return a full length contig.
graph, contig, L, HDN, R, tip = left_tip_structure
asm = khmer.LinearAssembler(graph)
stop_bf = khmer.Nodegraph(K, 1e5, 4)
stop_bf.count(tip)
path = asm.assemble(revcomp(HDN), stop_bf)
assert len(path) == len(contig)
assert utils._equals_rc(path, contig)
def test_from_branch_to_ends_with_stopbf_revcomp(self, left_tip_structure):
# block the tip with the stop_bf. should return a full length contig.
graph, contig, L, HDN, R, tip = left_tip_structure
asm = khmer.LinearAssembler(graph)
stop_bf = khmer.Nodegraph(K, 1e5, 4)
stop_bf.count(tip)
path = asm.assemble(revcomp(HDN), stop_bf)
assert len(path) == len(contig)
assert utils._equals_rc(path, contig)
def add_seen(kmer):
seen.add(kmer)
seen.add(revcomp(kmer))
def _contains_rc(match, query):
return (query in match) or (revcomp(query) in match)
def _equals_rc(query, match):
return (query == match) or (revcomp(query) == match)
def _contains_rc(match, query):
return (query in match) or (revcomp(query) in match)
def _equals_rc(query, match):
return (query == match) or (revcomp(query) == match)
def add_seen(kmer):
seen.add(kmer)
seen.add(revcomp(kmer))