def testCase(self, instance):
data = TokenReader(StringIO(" ".join(instance)))
dataset = TestDataset.loadStructure(data)
disjointigs = DisjointigCollection()
for dis in dataset.disjointigs:
disjointigs.addNew(dis.seq, dis.id)
dp = DotPlot(disjointigs)
dp.construct(self.aligner)
save = StringIO()
save_handler = TokenWriter(save)
dp.save(save_handler)
tmp = save.getvalue()
test_result = tmp.replace(" ", "").replace("\n", "")
ethalon = data.readToken()
if test_result != ethalon:
for dis in disjointigs:
print list(dp.allInter(dis.asSegment()))
assert test_result == ethalon, "\n" + test_result + "\n" + ethalon
def genAll(self, aligner):
# type: (Aligner) -> Tuple[NewLineStorage, LineDotPlot, ReadCollection]
disjointigs = DisjointigCollection()
for dis in self.disjointigs:
disjointigs.addNew(dis.seq, dis.id)
from disjointig_resolve.line_storage import NewLineStorage
lines = NewLineStorage(disjointigs, aligner)
lines.name_printer = lambda line: line.id + "_" + self.translateBack(
line, aligner)
for line in self.contigs:
new_line = lines.addNew(line.seq, line.id)
new_line.initial.add(
AlignmentPiece.Identical(
new_line.asSegment().asContig().asSegment(),
new_line.asSegment()))
dp = LineDotPlot(lines, aligner)
dp.construct(aligner)
lines.alignDisjointigs()
reads = ReadCollection()
for read in self.reads:
reads.addNewRead(read)
disjointigs.addAlignments(aligner.localAlign(reads, disjointigs))
return lines, dp, reads