Ejemplo n.º 1
0
def test_partition_nodedup_minabund(capsys):
    infile = kevlar.tests.data_file('dupl-part-2reads.augfastq.gz')
    readstream = kevlar.parse_augmented_fastx(kevlar.open(infile, 'r'))
    partitioner = partition(readstream, minabund=5, dedup=False)
    partitions = list(partitioner)
    assert len(partitions) == 0
Ejemplo n.º 2
0
def test_pico_ccs():
    infile = kevlar.tests.data_file('pico-filtered.fq.gz')
    readstream = kevlar.parse_augmented_fastx(kevlar.open(infile, 'r'))
    partitions = [p for p in partition(readstream, minabund=6)]
    assert len(partitions) == 10
Ejemplo n.º 3
0
                       ksize=ksize,
                       casemin=casemin,
                       ctrlmax=ctrlmax,
                       updateint=100000,
                       logstream=logstream)
    filterer = kfilter(discoverer,
                       mask=mask,
                       casemin=casemin,
                       ctrlmax=ctrlmax,
                       ksize=ksize,
                       memory=filtermem,
                       maxfpr=filterfpr,
                       logstream=logstream)
    partitioner = partition(filterer,
                            dedup=dedup,
                            minabund=partminabund,
                            maxabund=partmaxabund,
                            logstream=logstream)

    caller = alac(partitioner,
                  refrfile,
                  threads=threads,
                  ksize=ksize,
                  delta=delta,
                  seedsize=seedsize,
                  match=match,
                  mismatch=mismatch,
                  gapopen=gapopen,
                  gapextend=gapextend,
                  logstream=logstream)