def test_count_first_pass():
mask = Nodetable.load(data_file('minitrio/mask.nt'))
counts = Counttable(31, 1e4, 4)
seqfile = data_file('minitrio/trio-proband.fq.gz')
count_first_pass([seqfile], counts, mask)
with NamedTemporaryFile(suffix='.ct') as countfile:
counts.save(countfile.name)
testcountfile = data_file('minitrio/trio-proband-mask-counts.ct')
assert filecmp.cmp(testcountfile, countfile.name) is True
def get_unique_seeds(recordstream, seedsize):
"""Grab all unique seeds from the specified sequence file."""
ct = Counttable(seedsize, 1, 1)
kmers = set()
for record in recordstream:
for kmer in ct.get_kmers(record.sequence):
minkmer = kevlar.revcommin(kmer)
if minkmer not in kmers:
kmers.add(minkmer)
yield kmer
def test_save_load(Tabletype):
kh = Tabletype(5)
ttype = type(kh)
savefile = utils.get_temp_filename('tablesave.out')
# test add(dna)
x = kh.add("ATGGC")
z = kh.get("ATGGC")
assert z == 1
kh.save(savefile)
# should we provide a single load function here? yes, probably. @CTB
if ttype == _Countgraph:
loaded = khmer.load_countgraph(savefile)
elif ttype == Counttable:
loaded = Counttable.load(savefile)
elif ttype == _SmallCountgraph:
loaded = khmer.load_countgraph(savefile, small=True)
elif ttype == SmallCounttable:
loaded = SmallCounttable.load(savefile)
elif ttype == _Nodegraph:
loaded = khmer.load_nodegraph(savefile)
elif ttype == Nodetable:
loaded = Nodetable.load(savefile)
else:
raise Exception("unknown tabletype")
z = loaded.get('ATGGC')
assert z == 1
def test_count_second_pass():
mask = Nodetable.load(data_file('minitrio/mask.nt'))
counts = Counttable.load(data_file('minitrio/trio-proband-mask-counts.ct'))
seqfile = data_file('minitrio/trio-proband.fq.gz')
abund = count_second_pass([seqfile], counts)
assert abund == {10: 6, 11: 10, 12: 12, 13: 18, 14: 16, 15: 11, 16: 9,
17: 9, 18: 11, 19: 8, 20: 9, 21: 7, 22: 3}
def test_assumptions(kmer):
ct = Counttable(27, 1e5, 2)
kmer_rc = kevlar.revcom(kmer)
assert ct.hash(kmer) == ct.hash(kmer_rc)
assert ct.get_kmer_hashes(kmer)[0] == ct.get_kmer_hashes(kmer_rc)[0]