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_load_sample_seqfile_withmask(count, smallcount, count_masked,
kpresent, kabsent):
mask = Nodetable(21, 1e4, 4)
mask.consume('CACCAATCCGTACGGAGAGCCGTATATATAGACTGCTATACTATTGGATCGTACGGGGC')
sketch = kevlar.count.load_sample_seqfile(
[data_file('bogus-genome/refr.fa')],
21,
1e6,
mask=mask,
consume_masked=count_masked,
count=count,
smallcount=smallcount,
)
assert sketch.get(kpresent) > 0
assert sketch.get(kabsent) == 0
assert sketch.get('GATTACAGATTACAGATTACA') == 0
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_count_cli_with_mask(capsys):
mask = Nodetable(21, 1e4, 4)
mask.consume('CACCAATCCGTACGGAGAGCCGTATATATAGACTGCTATACTATTGGATCGTACGGGGC')
with NamedTemporaryFile(suffix='.nt') as maskfile, \
NamedTemporaryFile(suffix='.sct') as countfile:
mask.save(maskfile.name)
arglist = [
'count', '--ksize', '21', '--mask', maskfile.name, '--memory',
'1M', countfile.name,
data_file('bogus-genome/refr.fa')
]
args = kevlar.cli.parser().parse_args(arglist)
kevlar.count.main(args)
out, err = capsys.readouterr()
assert '36898 distinct k-mers stored' in err