def test_count_threading():
with NamedTemporaryFile(suffix='.counttable') as ctrl1out, \
NamedTemporaryFile(suffix='.counttable') as ctrl2out, \
NamedTemporaryFile(suffix='.counttable') as caseout:
case = data_file('trio1/case1.fq')
ctrls = data_glob('trio1/ctrl[1,2].fq')
arglist = [
'count',
'--ksize',
'19',
'--memory',
'500K',
'--threads',
'2',
'--case',
caseout.name,
case,
'--control',
ctrl1out.name,
ctrls[0],
'--control',
ctrl2out.name,
ctrls[1],
]
args = kevlar.cli.parser().parse_args(arglist)
kevlar.count.main(args)
def test_count_simple(numbands, band, kmers_stored, capsys):
with NamedTemporaryFile(suffix='.counttable') as ctrl1out, \
NamedTemporaryFile(suffix='.counttable') as ctrl2out, \
NamedTemporaryFile(suffix='.counttable') as caseout:
case = data_file('simple-genome-case-reads.fa.gz')
ctrls = data_glob('simple-genome-ctrl[1,2]-reads.fa.gz')
arglist = [
'count',
'--case',
caseout.name,
case,
'--control',
ctrl1out.name,
ctrls[0],
'--control',
ctrl2out.name,
ctrls[1],
'--ksize',
'25',
'--memory',
'5K',
'--ctrl-max',
'0',
'--num-bands',
str(numbands),
'--band',
str(band),
]
args = kevlar.cli.parser().parse_args(arglist)
kevlar.count.main(args)
def test_unband_beta():
infiles = data_glob('collect.beta.?.txt')
instream = kevlar.seqio.afxstream(infiles)
merger = kevlar.unband.unband(instream, numbatches=2)
reads = list(merger)
reads.sort(key=lambda r: r.name)
assert len(reads) == 8
assert len(reads[0].annotations) == 4
def test_unband_cli(capsys):
infiles = data_glob('helium-unband/novel.band?.augfastq.gz')
arglist = ['unband'] + infiles
args = kevlar.cli.parser().parse_args(arglist)
kevlar.unband.main(args)
out, err = capsys.readouterr()
outlines = out.strip().split('\n')
qualdeflines = [ln for ln in outlines if ln == '+']
assert len(qualdeflines) == 135
def test_unband_helium():
infiles = data_glob('helium-unband/novel.band?.augfastq.gz')
instream = kevlar.seqio.afxstream(infiles)
merger = kevlar.unband.unband(instream, numbatches=16)
reads = list(merger)
assert len(reads) == 135
readname = 'seq1_haplo1_285110_285519_1:0:0_0:0:0_2dbcd/1'
someread = [r for r in reads if r.name == readname][0]
assert len(someread.annotations) == 75
def test_load_threading(mask, numbands, band):
# Smoke test: make sure things don't explode when run in "threaded" mode.
infiles = data_glob('trio1/case1.fq')
sketch = kevlar.count.load_sample_seqfile(infiles,
19,
1e7,
mask=mask,
numbands=numbands,
band=band,
numthreads=2)
def test_novel_load_counts(capsys):
file1 = data_file('simple-genome-case-reads.fa.gz')
file2 = data_file('ambig.fasta')
file3 = data_file('simple-genome-case.ct')
file4, file5 = data_glob('simple-genome-ctrl?.ct')
arglist = [
'novel', '-k', '25', '--case', file1, file2, '--case-counts', file3,
'--control-counts', file4, file5
]
args = kevlar.cli.parser().parse_args(arglist)
kevlar.novel.main(args)
out, err = capsys.readouterr()
assert 'counttables for 2 sample(s) provided' in err
filterfpr=0.005,
logstream=sys.stderr)
variants = [v for v in workflow]
variants = sorted(variants, key=lambda v: v._pos)
startpos = [v._pos + 1 for v in variants]
teststartpos = [
4073, 185752, 226611, 636699, 834646, 901124, 1175768, 1527139,
1631013, 2265795
]
assert len(variants) == 10
assert startpos == teststartpos
def test_simplex_trio1(capsys):
case = data_file('trio1/case1.fq')
controls = data_glob('trio1/ctrl[1,2].fq')
refr = data_file('bogus-genome/refr.fa')
arglist = [
'simplex', '--case', case, '--control', controls[0], '--control',
controls[1], '--case-min', '6', '--ctrl-max', '0', '--novel-memory',
'1M', '--novel-fpr', '0.2', '--filter-memory', '50K', '--mask-files',
refr, '--mask-memory', '1M', '--filter-fpr', '0.005', '--ksize', '21',
refr
]
args = kevlar.cli.parser().parse_args(arglist)
kevlar.simplex.main(args)
out, err = capsys.readouterr()
testvcf = '\t'.join([
'bogus-genome-chr1', '3567', '.', 'A', 'C', '.', 'PASS', 'RW=GAAGGGCAC'
'ACCTAACCGCAACATTTGCCGTGGAAGCATAA;VW=GAAGGGCACACCTAACCGCACCATTTGCCGTGG'
def test_load_sketches_fpr_fail():
infiles = data_glob('test.counttable')
with pytest.raises(kevlar.sketch.KevlarUnsuitableFPRError) as e:
sketches = kevlar.sketch.load_sketchfiles(infiles, maxfpr=0.001)
assert 'FPR too high, bailing out!!!' in str(e)
def test_load_sketches():
infiles = data_glob('test.counttable')
sketches = kevlar.sketch.load_sketchfiles(infiles, maxfpr=0.5)
for sketch in sketches:
assert sketch.get('CCTGATATCCGGAATCTTAGC') > 0
assert sketch.get('GATTACA' * 3) == 0
def test_load_sketches_fpr_fail():
infiles = data_glob('test.counttable')
errormsg = r'FPR too high, bailing out!!!'
with pytest.raises(kevlar.sketch.KevlarUnsuitableFPRError, match=errormsg):
sketches = kevlar.sketch.load_sketchfiles(infiles, maxfpr=0.001)