def test_novel_output_has_mates():
kid = data_file('microtrios/trio-na-proband.fq.gz')
mom = data_file('microtrios/trio-na-mother.fq.gz')
dad = data_file('microtrios/trio-na-father.fq.gz')
testnovel = data_file('microtrios/novel-na.augfastq.gz')
with NamedTemporaryFile(suffix='.augfastq') as novelfile:
arglist = [
'novel', '--out', novelfile.name, '--case', kid, '--case-min', '5',
'--control', mom, '--control', dad, '--ctrl-max', '1', '--memory',
'500K'
]
args = kevlar.cli.parser().parse_args(arglist)
kevlar.novel.main(args)
intread_ids = set()
mate_seqs = set()
stream = kevlar.parse_augmented_fastx(kevlar.open(novelfile.name, 'r'))
for read in stream:
intread_ids.add(read.name)
mate_seqs.update(read.mates)
stream = kevlar.parse_augmented_fastx(kevlar.open(testnovel, 'r'))
test_ids = set([r.name for r in stream])
assert intread_ids == test_ids
stream = kevlar.parse_augmented_fastx(kevlar.open(testnovel, 'r'))
test_mate_seqs = set([m for r in stream for m in r.mates])
assert mate_seqs == test_mate_seqs
def main(args):
readstream = kevlar.parse_augmented_fastx(kevlar.open(args.infile, 'r'))
if args.part_id:
pstream = kevlar.parse_single_partition(readstream, args.part_id)
else:
pstream = kevlar.parse_partitioned_reads(readstream)
outstream = kevlar.open(args.out, 'w')
workflow = alac(pstream,
args.refr,
threads=args.threads,
ksize=args.ksize,
bigpart=args.bigpart,
delta=args.delta,
seedsize=args.seed_size,
maxdiff=args.max_diff,
match=args.match,
mismatch=args.mismatch,
gapopen=args.open,
gapextend=args.extend,
min_ikmers=args.min_ikmers,
logstream=args.logfile)
writer = kevlar.vcf.VCFWriter(
outstream,
source='kevlar::alac',
refr=args.refr,
)
writer.write_header()
for varcall in workflow:
writer.write(varcall)
def test_call_max_target_length(contigs, gdnas, maxtargetlen, numpassing):
contigfile = data_file(contigs)
contigstream = kevlar.parse_augmented_fastx(kevlar.open(contigfile, 'r'))
partstream = kevlar.parse_partitioned_reads(contigstream)
contigs = kevlar.call.load_contigs(partstream)
gdnafile = data_file(gdnas)
gdnastream = kevlar.reference.load_refr_cutouts(kevlar.open(gdnafile, 'r'))
partstream = kevlar.parse_partitioned_reads(gdnastream)
targets = kevlar.call.load_contigs(partstream)
calls = list()
for partid in contigs:
contiglist = contigs[partid]
gdnalist = targets[partid]
caller = kevlar.call.call(
gdnalist, contiglist, partid=partid, maxtargetlen=maxtargetlen
)
calls.extend(list(caller))
nocalls = [c for c in calls if c.seqid == '.']
passcalls = [c for c in calls if c.seqid != '.']
assert len(passcalls) == numpassing
for c in nocalls:
assert c.seqid == c.position == '.'
assert sorted(c.info.keys()) == ['CONTIG', 'IKMERS', 'PART']
def main(args):
if args.split:
kevlar.mkdirp(args.split, trim=True)
outstream = None if args.split else kevlar.open(args.out, 'w')
readstream = kevlar.parse_augmented_fastx(kevlar.open(args.infile, 'r'))
partitioner = partition(readstream,
strict=args.strict,
minabund=args.min_abund,
maxabund=args.max_abund,
dedup=args.dedup,
gmlfile=args.gml,
logstream=args.logfile)
partnum = 0
numreads = 0
for partnum, part in enumerate(partitioner, 1):
numreads += len(part)
if args.split:
ofname = '{:s}.cc{:d}.augfastq.gz'.format(args.split, partnum)
with kevlar.open(ofname, 'w') as outfile:
for read in part:
kevlar.print_augmented_fastx(read, outfile)
else:
for read in part:
read.name += ' kvcc={:d}'.format(partnum)
kevlar.print_augmented_fastx(read, outstream)
message = '[kevlar::partition] grouped {:d} reads'.format(numreads)
message += ' into {:d} connected components'.format(partnum)
print(message, file=args.logfile)
def test_split_cli():
infile = data_file('fiveparts.augfastq.gz')
tempdir = mkdtemp()
print(tempdir)
arglist = ['split', infile, '3', tempdir + '/out']
args = kevlar.cli.parser().parse_args(arglist)
kevlar.split.main(args)
outfile = tempdir + '/out.0.augfastx.gz'
readstream = kevlar.parse_augmented_fastx(kevlar.open(outfile, 'r'))
partstream = kevlar.parse_partitioned_reads(readstream)
partitions = list(partstream)
partitions = [part for partid, part in partitions]
assert len(partitions) == 2
assert len(partitions[0]) == 67
assert len(partitions[1]) == 12
outfile = tempdir + '/out.1.augfastx.gz'
readstream = kevlar.parse_augmented_fastx(kevlar.open(outfile, 'r'))
partstream = kevlar.parse_partitioned_reads(readstream)
partitions = list(partstream)
partitions = [part for partid, part in partitions]
assert len(partitions) == 2
assert len(partitions[0]) == 23
assert len(partitions[1]) == 11
outfile = tempdir + '/out.2.augfastx.gz'
readstream = kevlar.parse_augmented_fastx(kevlar.open(outfile, 'r'))
partstream = kevlar.parse_partitioned_reads(readstream)
partitions = list(partstream)
partitions = [part for partid, part in partitions]
assert len(partitions) == 1
assert len(partitions[0]) == 15
rmtree(tempdir)
def test_call_homopolymer_filter_disabled():
contigfile = data_file('homopolymer/12175-3parts.contigs.augfasta')
contigstream = kevlar.parse_augmented_fastx(kevlar.open(contigfile, 'r'))
partstream = kevlar.parse_partitioned_reads(contigstream)
contigs = kevlar.call.load_contigs(partstream)
gdnafile = data_file('homopolymer/12175-3parts.targets.fasta')
gdnastream = kevlar.reference.load_refr_cutouts(kevlar.open(gdnafile, 'r'))
partstream = kevlar.parse_partitioned_reads(gdnastream)
targets = kevlar.call.load_contigs(partstream)
prelimcalls = list()
for partid in contigs:
contiglist = contigs[partid]
gdnalist = targets[partid]
caller = kevlar.call.call(
gdnalist, contiglist, partid=partid, homopolyfilt=False
)
prelimcalls.extend(list(caller))
kid = kevlar.sketch.load(data_file('homopolymer/12175-kid.sct'))
mom = kevlar.sketch.load(data_file('homopolymer/12175-mom.sct'))
dad = kevlar.sketch.load(data_file('homopolymer/12175-dad.sct'))
refr = kevlar.sketch.load(data_file('homopolymer/12175-refr.sct'))
scorer = kevlar.simlike.simlike(
prelimcalls, kid, [mom, dad], refr,
samplelabels=['Proband', 'Mother', 'Father'],
)
calls = list(scorer)
assert len(calls) == 6
for c in calls:
assert 'Homopolymer' not in c.filterstr
def main(args):
augseqs = kevlar.parse_augmented_fastx(kevlar.open(args.augseqs, 'r'))
nakedseqs = kevlar.parse_augmented_fastx(kevlar.open(args.seqs, 'r'))
outstream = kevlar.open(args.out, 'w')
docollapse = args.collapse_mates
for record in augment(augseqs, nakedseqs, collapsemates=docollapse):
kevlar.print_augmented_fastx(record, outstream)
def test_nocall():
# Intentionally mismatched
qfile = data_file('phony-deletion-01.contig.fa')
tfile = data_file('phony-insertion-01.gdna.fa')
qinstream = kevlar.parse_augmented_fastx(kevlar.open(qfile, 'r'))
query = [record for record in qinstream][0]
tinstream = kevlar.reference.load_refr_cutouts(kevlar.open(tfile, 'r'))
target = [record for record in tinstream][0]
aln = VariantMapping(query, target, 1e6, '25D5M22I5M46D8M13D2M35I')
assert aln.offset is None
assert aln.targetshort is None
assert aln.match is None
assert aln.leftflank is None
assert aln.indel is None
assert aln.indeltype is None
assert aln.rightflank is None
variants = list(aln.call_variants(21))
assert len(variants) == 1
assert variants[0].vcf == (
'yourchr\t801\t.\t.\t.\t.\tInscrutableCigar\t'
'CIGAR=25D5M22I5M46D8M13D2M35I;KSW2=1000000.0;CONTIG=AACTGGTGGGCTCAAGA'
'CTAAAAAGACTTTTTTGGTGACAAGCAGGGCGGCCTGCCCTTCCTGTAGTGCAAGAAAAT')
def main(args):
print('[kevlar::mutate] loading mutations', file=args.logfile)
mutations = load_mutations(kevlar.open(args.mutations, 'r'), args.logfile)
print('[kevlar::mutate] mutating genome', file=args.logfile)
for record in mutate_genome(args.genome, mutations):
write_record(record, kevlar.open(args.out, 'w'))
def test_augment_contig_mates():
augfh = kevlar.open(data_file('deadbeef.augfastq.gz'), 'r')
augreads = kevlar.parse_augmented_fastx(augfh)
nakedfh = kevlar.open(data_file('deadbeef.contig.fa'), 'r')
nakedseq = kevlar.parse_augmented_fastx(nakedfh)
contigs = list(augment(augreads, nakedseq))
assert len(contigs) == 1
assert len(contigs[0].annotations) == 74
def main(args):
contigstream = kevlar.parse_augmented_fastx(kevlar.open(args.contigs, 'r'))
outstream = kevlar.open(args.out, 'w')
for record in localize(contigstream,
args.refr,
ksize=args.ksize,
delta=args.delta):
khmer.utils.write_record(record, outstream)
def main(args):
reader = kevlar.vcf.vcfstream(args.vcf)
bedstream = kevlar.parse_bed(kevlar.open(args.filt, 'r'))
outstream = kevlar.open(args.out, 'w')
writer = kevlar.vcf.VCFWriter(outstream, source='kevlar::varfilter')
writer.write_header()
for varcall in varfilter(reader, bedstream):
writer.write(varcall)
def test_suffix():
bamstream = kevlar.open(data_file('nopair.sam'), 'r')
refrstream = kevlar.open(data_file('bogus-genome/refr.fa'), 'r')
refr = kevlar.seqio.parse_seq_dict(refrstream)
records = [r for r in kevlar.dump.dump(bamstream, refr)]
assert len(records) == 1
assert records[0].name.endswith('/1') or records[0].name.endswith('/2')
def test_kevlar_open():
thefile = kevlar.tests.data_file('wasp-pass.contig.augfasta')
filehandle = kevlar.open(thefile, 'r')
filecontents = filehandle.read()
assert len(filecontents.strip().split('\n')) == 9
with pytest.raises(ValueError, match=r'invalid mode "p"'):
filehandle = kevlar.open(thefile, 'p')
def test_nomargin():
qfile = kevlar.open(data_file('nomargin-r-indel-contigs.augfasta'), 'r')
tfile = kevlar.open(data_file('nomargin-r-gdna.fa'), 'r')
query = next(kevlar.parse_augmented_fastx(qfile))
target = next(kevlar.parse_augmented_fastx(tfile))
cigar, score = kevlar.align(target.sequence, query.sequence)
tok = AlignmentTokenizer(query.sequence, target.sequence, cigar)
assert tok._cigar == tok._origcigar
def test_compact():
bedstream = kevlar.open(data_file('compact-test-refr.bed.gz'), 'r')
index = kevlar.evaluate.populate_index_from_bed(bedstream)
vcfstream = kevlar.open(data_file('compact-test-pred.vcf.gz'), 'r')
reader = kevlar.vcf.VCFReader(vcfstream)
compactor = kevlar.evaluate.compact(reader, index, delta=10)
calls = list(compactor)
assert len(calls) == 33
def test_augment_reads_mates():
augfh = kevlar.open(data_file('deadbeef.augfastq.gz'), 'r')
augreads = list(kevlar.parse_augmented_fastx(augfh))
nakedfh = kevlar.open(data_file('deadbeef.fq.gz'), 'r')
nakedseq = kevlar.parse_augmented_fastx(nakedfh)
newreads = list(augment(augreads, nakedseq, upint=5))
for oldread, newread in zip(augreads, newreads):
assert oldread.sequence == newread.sequence
assert oldread.annotations == newread.annotations
def main(args):
fastq = kevlar.open(args.out, 'w')
refr = None
if args.refr:
print('[kevlar::dump] Loading reference sequence', file=args.logfile)
refrstream = kevlar.open(args.refr, 'r')
refr = kevlar.seqio.parse_seq_dict(refrstream)
for read in dump(args.reads, refr, args.pair_mode, logstream=args.logfile):
write_record(read, fastq)
def main_greedy(args):
readstream = kevlar.parse_augmented_fastx(kevlar.open(args.augfastq, 'r'))
outstream = None # Only create output file if there are contigs
contigstream = assemble_greedy(readstream, args.gml, args.debug,
args.logfile)
for contig in contigstream:
if outstream is None:
outstream = kevlar.open(args.out, 'w')
kevlar.print_augmented_fastx(contig, outstream)
def test_gap_center_aligned(contig, gdna, newcigar, origcigar, nblocks):
qfile = kevlar.open(data_file('cigar/' + contig), 'r')
tfile = kevlar.open(data_file('cigar/' + gdna), 'r')
query = next(kevlar.parse_augmented_fastx(qfile))
target = next(kevlar.parse_augmented_fastx(tfile))
cigar, score = kevlar.align(target.sequence, query.sequence)
tok = AlignmentTokenizer(query.sequence, target.sequence, cigar)
assert len(tok.blocks) == nblocks
assert tok._cigar == newcigar
assert tok._origcigar == origcigar
def main(args):
readstream = kevlar.parse_augmented_fastx(kevlar.open(args.augfastq, 'r'))
if args.part_id:
pstream = kevlar.parse_single_partition(readstream, args.part_id)
else:
pstream = kevlar.parse_partitioned_reads(readstream)
outstream = kevlar.open(args.out, 'w')
assembler = assemble(pstream, maxreads=args.max_reads)
for partid, contig in assembler:
kevlar.print_augmented_fastx(contig, outstream)
def test_call_near_end(query, target, dist, n, trimcount):
contig = next(
kevlar.parse_augmented_fastx(kevlar.open(data_file(query), 'r')))
cutout = next(
kevlar.reference.load_refr_cutouts(kevlar.open(data_file(target),
'r')))
aln = VariantMapping(contig, cutout)
calls = list(aln.call_variants(31, mindist=dist))
assert len(calls) == n
assert aln.trimmed == trimcount
def main(args):
partfile = kevlar.open(args.infile, 'r')
readstream = kevlar.parse_augmented_fastx(partfile)
partstream = kevlar.parse_partitioned_reads(readstream)
outstreams = list()
for i in range(args.numfiles):
outfile = '{:s}.{:d}'.format(args.base, i + 1)
os = kevlar.open(outfile, 'w')
outstreams.append(os)
split(partstream, outstreams)
def test_call_num_interesting_kmers():
contig = next(
kevlar.parse_augmented_fastx(
kevlar.open(data_file('iktest.contig.fa'), 'r')))
cutout = next(
kevlar.reference.load_refr_cutouts(
kevlar.open(data_file('iktest.gdna.fa'), 'r')))
aln = VariantMapping(contig, cutout)
calls = list(aln.call_variants(29))
assert len(calls) == 1
assert calls[0].attribute('IKMERS') == '1'
def test_varfilter_single():
bedstream = kevlar.parse_bed(
kevlar.open(data_file('fiveparts-ignore-single.bed'), 'r'))
vcffile = data_file('five-snvs-with-likelihood.vcf')
with kevlar.open(vcffile, 'r') as vcfstream:
reader = kevlar.vcf.VCFReader(vcfstream)
varcalls = list(kevlar.varfilter.varfilter(reader, bedstream))
assert len(varcalls) == 5
filtered = [vc for vc in varcalls if vc.filterstr != 'PASS']
assert len(filtered) == 1
assert filtered[0].position == 36385017
def test_augment_contigs():
augfh = kevlar.open(data_file('snorkel.augfastq'), 'r')
augreads = kevlar.parse_augmented_fastx(augfh)
nakedfh = kevlar.open(data_file('snorkel-contig.fasta'), 'r')
nakedseq = kevlar.parse_augmented_fastx(nakedfh)
augseqs = list(augment(augreads, nakedseq))
assert len(augseqs) == 1
assert len(augseqs[0].annotations) == 3
offsets = [k.offset for k in augseqs[0].annotations]
assert offsets == [17, 20, 22]
def filter(readfile, mask=None, memory=1e6, maxfpr=0.01, casemin=6, ctrlmax=1):
timer = kevlar.Timer()
timer.start()
reader = kevlar.parse_augmented_fastx(kevlar.open(readfile, 'r'))
counts = first_pass(reader, mask, memory, timer)
check_fpr(counts, maxfpr)
reader = kevlar.parse_augmented_fastx(kevlar.open(readfile, 'r'))
for read in second_pass(reader, counts, casemin, ctrlmax, timer):
yield read
total = timer.stop()
message = 'Total time: {:.2f} seconds'.format(total)
kevlar.plog('[kevlar::filter]', message)
def test_call_pico_indel(ccid, varcall):
qfile = data_file('pico' + ccid + '.contig.augfasta')
tfile = data_file('pico' + ccid + '.gdna.fa')
qinstream = kevlar.parse_augmented_fastx(kevlar.open(qfile, 'r'))
queries = [record for record in qinstream]
tinstream = kevlar.reference.load_refr_cutouts(kevlar.open(tfile, 'r'))
targets = [record for record in tinstream]
calls = list(call(targets, queries))
assert len(calls) == 1
assert str(calls[0]) == varcall
def test_gap_center_aligned():
query = next(
kevlar.parse_augmented_fastx(
kevlar.open(data_file('cigar/b.contig.fa'), 'r')))
target = next(
kevlar.parse_augmented_fastx(
kevlar.open(data_file('cigar/b.gdna.fa'), 'r')))
cigar, score = kevlar.align(target.sequence, query.sequence)
tok = AlignmentTokenizer(query.sequence, target.sequence, cigar)
assert len(tok.blocks) == 3
assert tok._cigar == '41D150M50D'
assert tok._origcigar == '41D144M50D6M'
def main(args):
contigstream = kevlar.parse_augmented_fastx(kevlar.open(args.contigs, 'r'))
outstream = kevlar.open(args.out, 'w')
localizer = localize(contigstream,
args.refr,
seedsize=args.seed_size,
delta=args.delta,
maxdiff=args.max_diff,
logstream=args.logfile)
for cutout in localizer:
record = Record(name=cutout.defline, sequence=cutout.sequence)
kevlar.sequence.write_record(record, outstream)