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 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 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_no_margin(query, target, refr, alt):
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))
assert len(calls) == 1
assert calls[0].filterstr == 'PASS'
assert calls[0]._refr == refr
assert calls[0]._alt == alt
def test_passenger_screen():
contig = next(
kevlar.parse_augmented_fastx(
kevlar.open(data_file('wasp-pass.contig.augfasta'), 'r')))
cutout = next(
kevlar.reference.load_refr_cutouts(
kevlar.open(data_file('wasp.gdna.fa'), 'r')))
aln = VariantMapping(contig, cutout)
calls = list(aln.call_variants(29))
assert len(calls) == 2
assert calls[0].filterstr == 'PASS'
assert calls[1].filterstr == 'PassengerVariant'
def test_variant_window(prefix, cigar, refrwindow, altwindow):
qfile = data_file(prefix + '.contig.fa')
tfile = data_file(prefix + '.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, cigar)
variants = list(aln.call_variants(21))
assert len(variants) == 1
assert variants[0].window == altwindow
assert variants[0].refrwindow == refrwindow
def test_call_ssc_1bpdel():
"""Test 1bp deletion"""
qfile = data_file('ssc218.contig.augfasta')
tfile = data_file('ssc218.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, '50D132M1D125M50D')
variants = list(aln.call_variants(31))
assert len(variants) == 1
assert str(variants[0]) == '6:23230160:1D'
def test_drop_numerous_mismatches():
contig = next(
kevlar.parse_augmented_fastx(
kevlar.open(data_file('drop-polysnp-contig.augfasta'), 'r')))
cutout = next(
kevlar.reference.load_refr_cutouts(
kevlar.open(data_file('drop-polysnp-gdna.fa'), 'r')))
aln = VariantMapping(contig, cutout)
calls = list(aln.call_variants(21))
for c in calls:
print(c.vcf)
assert len(calls) == 1
assert calls[0].filterstr == 'NumerousMismatches'
assert calls[0]._refr == '.'
assert calls[0]._alt == '.'
def prelim_call(targetlist, querylist, match=1, mismatch=2, gapopen=5,
gapextend=0, ksize=31, refrfile=None, debug=False, mindist=5,
logstream=sys.stderr):
"""Implement the `kevlar call` procedure as a generator function."""
for query in sorted(querylist, reverse=True, key=len):
alignments = list()
for target in sorted(targetlist, key=lambda cutout: cutout.defline):
mapping = VariantMapping(
query, target, match=match, mismatch=mismatch, gapopen=gapopen,
gapextend=gapextend
)
alignments.append(mapping)
aligns2report = alignments_to_report(alignments)
if len(aligns2report) > 1:
if refrfile and len(query.mates) > 0:
mate_pos = list(align_mates(query, refrfile))
if len(mate_pos) > 0:
for aln in aligns2report:
aln.matedist = mate_distance(mate_pos, aln.interval)
aligns2report.sort(key=lambda aln: aln.matedist)
for n, alignment in enumerate(aligns2report):
if debug:
print('DEBUG ', alignment.cutout.defline, ' vs ',
alignment.contig.name, '\n', str(alignment), sep='',
end='\n\n', file=logstream)
for varcall in alignment.call_variants(ksize, mindist, logstream):
if alignment.matedist:
varcall.annotate('MATEDIST', alignment.matedist)
yield varcall
def test_call_ssc_two_proximal_snvs():
"""Test two proximal SNVs
Currently this serves as a negative control for calling isolated SNVs, but
distinguishing which (if any) of a set of proximal SNVs is novel will be
supported soon, and this test will need to be updated.
"""
qfile = data_file('ssc107.contig.augfasta.gz')
tfile = data_file('ssc107.gdna.fa.gz')
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, '25D263M25D')
variants = list(aln.call_variants(31))
assert len(variants) == 2
def test_call_truncated_windows(query, target, vw, rw):
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)
if aln.vartype == 'snv':
assert aln.leftflank is None
assert aln.indeltype is None
assert aln.indel is None
assert aln.rightflank is None
calls = list(aln.call_variants(31))
assert len(calls) == 1
print('VW:', calls[0].window, file=sys.stderr)
print('RW:', calls[0].refrwindow, file=sys.stderr)
assert calls[0].window == vw
assert calls[0].refrwindow == rw
def test_call_indel_snv():
contig = next(
kevlar.parse_augmented_fastx(
kevlar.open(data_file('indel-snv.contig.augfasta'), 'r')))
cutout = next(
kevlar.reference.load_refr_cutouts(
kevlar.open(data_file('indel-snv.gdna.fa'), 'r')))
aln = VariantMapping(contig, cutout)
calls = list(aln.call_variants(31))
assert len(calls) == 2
assert calls[0]._refr == 'CA'
assert calls[0]._alt == 'C'
assert calls[0]._pos == 501 - 1
assert calls[1]._refr == 'C'
assert calls[1]._alt == 'A'
assert calls[1]._pos == 474 - 1
calls = list(aln.call_variants(31, mindist=None))
assert len(calls) == 2
def test_variant_mapping():
contig = screed.Record(
name='contig1',
sequence='CCTGAGCCCTCTCAAGTCGGGTCCTGGCCCGGTCTGCCCATGAGGCTGGGCCTGAGCCCC'
)
cutout = kevlar.reference.ReferenceCutout(
defline='chr1_10000-10060',
sequence='CCTGAGCCCTCTCAAGTCGGGTCCTGGCCCAGTCTGCCCATGAGGCTGGGCCTGAGCCCC'
)
mapping = VariantMapping(contig, cutout, score=1e6, cigar='60M')
assert mapping.seqid == 'chr1'
assert mapping.interval == ('chr1', 10000, 10060)
def test_varmap_str():
contig = next(
kevlar.parse_augmented_fastx(
kevlar.open(data_file('wasp-pass.contig.augfasta'), 'r')))
cutout = next(
kevlar.reference.load_refr_cutouts(
kevlar.open(data_file('wasp.gdna.fa'), 'r')))
aln = VariantMapping(contig, cutout)
alignstr = kevlar.open(data_file('wasp-align.txt'), 'r').read().strip()
print(str(aln), file=sys.stderr)
print(alignstr, file=sys.stderr)
assert str(aln) == alignstr
def prelim_call(targetlist,
querylist,
partid=None,
match=1,
mismatch=2,
gapopen=5,
gapextend=0,
ksize=31,
refrfile=None,
debug=False,
mindist=5,
homopolyfilt=True,
maxtargetlen=10000):
"""Implement the `kevlar call` procedure as a generator function."""
for query in sorted(querylist, reverse=True, key=len):
alignments = list()
for target in sorted(targetlist, key=lambda cutout: cutout.defline):
nocall = False
if maxtargetlen and len(target) > maxtargetlen:
nocall = True
mapping = VariantMapping(
query,
target,
match=match,
mismatch=mismatch,
gapopen=gapopen,
gapextend=gapextend,
homopolyfilt=homopolyfilt,
nocall=nocall,
)
alignments.append(mapping)
aligns2report = alignments_to_report(alignments)
for n, alignment in enumerate(aligns2report):
if debug:
kevlar.plog(
'DEBUG ',
alignment.cutout.defline,
' vs ',
alignment.contig.name,
'\n',
str(alignment),
sep='',
end='\n\n',
)
for varcall in alignment.call_variants(ksize, mindist):
if partid is not None:
varcall.annotate('PART', partid)
yield varcall