def test_wrong_chromosome(): with TemporaryDirectory() as tempdir: outvcf = tempdir + '/output.vcf' with raises(SystemExit): run_genotype(phase_input_files=[short_bamfile], ignore_read_groups=True, variant_file='tests/data/short-genome/wrongchromosome.vcf', output=outvcf)
def test_GtQualThreshold():
for threshold in [0,2,3,6,13,50]:
with TemporaryDirectory() as tempdir:
thres = 1-10**(-threshold/10.0)
out_vcf = tempdir + '/out.vcf'
priors_vcf = tempdir + '/priors.vcf'
run_genotype(phase_input_files=[trio_bamfile], variant_file='tests/data/trio.vcf',
output=out_vcf, gt_qual_threshold=threshold, indels=False, prioroutput=priors_vcf)
for out in [open(out_vcf,'r'), open(priors_vcf,'r')]:
out.seek(0)
lines = [line for line in out.readlines() if not line.startswith('#')]
for line in lines:
entries = line.split()
likelihood_str = entries[9].split(':')[-1:][0]
likelihoods = [float(i) for i in likelihood_str.split(',')]
genotype = entries[9].split(':')[0]
if not genotype == '.':
genotype = int(genotype[0]) + int(genotype[2])
gt = likeliest_genotype(likelihoods[0], likelihoods[1], likelihoods[2], thres)
print(likelihoods[0], likelihoods[1], likelihoods[2], gt, genotype, thres)
assert(gt == genotype)
def test_genotype_log_likelihoods_given():
with TemporaryDirectory() as tempdir:
outvcf = tempdir + '/output_gl_log.vcf'
outpriors = tempdir + '/priors.vcf'
run_genotype(phase_input_files=[trio_bamfile], variant_file='tests/data/trio_genotype_log_likelihoods.vcf', output=outvcf,
ped='tests/data/trio.ped', genmap='tests/data/trio.map', gt_qual_threshold=0, prioroutput=outpriors)
for outfile in [outvcf, outpriors]:
assert os.path.isfile(outfile)
tables = list(VcfReader(outfile, phases=True, genotype_likelihoods=True))
assert len(tables) == 1
table = tables[0]
assert table.chromosome == '1'
assert len(table.variants) == 5
assert table.samples == ['HG004', 'HG003', 'HG002']
# check if GL likelihoods were replaced
vcf_reader = vcf.Reader(filename=outfile)
print(vcf_reader.samples, outfile)
for record in vcf_reader:
for call in record.samples:
GL = getattr(call.data, 'GL', None)
GQ = getattr(call.data, 'GQ', None)
print('GL:', GL, 'GQ', GQ)
assert(GL != [-1,-1,-1])
assert(GQ != 100)
def test_genotyping_specific_chromosome(): for requested_chromosome in ['1','2']: with TemporaryDirectory() as tempdir: outvcf = tempdir + '/output.vcf' outpriors = tempdir + '/priors.vcf' run_genotype(phase_input_files=[trio_bamfile], variant_file='tests/data/trio-two-chromosomes.vcf', output=outvcf, ped='tests/data/trio.ped', genmap='tests/data/trio.map', chromosomes=[requested_chromosome], prioroutput=outpriors) for outfile in [outvcf, outpriors]: assert os.path.isfile(outfile) tables = list(VcfReader(outfile, genotype_likelihoods=True)) assert len(tables) == 2 for table in tables: assert len(table.variants) == 5 assert table.samples == ['HG004', 'HG003', 'HG002'] index = 0 if requested_chromosome == '1': index = 1 # should be no genotype likelihoods for skipped chromosomes for s in tables[index].samples: tables[index].genotype_likelihoods_of(s) == [None] * 5 tables[not index].genotype_likelihoods_of(s) != [None] * 5
def test_empty_format_field(): with TemporaryDirectory() as tempdir: outvcf = tempdir + '/output_empty_format.vcf' run_genotype(phase_input_files=[trio_bamfile], variant_file='tests/data/empty_format.vcf', output=outvcf, gt_qual_threshold=0) # check if sample fields now contain information assert os.path.isfile(outvcf) vcf_reader = vcf.Reader(filename=outvcf) for record in vcf_reader: print(record.samples, outvcf) assert(len(record.samples) == 3)
def test_phase_trio_paired_end_reads(): with TemporaryDirectory() as tempdir: outvcf = tempdir + '/output-paired_end.vcf' run_genotype(phase_input_files=[trio_paired_end_bamfile], variant_file='tests/data/paired_end.sorted.vcf', output=outvcf, ped='tests/data/trio_paired_end.ped', genmap='tests/data/trio.map') assert os.path.isfile(outvcf) tables = list(VcfReader(outvcf, phases=True)) assert len(tables) == 1 table = tables[0] assert table.chromosome == '1' assert len(table.variants) == 3 assert table.samples == ['mother', 'father', 'child']
def test_genotyping_trio(): with TemporaryDirectory() as tempdir: outvcf = tempdir + '/output.vcf' outpriors = tempdir + 'priors.vcf' run_genotype(phase_input_files=[trio_bamfile], variant_file='tests/data/trio.vcf', output=outvcf, ped='tests/data/trio.ped', genmap='tests/data/trio.map', prioroutput=outpriors) for outfile in [outvcf,outpriors]: assert os.path.isfile(outfile) tables = list(VcfReader(outfile, phases=True)) assert len(tables) == 1 table = tables[0] assert table.chromosome == '1' assert len(table.variants) == 5 assert table.samples == ['HG004', 'HG003', 'HG002']
def test_use_ped_samples():
with TemporaryDirectory() as tempdir:
outvcf = tempdir + '/output_ped_samples.vcf'
run_genotype(phase_input_files=[ped_samples_bamfile], variant_file='tests/data/ped_samples.vcf', output=outvcf,
ped='tests/data/trio.ped', genmap='tests/data/trio.map', use_ped_samples=True)
assert os.path.isfile(outvcf)
tables = list(VcfReader(outvcf, phases=True, genotype_likelihoods=True))
assert len(tables) == 1
table = tables[0]
assert table.chromosome == '1'
assert len(table.variants) == 5
assert table.samples == ['HG004', 'HG003', 'HG002', 'orphan']
default_l = math.log10(1/3.0)
for var in table.genotype_likelihoods_of('orphan'):
assert(var.log10_probs() == (default_l, default_l, default_l))
def test_adding_constant():
for const in [0.1,0.2,0.3,0.5,0.7,1,2,5,10,20,100]:
with TemporaryDirectory() as tempdir:
priors_raw_vcf = tempdir + '/output.raw_priors.vcf'
outvcf_raw_vcf = tempdir + '/output_raw.vcf'
priors_const_vcf = tempdir + '/output.const_priors.vcf'
outvcf_const_vcf = tempdir + '/output_raw.vcf'
# run genotyping without adding constant to priors
run_genotype(phase_input_files=[trio_bamfile], variant_file='tests/data/trio.vcf',
prioroutput=priors_raw_vcf, output=outvcf_raw_vcf, indels=False)
# run genotyping with modified priors
run_genotype(phase_input_files=[trio_bamfile], variant_file='tests/data/trio.vcf',
prioroutput=priors_const_vcf, output=outvcf_const_vcf, indels=False, constant=const)
# check if priors were modified properly
priors_raw = open(priors_raw_vcf, 'r')
priors_const = open(priors_const_vcf, 'r')
priors_raw.seek(0)
priors_const.seek(0)
lines_raw = [line for line in priors_raw.readlines() if not line.startswith('#')]
lines_const = [line for line in priors_const.readlines() if not line.startswith('#')]
assert(len(lines_raw) == len(lines_const))
for i in range(len(lines_raw)):
likelihoods_raw = extract_likelihoods(lines_raw[i])
likelihoods_const = extract_likelihoods(lines_const[i])
norm_sum = likelihoods_raw[0]+likelihoods_raw[1]+likelihoods_raw[2] + 3.0*const
#print('raw likelihoods: ', likelihoods_raw, ' modified likelihoods: ', likelihoods_const)
print(float(likelihoods_const[0]),float((likelihoods_raw[0] + const)/norm_sum))
print(float(likelihoods_const[1]),float((likelihoods_raw[1] + const)/norm_sum))
print(float(likelihoods_const[2]),float((likelihoods_raw[2] + const)/norm_sum))
for j in range(3):
assert(round(likelihoods_const[j],10) == round((likelihoods_raw[j] + const)/norm_sum,10))
priors_raw.close()
priors_const.close()
def test_genotyping_one_of_three_individuals():
with TemporaryDirectory() as tempdir:
outvcf = tempdir + '/output.vcf'
outpriors = tempdir + '/priors.vcf'
run_genotype(phase_input_files=[trio_bamfile], variant_file='tests/data/trio.vcf', output=outvcf, samples=['HG003'],
prioroutput=outpriors)
for outfile in [outvcf, outpriors]:
assert os.path.isfile(outfile)
tables = list(VcfReader(outfile, phases=True,genotype_likelihoods=True))
assert len(tables) == 1
table = tables[0]
assert table.chromosome == '1'
assert len(table.variants) == 5
assert table.samples == ['HG004', 'HG003', 'HG002']
# there should be no genotype predicitons for HG003/HG002
default_l = math.log10(1/3.0)
for l in [table.genotype_likelihoods_of('HG002'), table.genotype_likelihoods_of('HG004')]:
for var in l:
assert(var.log10_probs() == (default_l, default_l, default_l))
def test_no_indels():
with TemporaryDirectory() as tempdir:
for priors in [[False, tempdir+'/priors.vcf'], [True,None]]:
outvcf = tempdir + '/output_gl.vcf'
run_genotype(phase_input_files=['tests/data/pacbio/pacbio.bam'], variant_file='tests/data/pacbio/variants.vcf',
reference='tests/data/pacbio/reference.fasta', output=outvcf, indels=False, nopriors=priors[0], prioroutput=priors[1])
result_vcfs = [outvcf]
if priors[0]:
result_vcfs.append(tempdir + '/priors.vcf')
# make sure indels not genotyped (also in priors.vcf if computed)
for o_vcf in result_vcfs:
vcf_reader = vcf.Reader(filename=o_vcf)
default_l = math.log10(1/3.0)
for record in vcf_reader:
if len(record.ALT[0]) > 1:
for call in record.samples:
GL = getattr(call.data, 'GL', None)
print('GL:', GL, record.POS)
assert(GL == [default_l, default_l, default_l])
def test_ped_sample(): with TemporaryDirectory() as tempdir: # running with --ped and --sample on subset of trio, should give same results as running with only --sample # the trio information should be ignored outvcf1 = tempdir + '/output1.vcf' outvcf2 = tempdir + '/output2.vcf' for sample_set in [['HG002'], ['HG003'], ['HG004'], ['HG002','HG003'], ['HG002','HG004'], ['HG003','HG004']]: run_genotype(phase_input_files=[ped_samples_bamfile], variant_file='tests/data/ped_samples.vcf', output=outvcf1, ped='tests/data/trio.ped', samples=sample_set) run_genotype(phase_input_files=[ped_samples_bamfile], variant_file='tests/data/ped_samples.vcf', output=outvcf2, samples=sample_set) assert os.path.isfile(outvcf1) assert os.path.isfile(outvcf2) tables1 = list(VcfReader(outvcf1, phases=True, genotype_likelihoods=True)) tables2 = list(VcfReader(outvcf2, phases=True, genotype_likelihoods=True)) assert( (len(tables1) == 1) and (len(tables2) == 1) ) table1, table2 = tables1[0], tables2[0] for individual in sample_set: for var1,var2 in zip(table1.genotype_likelihoods_of(individual), table2.genotype_likelihoods_of(individual)): print(var1, var2) assert(var1.log10_probs() == var2.log10_probs())
def test_genotype_likelihoods_given():
with TemporaryDirectory() as tempdir:
outvcf = tempdir + '/output_gl.vcf'
run_genotype(phase_input_files=[trio_bamfile], variant_file='tests/data/trio_genotype_likelihoods.vcf', output=outvcf,
ped='tests/data/trio.ped', genmap='tests/data/trio.map')
assert os.path.isfile(outvcf)
tables = list(VcfReader(outvcf, phases=True, genotype_likelihoods=True))
assert len(tables) == 1
table = tables[0]
assert table.chromosome == '1'
assert len(table.variants) == 5
assert table.samples == ['HG004', 'HG003', 'HG002']
# check if PL likelihoods (that were present before) are deleted
vcf_reader = vcf.Reader(filename=outvcf)
print(vcf_reader.samples, outvcf)
for record in vcf_reader:
for call in record.samples:
PL = getattr(call.data, 'PL', None)
GL = getattr(call.data, 'GL', None)
print('GL:', GL, 'PL:', PL)
assert(PL==None)
assert(GL != None)
def test_with_reference(): run_genotype(phase_input_files=['tests/data/pacbio/pacbio.bam'], variant_file='tests/data/pacbio/variants.vcf', reference='tests/data/pacbio/reference.fasta')
def test_requested_sample_not_found(): with raises(SystemExit): run_genotype(phase_input_files=['tests/data/oneread.bam'], variant_file='tests/data/onevariant.vcf', output='/dev/null', samples=['DOES_NOT_EXIST'])
def test_bam_without_readgroup(): run_genotype(phase_input_files=['tests/data/no-readgroup.bam'], variant_file='tests/data/onevariant.vcf', output='/dev/null', ignore_read_groups=True)
def test_default_output(): """Output to stdout""" run_genotype(phase_input_files=['tests/data/oneread.bam'], variant_file='tests/data/onevariant.vcf')
def test_one_variant(): run_genotype(phase_input_files=['tests/data/oneread.bam'], variant_file='tests/data/onevariant.vcf', output='/dev/null')
