def setUpClass(cls):
cls.project = create_project_with_name('my project')
cls.chr_run = create_run_with_uri(cls.project['id'], '/tests/data/diverse.vcf')
_extract(cls.chr_run['id'])
cls.no_chr_run = create_run_with_uri(cls.project['id'], '/tests/data/diverse.nochr.vcf')
_extract(cls.no_chr_run['id'])
return super(TestGenotypesAPI, cls).setUpClass()
def setUpClass(cls):
cls.project = create_project_with_name('Downloadable project')
cls.run = create_run_with_uri(cls.project['id'],
'/tests/data/somatic_hg19_14muts.vcf')
_extract(cls.run['id'])
return super(TestDownload, cls).setUpClass()
def setUpClass(cls):
cls.project = create_project_with_name('my project')
cls.chr_run = create_run_with_uri(cls.project['id'], '/tests/data/diverse.vcf')
_extract(cls.chr_run['id'])
cls.no_chr_run = create_run_with_uri(cls.project['id'], '/tests/data/diverse.nochr.vcf')
_extract(cls.no_chr_run['id'])
def test_extraction(self):
_extract(self.run['id'])
with tables(db.engine, 'vcfs', 'genotypes') as (con, vcfs, genotypes):
vcf = vcfs.select(vcfs.c.id == self.run['id']).execute().fetchone()
variants = genotypes.select(
genotypes.c.vcf_id == self.run['id']).execute().fetchall()
variants = [dict(v) for v in variants]
expected_extant_columns = set(["sample:GT", "sample:RD", "sample:FREQ",
"info:SSC", "sample:DP", "sample:DP4",
"info:DP", "info:SS", "info:GPV", "sample:AD",
"info:SPV"])
extant_columns = set(ast.literal_eval(vcf['extant_columns']))
asserts.eq_(extant_columns, expected_extant_columns)
# 10 variants x 2 for the two samples in this file, NORMAL & TUMOR
asserts.eq_(vcf['genotype_count'], 20)
asserts.eq_(vcf['genotype_count'], len(variants))
with open('tests/data/snv.vcf', 'r') as vcffile:
vcflines = vcffile.readlines()
expected_vcf_header = ''.join([l for l in vcflines
if l.startswith('#')])
asserts.eq_(vcf['vcf_header']+'\n', unicode(expected_vcf_header))
with open('tests/data/snv.vcf') as vcffile:
vcfreader = pyvcf.Reader(vcffile)
expected_pyvcf_variants = [r for r in vcfreader]
# Make sure we have the same (chromosome, position, ref, alt) variants
assert_keys_in_variants(expected_pyvcf_variants, variants)
# Make sure we've got the INFO fields we expect
pyvcf_getters = [lambda v: v.INFO['DP'],
lambda v: v.INFO['SS'],
lambda v: v.INFO['SSC'],
lambda v: v.INFO['GPV'],
lambda v: v.INFO['SPV']]
db_variant_getters = [lambda v: int(v['info:DP']),
lambda v: v['info:SS'],
lambda v: v['info:SSC'],
lambda v: float(v['info:GPV']),
lambda v: float(v['info:SPV'])]
assert_keys_in_variants(expected_pyvcf_variants, variants,
expected_getters=pyvcf_getters,
actual_getters=db_variant_getters)
# Make sure we've got the samples we expect (namely, TUMOR & NORMAL)
asserts.eq_(set(vcfreader.samples),
set([v['sample_name'] for v in variants]))
# Make sure all the NORMAL & TUMOR samples have the same fields with the same values
def ensure_samples_equivalent(sample_name):
def get_sample_data(attr):
def get_from_variant(variant):
sample = find(variant.samples, lambda x: x.sample == sample_name)
return getattr(sample.data, attr)
return get_from_variant
pyvcf_getters = [get_sample_data('GT'),
get_sample_data('GQ'),
get_sample_data('DP'),
get_sample_data('RD'),
get_sample_data('AD'),
get_sample_data('FREQ'),
lambda v: tuple(get_sample_data('DP4')(v))]
db_variant_getters = [lambda v: v['sample:GT'],
# GQ is actually None on all variants in snv.vcf
lambda v: int(v['sample:GQ']) if v['sample:GQ'] else None,
lambda v: int(v['sample:DP']),
lambda v: int(v['sample:RD']),
lambda v: int(v['sample:AD']),
lambda v: v['sample:FREQ'],
lambda v: tuple(ast.literal_eval(v['sample:DP4']))]
actual_db_variants = [v for v in variants
if v['sample_name'] == sample_name]
assert_keys_in_variants(expected_pyvcf_variants, actual_db_variants,
expected_getters=pyvcf_getters,
actual_getters=db_variant_getters)
ensure_samples_equivalent('NORMAL')
ensure_samples_equivalent('TUMOR')
