def test_info():
a = info('fixture/sample.vcf', arities={'AC': 2})
print repr(a)
eq_(3, a[2]['NS'])
eq_(.5, a[2]['AF'])
eq_(True, a[2]['DB'])
eq_((3, 1), tuple(a[6]['AC']))
def test_condition():
v = variants('fixture/sample.vcf')
eq_(9, len(v))
c = calldata('fixture/sample.vcf', condition=v['FILTER']['PASS'])
eq_(5, len(c))
i = info('fixture/sample.vcf', condition=v['FILTER']['PASS'])
eq_(5, len(i))
vf = variants('fixture/sample.vcf', condition=v['FILTER']['PASS'])
eq_(5, len(vf))
def build_arrays(vcf_fn, region, samples=None, force=False):
variants_array_fn = vcf_fn + '.' + region.replace('-:', '_') + '.variants.npy'
if force or not os.path.exists(variants_array_fn):
print >>sys.stderr, 'building', variants_array_fn
V = vcfnp.variants(vcf_fn, region=region, progress=20000)
np.save(variants_array_fn, V)
else:
print >>sys.stderr, 'skipping', variants_array_fn
info_array_fn = vcf_fn + '.' + region.replace('-:', '_') + '.info.npy'
if force or not os.path.exists(info_array_fn):
print >>sys.stderr, 'building', info_array_fn
I = vcfnp.info(vcf_fn, region=region, progress=20000, fields=['NS', 'UQ', 'CODING', 'DP', 'AD'], vcf_types={'DP': 'Integer', 'AD': 'Integer'}, arities={'AD': 2})
np.save(info_array_fn, I)
else:
print >>sys.stderr, 'skipping', info_array_fn
def profile():
a = vcfnp.info(sys.argv[1], count=int(sys.argv[2]))
def profile():
a = vcfnp.info(sys.argv[1], count=int(sys.argv[2]))
