def test_fromvcfinfo_override_fields():
# default array
a = vcfarray.fromvcfinfo('fixture/example-4.1.vcf', fields=['CHROM', 'POS', 'DP']).view(np.recarray)
eq_('20', a.CHROM[0])
eq_(14370, a.POS[0])
eq_(14, a.DP[0])
for f in ('ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'NS', 'AF', 'DB', 'H2'):
assert not hasattr(a, f), 'unexpected attribute on array: %s' % f
def test_fromvcfinfo_override_fields():
# default array
a = vcfarray.fromvcfinfo('fixture/example-4.1.vcf',
fields=['CHROM', 'POS', 'DP']).view(np.recarray)
eq_('20', a.CHROM[0])
eq_(14370, a.POS[0])
eq_(14, a.DP[0])
for f in ('ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'NS', 'AF', 'DB', 'H2'):
assert not hasattr(a, f), 'unexpected attribute on array: %s' % f
def test_fromvcfinfo_default():
# default array
a = vcfarray.fromvcfinfo('fixture/example-4.1.vcf').view(np.recarray)
# check fixed fields
eq_('20', a.CHROM[0])
eq_(14370, a.POS[0])
eq_('rs6054257', a.ID[0])
eq_('G', a.REF[0])
eq_('A', a.ALT[0])
eq_(29, a.QUAL[0])
# check FILTER field
eq_(True, a.FILTER.PASS[0])
eq_(False, a.FILTER.PASS[1])
eq_(False, a.FILTER.q10[0])
eq_(True, a.FILTER.q10[1])
# check other attributes
eq_(True, a.is_snp[0])
eq_(False, a.is_indel[0])
eq_(False, a.is_deletion[0])
eq_(True, a.is_transition[0])
eq_(3, a.num_called[0])
eq_(0, a.num_unknown[0])
eq_(1., a.call_rate[0])
# check special attributes
eq_(2, a.num_alleles[0])
eq_(3, a.num_alleles[2])
# check INFO fields
eq_(3, a.NS[0])
eq_(14, a.DP[0])
eq_(.5, a.AF[0])
eq_(True, a.DB[0])
eq_(True, a.H2[0])
def test_fromvcfinfo_default():
# default array
a = vcfarray.fromvcfinfo('fixture/example-4.1.vcf').view(np.recarray)
# check fixed fields
eq_('20', a.CHROM[0])
eq_(14370, a.POS[0])
eq_('rs6054257', a.ID[0])
eq_('G', a.REF[0])
eq_('A', a.ALT[0])
eq_(29, a.QUAL[0])
# check FILTER field
eq_(True, a.FILTER.PASS[0])
eq_(False, a.FILTER.PASS[1])
eq_(False, a.FILTER.q10[0])
eq_(True, a.FILTER.q10[1])
# check other attributes
eq_(True, a.is_snp[0])
eq_(False, a.is_indel[0])
eq_(False, a.is_deletion[0])
eq_(True, a.is_transition[0])
eq_(3, a.num_called[0])
eq_(0, a.num_unknown[0])
eq_(1., a.call_rate[0])
# check special attributes
eq_(2, a.num_alleles[0])
eq_(3, a.num_alleles[2])
# check INFO fields
eq_(3, a.NS[0])
eq_(14, a.DP[0])
eq_(.5, a.AF[0])
eq_(True, a.DB[0])
eq_(True, a.H2[0])
def profile():
a = vcfarray.fromvcfinfo(sys.argv[1])
