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))
vf = variants('fixture/sample.vcf', condition=v['FILTER']['PASS'])
eq_(5, len(vf))
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))
vf = variants('fixture/sample.vcf', condition=v['FILTER']['PASS'])
eq_(5, len(vf))
def test_override_vcf_types():
v = variants('fixture/test4.vcf')
eq_(0, v['MQ0FractionTest'][2])
v = variants('fixture/test4.vcf', vcf_types={'MQ0FractionTest': 'Float'})
assert_almost_equal(
0.03,
v['MQ0FractionTest'][2],
)
def test_missing_info_definition():
# INFO field DP not declared in VCF header
v = variants('fixture/test14.vcf', fields=['DP'])
eq_(b'14', v[2]['DP']) # default is string
v = variants('fixture/test14.vcf', fields=['DP'],
vcf_types={'DP': 'Integer'})
eq_(14, v[2]['DP'])
# what about a field which isn't present at all?
v = variants('fixture/test14.vcf', fields=['FOO'])
eq_(b'', v[2]['FOO']) # default missing value for string field
def test_missing_info_definition():
# INFO field DP not declared in VCF header
v = variants('fixture/test14.vcf', fields=['DP'])
eq_(b'14', v[2]['DP']) # default is string
v = variants('fixture/test14.vcf',
fields=['DP'],
vcf_types={'DP': 'Integer'})
eq_(14, v[2]['DP'])
# what about a field which isn't present at all?
v = variants('fixture/test14.vcf', fields=['FOO'])
eq_(b'', v[2]['FOO']) # default missing value for string field
def test_svlen():
v = variants('fixture/test13.vcf').view(np.recarray)
assert hasattr(v, 'svlen')
eq_(0, v.svlen[0])
eq_(1, v.svlen[1])
eq_(-1, v.svlen[2])
eq_(3, v.svlen[3])
eq_(3, v.svlen[4])
v = variants('fixture/test13.vcf', arities={'svlen': 2}).view(np.recarray)
assert hasattr(v, 'svlen')
eq_((3, 0), tuple(v.svlen[3]))
eq_((3, -2), tuple(v.svlen[4]))
def test_variants_transformers_eff():
def _test(v):
eq_(b'STOP_GAINED', v['EFF']['Effect'][0])
eq_(b'HIGH', v['EFF']['Effect_Impact'][0])
eq_(b'NONSENSE', v['EFF']['Functional_Class'][0])
eq_(b'Cag/Tag', v['EFF']['Codon_Change'][0])
eq_(b'Q236*', v['EFF']['Amino_Acid_Change'][0])
eq_(749, v['EFF']['Amino_Acid_Length'][0])
eq_(b'NOC2L', v['EFF']['Gene_Name'][0])
eq_(b'.', v['EFF']['Transcript_BioType'][0])
eq_(1, v['EFF']['Gene_Coding'][0])
eq_(b'NM_015658', v['EFF']['Transcript_ID'][0])
eq_(-1, v['EFF']['Exon'][0])
eq_(b'NON_SYNONYMOUS_CODING', v['EFF']['Effect'][1])
eq_(b'MODERATE', v['EFF']['Effect_Impact'][1])
eq_(b'MISSENSE', v['EFF']['Functional_Class'][1])
eq_(b'gTt/gGt', v['EFF']['Codon_Change'][1])
eq_(b'V155G', v['EFF']['Amino_Acid_Change'][1])
eq_(-1, v['EFF']['Amino_Acid_Length'][1])
eq_(b'PF3D7_0108900', v['EFF']['Gene_Name'][1])
eq_(b'.', v['EFF']['Transcript_BioType'][1])
eq_(-1, v['EFF']['Gene_Coding'][1])
eq_(b'rna_PF3D7_0108900-1', v['EFF']['Transcript_ID'][1])
eq_(1, v['EFF']['Exon'][1])
eq_(b'.', v['EFF']['Effect'][2])
eq_(b'.', v['EFF']['Effect_Impact'][2])
eq_(b'.', v['EFF']['Functional_Class'][2])
eq_(b'.', v['EFF']['Codon_Change'][2])
eq_(b'.', v['EFF']['Amino_Acid_Change'][2])
eq_(-1, v['EFF']['Amino_Acid_Length'][2])
eq_(b'.', v['EFF']['Gene_Name'][2])
eq_(b'.', v['EFF']['Transcript_BioType'][2])
eq_(-1, v['EFF']['Gene_Coding'][2])
eq_(b'.', v['EFF']['Transcript_ID'][2])
eq_(-1, v['EFF']['Exon'][2])
varr = variants('fixture/test12.vcf',
dtypes={'EFF': vcfnp.eff.EFF_DEFAULT_DTYPE},
arities={'EFF': 1},
transformers={'EFF': vcfnp.eff.eff_default_transformer()})
_test(varr)
# test EFF is included in defaults
varr = variants('fixture/test12.vcf')
_test(varr)
def test_variants_transformers_eff():
def _test(v):
eq_(b'STOP_GAINED', v['EFF']['Effect'][0])
eq_(b'HIGH', v['EFF']['Effect_Impact'][0])
eq_(b'NONSENSE', v['EFF']['Functional_Class'][0])
eq_(b'Cag/Tag', v['EFF']['Codon_Change'][0])
eq_(b'Q236*', v['EFF']['Amino_Acid_Change'][0])
eq_(749, v['EFF']['Amino_Acid_Length'][0])
eq_(b'NOC2L', v['EFF']['Gene_Name'][0])
eq_(b'.', v['EFF']['Transcript_BioType'][0])
eq_(1, v['EFF']['Gene_Coding'][0])
eq_(b'NM_015658', v['EFF']['Transcript_ID'][0])
eq_(-1, v['EFF']['Exon'][0])
eq_(b'NON_SYNONYMOUS_CODING', v['EFF']['Effect'][1])
eq_(b'MODERATE', v['EFF']['Effect_Impact'][1])
eq_(b'MISSENSE', v['EFF']['Functional_Class'][1])
eq_(b'gTt/gGt', v['EFF']['Codon_Change'][1])
eq_(b'V155G', v['EFF']['Amino_Acid_Change'][1])
eq_(-1, v['EFF']['Amino_Acid_Length'][1])
eq_(b'PF3D7_0108900', v['EFF']['Gene_Name'][1])
eq_(b'.', v['EFF']['Transcript_BioType'][1])
eq_(-1, v['EFF']['Gene_Coding'][1])
eq_(b'rna_PF3D7_0108900-1', v['EFF']['Transcript_ID'][1])
eq_(1, v['EFF']['Exon'][1])
eq_(b'.', v['EFF']['Effect'][2])
eq_(b'.', v['EFF']['Effect_Impact'][2])
eq_(b'.', v['EFF']['Functional_Class'][2])
eq_(b'.', v['EFF']['Codon_Change'][2])
eq_(b'.', v['EFF']['Amino_Acid_Change'][2])
eq_(-1, v['EFF']['Amino_Acid_Length'][2])
eq_(b'.', v['EFF']['Gene_Name'][2])
eq_(b'.', v['EFF']['Transcript_BioType'][2])
eq_(-1, v['EFF']['Gene_Coding'][2])
eq_(b'.', v['EFF']['Transcript_ID'][2])
eq_(-1, v['EFF']['Exon'][2])
varr = variants('fixture/test12.vcf',
dtypes={'EFF': vcfnp.eff.EFF_DEFAULT_DTYPE},
arities={'EFF': 1},
transformers={'EFF': vcfnp.eff.eff_default_transformer()})
_test(varr)
# test EFF is included in defaults
varr = variants('fixture/test12.vcf')
_test(varr)
def test_variants_flatten_filter():
a = variants('fixture/sample.vcf', flatten_filter=True)
debug(a)
debug(a.dtype)
eq_(True, a[2]['FILTER_PASS'])
eq_(False, a[3]['FILTER_PASS'])
eq_(True, a[3]['FILTER_q10'])
def test_caching_cachedir():
vcf_fn = 'fixture/sample.vcf.gz'
cachedir = 'fixture/custom.vcfnp_cache/foo'
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn,
array_type='variants',
cachedir=cachedir)
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = variants(vcf_fn, cache=True, verbose=True, cachedir=cachedir)
a2 = np.load(cache_fn)
assert np.all(a == a2)
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn,
array_type='calldata',
cachedir=cachedir)
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = calldata(vcf_fn, cache=True, verbose=True, cachedir=cachedir)
a2 = np.load(cache_fn)
assert np.all(a == a2)
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn,
array_type='calldata_2d',
cachedir=cachedir)
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = calldata_2d(vcf_fn, cache=True, verbose=True, cachedir=cachedir)
a2 = np.load(cache_fn)
assert np.all(a == a2)
def test_caching_cachedir():
vcf_fn = 'fixture/sample.vcf.gz'
cachedir = 'fixture/custom.vcfnp_cache/foo'
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn, array_type='variants',
cachedir=cachedir)
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = variants(vcf_fn, cache=True, verbose=True, cachedir=cachedir)
a2 = np.load(cache_fn)
assert_array_equal(a, a2)
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn, array_type='calldata',
cachedir=cachedir)
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = calldata(vcf_fn, cache=True, verbose=True, cachedir=cachedir)
a2 = np.load(cache_fn)
assert_array_equal(a, a2)
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn, array_type='calldata_2d',
cachedir=cachedir)
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = calldata_2d(vcf_fn, cache=True, verbose=True, cachedir=cachedir)
a2 = np.load(cache_fn)
assert_array_equal(a, a2)
def test_variants_flatten_filter():
a = variants('fixture/sample.vcf', flatten_filter=True)
debug(a)
debug(a.dtype)
eq_(True, a[2]['FILTER_PASS'])
eq_(False, a[3]['FILTER_PASS'])
eq_(True, a[3]['FILTER_q10'])
def test_caching():
vcf_fn = 'fixture/sample.vcf.gz'
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn, array_type='variants')
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = variants(vcf_fn, cache=True, verbose=True)
a2 = np.load(cache_fn)
assert np.all(a == a2)
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn, array_type='calldata')
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = calldata(vcf_fn, cache=True, verbose=True)
a2 = np.load(cache_fn)
assert np.all(a == a2)
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn, array_type='calldata_2d')
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = calldata_2d(vcf_fn, cache=True, verbose=True)
a2 = np.load(cache_fn)
assert np.all(a == a2)
def test_caching_compression():
vcf_fn = 'fixture/sample.vcf.gz'
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn, array_type='variants',
compress=True)
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = variants(vcf_fn, cache=True, compress_cache=True, verbose=True)
a2 = np.load(cache_fn)['data']
assert_array_equal(a, a2)
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn, array_type='calldata',
compress=True)
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = calldata(vcf_fn, cache=True, compress_cache=True, verbose=True)
a2 = np.load(cache_fn)['data']
assert_array_equal(a, a2)
cache_fn = vcfnp.array._mk_cache_fn(vcf_fn, array_type='calldata_2d',
compress=True)
debug(cache_fn)
if os.path.exists(cache_fn):
os.remove(cache_fn)
a = calldata_2d(vcf_fn, cache=True, compress_cache=True, verbose=True)
a2 = np.load(cache_fn)['data']
assert_array_equal(a, a2)
def test_svlen():
# v = variants('fixture/test13.vcf').view(np.recarray)
# assert hasattr(v, 'svlen')
# eq_(0, v.svlen[0])
# eq_(1, v.svlen[1])
# eq_(-1, v.svlen[2])
# eq_(3, v.svlen[3])
# eq_(3, v.svlen[4])
v = variants('fixture/test13.vcf', arities={'svlen': 2}).view(np.recarray)
def test_svlen():
# v = variants('fixture/test13.vcf').view(np.recarray)
# assert hasattr(v, 'svlen')
# eq_(0, v.svlen[0])
# eq_(1, v.svlen[1])
# eq_(-1, v.svlen[2])
# eq_(3, v.svlen[3])
# eq_(3, v.svlen[4])
v = variants('fixture/test13.vcf', arities={'svlen': 2}).view(np.recarray)
def test_truncate():
# https://github.com/alimanfoo/vcfnp/issues/54
vcf_fn = 'fixture/test54.vcf.gz'
# truncate by default
v = variants(vcf_fn, region='chr1:10-100')
eq_(2, len(v))
c = calldata(vcf_fn, region='chr1:10-100')
eq_(2, len(c))
c2d = calldata_2d(vcf_fn, region='chr1:10-100')
eq_(2, len(c2d))
# don't truncate
v = variants(vcf_fn, region='chr1:10-100', truncate=False)
eq_(3, len(v))
c = calldata(vcf_fn, region='chr1:10-100', truncate=False)
eq_(3, len(c))
c2d = calldata_2d(vcf_fn, region='chr1:10-100', truncate=False)
eq_(3, len(c2d))
def test_truncate():
# https://github.com/alimanfoo/vcfnp/issues/54
vcf_fn = 'fixture/test54.vcf.gz'
# truncate by default
v = variants(vcf_fn, region='chr1:10-100')
eq_(2, len(v))
c = calldata(vcf_fn, region='chr1:10-100')
eq_(2, len(c))
c2d = calldata_2d(vcf_fn, region='chr1:10-100')
eq_(2, len(c2d))
# don't truncate
v = variants(vcf_fn, region='chr1:10-100', truncate=False)
eq_(3, len(v))
c = calldata(vcf_fn, region='chr1:10-100', truncate=False)
eq_(3, len(c))
c2d = calldata_2d(vcf_fn, region='chr1:10-100', truncate=False)
eq_(3, len(c2d))
def test_variants():
a = variants('fixture/sample.vcf', arities={'ALT': 2, 'AC': 2})
debug(repr(a))
eq_(9, len(a))
eq_(b'19', a[0]['CHROM'])
eq_(111, a[0]['POS'])
eq_(b'rs6054257', a[2]['ID'])
eq_(b'A', a[0]['REF'])
eq_(b'ATG', a[8]['ALT'][1])
eq_(10.0, a[1]['QUAL'])
eq_(True, a[2]['FILTER']['PASS'])
eq_(False, a[3]['FILTER']['PASS'])
eq_(True, a[3]['FILTER']['q10'])
eq_(2, a[0]['num_alleles'])
eq_(False, a[5]['is_snp'])
# INFO fields
eq_(3, a[2]['NS'])
eq_(.5, a[2]['AF'])
eq_(True, a[2]['DB'])
eq_((3, 1), tuple(a[6]['AC']))
def test_variants():
a = variants('fixture/sample.vcf', arities={'ALT': 2, 'AC': 2})
debug(repr(a))
eq_(9, len(a))
eq_(b'19', a[0]['CHROM'])
eq_(111, a[0]['POS'])
eq_(b'rs6054257', a[2]['ID'])
eq_(b'A', a[0]['REF'])
eq_(b'ATG', a[8]['ALT'][1])
eq_(10.0, a[1]['QUAL'])
eq_(True, a[2]['FILTER']['PASS'])
eq_(False, a[3]['FILTER']['PASS'])
eq_(True, a[3]['FILTER']['q10'])
eq_(2, a[0]['num_alleles'])
eq_(False, a[5]['is_snp'])
# INFO fields
eq_(3, a[2]['NS'])
eq_(.5, a[2]['AF'])
eq_(True, a[2]['DB'])
eq_((3, 1), tuple(a[6]['AC']))
def test_variants_region_empty():
a = variants('fixture/sample.vcf.gz', region='18')
eq_(0, len(a))
a = variants('fixture/sample.vcf.gz', region='19:113-200')
eq_(0, len(a))
def test_variants_transformers_ann():
def _test(v):
eq_(b'T', v['ANN']['Allele'][0])
eq_(b'intergenic_region', v['ANN']['Annotation'][0])
eq_(b'MODIFIER', v['ANN']['Annotation_Impact'][0])
eq_(b'AGAP004677', v['ANN']['Gene_Name'][0])
eq_(b'AGAP004677', v['ANN']['Gene_ID'][0])
eq_(b'intergenic_region', v['ANN']['Feature_Type'][0])
eq_(b'AGAP004677', v['ANN']['Feature_ID'][0])
eq_(b'.', v['ANN']['Transcript_BioType'][0])
eq_(-1, v['ANN']['Rank'][0])
eq_(b'.', v['ANN']['HGVS_c'][0])
eq_(b'.', v['ANN']['HGVS_p'][0])
eq_(-1, v['ANN']['cDNA_pos'][0])
eq_(-1, v['ANN']['cDNA_length'][0])
eq_(-1, v['ANN']['CDS_pos'][0])
eq_(-1, v['ANN']['CDS_length'][0])
eq_(-1, v['ANN']['AA_pos'][0])
eq_(-1, v['ANN']['AA_length'][0])
eq_(-1, v['ANN']['Distance'][0])
eq_(b'.', v['ANN']['Allele'][1])
eq_(b'.', v['ANN']['Annotation'][1])
eq_(b'.', v['ANN']['Annotation_Impact'][1])
eq_(b'.', v['ANN']['Gene_Name'][1])
eq_(b'.', v['ANN']['Gene_ID'][1])
eq_(b'.', v['ANN']['Feature_Type'][1])
eq_(b'.', v['ANN']['Feature_ID'][1])
eq_(b'.', v['ANN']['Transcript_BioType'][1])
eq_(-1, v['ANN']['Rank'][1])
eq_(b'.', v['ANN']['HGVS_c'][1])
eq_(b'.', v['ANN']['HGVS_p'][1])
eq_(-1, v['ANN']['cDNA_pos'][1])
eq_(-1, v['ANN']['cDNA_length'][1])
eq_(-1, v['ANN']['CDS_pos'][1])
eq_(-1, v['ANN']['CDS_length'][1])
eq_(-1, v['ANN']['AA_pos'][1])
eq_(-1, v['ANN']['AA_length'][1])
eq_(-1, v['ANN']['Distance'][1])
eq_(b'T', v['ANN']['Allele'][2])
eq_(b'missense_variant', v['ANN']['Annotation'][2])
eq_(b'MODERATE', v['ANN']['Annotation_Impact'][2])
eq_(b'AGAP005273', v['ANN']['Gene_Name'][2])
eq_(b'AGAP005273', v['ANN']['Gene_ID'][2])
eq_(b'transcript', v['ANN']['Feature_Type'][2])
eq_(b'AGAP005273-RA', v['ANN']['Feature_ID'][2])
eq_(b'VectorBase', v['ANN']['Transcript_BioType'][2])
eq_(1, v['ANN']['Rank'][2])
eq_(b'n.17A>T', v['ANN']['HGVS_c'][2])
eq_(b'p.Asp6Val', v['ANN']['HGVS_p'][2])
eq_(17, v['ANN']['cDNA_pos'][2])
eq_(4788, v['ANN']['cDNA_length'][2])
eq_(17, v['ANN']['CDS_pos'][2])
eq_(-1, v['ANN']['CDS_length'][2])
eq_(6, v['ANN']['AA_pos'][2])
eq_(-1, v['ANN']['AA_length'][2])
eq_(-1, v['ANN']['Distance'][2])
varr = variants('fixture/test_ann.vcf',
dtypes={'ANN': vcfnp.eff.ANN_DEFAULT_DTYPE},
arities={'ANN': 1},
transformers={'ANN': vcfnp.eff.ann_default_transformer()})
_test(varr)
# test ANN is included in defaults
varr = variants('fixture/test_ann.vcf')
_test(varr)
def test_explicit_pass_definition():
# explicit PASS FILTER definition
variants('fixture/test16.vcf')
def test_duplicate_field_definitions():
variants('fixture/test10.vcf')
# should not raise, but print useful message to stderr
calldata('fixture/test10.vcf')
def test_duplicate_field_definitions():
variants('fixture/test10.vcf')
# should not raise, but print useful message to stderr
calldata('fixture/test10.vcf')
def test_explicit_pass_definition():
# explicit PASS FILTER definition
variants('fixture/test16.vcf')
def test_variants_transformers_ann():
def _test(v):
eq_(b'T', v['ANN']['Allele'][0])
eq_(b'intergenic_region', v['ANN']['Annotation'][0])
eq_(b'MODIFIER', v['ANN']['Annotation_Impact'][0])
eq_(b'AGAP004677', v['ANN']['Gene_Name'][0])
eq_(b'AGAP004677', v['ANN']['Gene_ID'][0])
eq_(b'intergenic_region', v['ANN']['Feature_Type'][0])
eq_(b'AGAP004677', v['ANN']['Feature_ID'][0])
eq_(b'.', v['ANN']['Transcript_BioType'][0])
eq_(-1, v['ANN']['Rank'][0])
eq_(b'.', v['ANN']['HGVS_c'][0])
eq_(b'.', v['ANN']['HGVS_p'][0])
eq_(-1, v['ANN']['cDNA_pos'][0])
eq_(-1, v['ANN']['cDNA_length'][0])
eq_(-1, v['ANN']['CDS_pos'][0])
eq_(-1, v['ANN']['CDS_length'][0])
eq_(-1, v['ANN']['AA_pos'][0])
eq_(-1, v['ANN']['AA_length'][0])
eq_(-1, v['ANN']['Distance'][0])
eq_(b'.', v['ANN']['Allele'][1])
eq_(b'.', v['ANN']['Annotation'][1])
eq_(b'.', v['ANN']['Annotation_Impact'][1])
eq_(b'.', v['ANN']['Gene_Name'][1])
eq_(b'.', v['ANN']['Gene_ID'][1])
eq_(b'.', v['ANN']['Feature_Type'][1])
eq_(b'.', v['ANN']['Feature_ID'][1])
eq_(b'.', v['ANN']['Transcript_BioType'][1])
eq_(-1, v['ANN']['Rank'][1])
eq_(b'.', v['ANN']['HGVS_c'][1])
eq_(b'.', v['ANN']['HGVS_p'][1])
eq_(-1, v['ANN']['cDNA_pos'][1])
eq_(-1, v['ANN']['cDNA_length'][1])
eq_(-1, v['ANN']['CDS_pos'][1])
eq_(-1, v['ANN']['CDS_length'][1])
eq_(-1, v['ANN']['AA_pos'][1])
eq_(-1, v['ANN']['AA_length'][1])
eq_(-1, v['ANN']['Distance'][1])
eq_(b'T', v['ANN']['Allele'][2])
eq_(b'missense_variant', v['ANN']['Annotation'][2])
eq_(b'MODERATE', v['ANN']['Annotation_Impact'][2])
eq_(b'AGAP005273', v['ANN']['Gene_Name'][2])
eq_(b'AGAP005273', v['ANN']['Gene_ID'][2])
eq_(b'transcript', v['ANN']['Feature_Type'][2])
eq_(b'AGAP005273-RA', v['ANN']['Feature_ID'][2])
eq_(b'VectorBase', v['ANN']['Transcript_BioType'][2])
eq_(1, v['ANN']['Rank'][2])
eq_(b'n.17A>T', v['ANN']['HGVS_c'][2])
eq_(b'p.Asp6Val', v['ANN']['HGVS_p'][2])
eq_(17, v['ANN']['cDNA_pos'][2])
eq_(4788, v['ANN']['cDNA_length'][2])
eq_(17, v['ANN']['CDS_pos'][2])
eq_(-1, v['ANN']['CDS_length'][2])
eq_(6, v['ANN']['AA_pos'][2])
eq_(-1, v['ANN']['AA_length'][2])
eq_(-1, v['ANN']['Distance'][2])
varr = variants('fixture/test_ann.vcf',
dtypes={'ANN': vcfnp.eff.ANN_DEFAULT_DTYPE},
arities={'ANN': 1},
transformers={'ANN': vcfnp.eff.ann_default_transformer()})
_test(varr)
# test ANN is included in defaults
varr = variants('fixture/test_ann.vcf')
_test(varr)
def test_override_vcf_types():
v = variants('fixture/test4.vcf')
eq_(0, v['MQ0FractionTest'][2])
v = variants('fixture/test4.vcf', vcf_types={'MQ0FractionTest': 'Float'})
assert_almost_equal(0.03, v['MQ0FractionTest'][2], )
def test_variants_region():
a = variants('fixture/sample.vcf.gz', region='20')
eq_(6, len(a))
def test_variants_exclude_fields():
a = variants('fixture/sample.vcf', exclude_fields=['ID', 'FILTER'])
assert 'CHROM' in a.dtype.names
assert 'ID' not in a.dtype.names
assert 'FILTER' not in a.dtype.names
def test_variants_region_empty():
a = variants('fixture/sample.vcf.gz', region='18')
eq_(0, len(a))
a = variants('fixture/sample.vcf.gz', region='19:113-200')
eq_(0, len(a))
def test_variants_region():
a = variants('fixture/sample.vcf.gz', region='20')
eq_(6, len(a))
def test_variants_count():
a = variants('fixture/sample.vcf', count=3)
eq_(3, len(a))
def test_variants_count():
a = variants('fixture/sample.vcf', count=3)
eq_(3, len(a))
def test_variants_exclude_fields():
a = variants('fixture/sample.vcf', exclude_fields=['ID', 'FILTER'])
assert 'CHROM' in a.dtype.names
assert 'ID' not in a.dtype.names
assert 'FILTER' not in a.dtype.names
def test_variants_slice():
a = variants('fixture/sample.vcf.gz')
eq_(b'rs6054257', a['ID'][2])
a = variants('fixture/sample.vcf.gz', slice_args=(0, None, 2))
eq_(b'rs6054257', a['ID'][1])
def test_variants_slice():
a = variants('fixture/sample.vcf.gz')
eq_(b'rs6054257', a['ID'][2])
a = variants('fixture/sample.vcf.gz', slice_args=(0, None, 2))
eq_(b'rs6054257', a['ID'][1])