def test_open_individual(self):
''' test that open_individual() works correctly
'''
# missing individual returns empty list
self.assertEqual(open_individual(None), [])
vcf = make_vcf_header()
vcf.append(make_vcf_line(pos=1, extra='HGNC=TEST;MAX_AF=0.0001'))
vcf.append(make_vcf_line(pos=2, extra='HGNC=ATRX;MAX_AF=0.0001'))
path = os.path.join(self.temp_dir, "temp.vcf")
write_temp_vcf(path, vcf)
person = Person('fam_id', 'sample', 'dad', 'mom', 'F', '2', path)
var1 = SNV(chrom="1", position=1, id=".", ref="G", alts="T",
qual='1000', filter="PASS", info="CQ=missense_variant;HGNC=TEST;MAX_AF=0.0001",
format="DP:GT", sample="50:0/1", gender="female", mnv_code=None)
var2 = SNV(chrom="1", position=2, id=".", ref="G", alts="T",
qual='1000', filter="PASS", info="CQ=missense_variant;HGNC=ATRX;MAX_AF=0.0001",
format="DP:GT", sample="50:0/1", gender="female", mnv_code=None)
self.assertEqual(open_individual(person), [var2])
# define a set of variants to automatically pass, and check that these
# variants pass.
child_keys = set([('1', 1), ('1', 2)])
self.assertEqual(open_individual(person,
child_variants=child_keys), [var1, var2])
def test_open_individual_with_mnvs(self):
''' test that open_individual works with MNVs
'''
vcf = make_vcf_header()
vcf.append(make_vcf_line(pos=1, cq='splice_region_variant',
extra='HGNC=ATRX;MAX_AF=0.0001'))
vcf.append(make_vcf_line(pos=2, cq='missense_variant',
extra='HGNC=ATRX;MAX_AF=0.0001'))
path = os.path.join(self.temp_dir, "temp.vcf.gz")
self.write_gzipped_vcf(path, vcf)
person = Person('fam_id', 'sample', 'dad', 'mom', 'F', '2', path)
args = {'chrom': "1", 'position': 1, 'id': ".", 'ref': "G", 'alts': "T",
'filter': "PASS", 'info': "CQ=splice_region_variant;HGNC=ATRX;MAX_AF=0.0001",
'format': "DP:GT", 'sample': "50:0/1", 'gender': "female",
'mnv_code': 'modified_protein_altering_mnv'}
var1 = SNV(**args)
args['position'] = 2
args['mnv_code'] = None
args['info'] = "CQ=missense_variant;HGNC=ATRX;MAX_AF=0.0001"
var2 = SNV(**args)
# by default only one variant passes
self.assertEqual(self.vcf_loader.open_individual(person), [var2])
# if we include MNVs, then the passing variants swap
self.assertEqual(self.vcf_loader.open_individual(person,
mnvs={('1', 1): 'modified_protein_altering_mnv',
('1', 2): 'modified_synonymous_mnv'}), [var1])
def test_open_individual(self):
''' test that open_individual() works correctly
'''
# missing individual returns empty list
self.assertEqual(self.vcf_loader.open_individual(None), [])
vcf = make_vcf_header()
vcf.append(make_vcf_line(pos=1, extra='HGNC=TEST;MAX_AF=0.0001'))
vcf.append(make_vcf_line(pos=2, extra='HGNC=ATRX;MAX_AF=0.0001'))
path = os.path.join(self.temp_dir, "temp.vcf")
self.write_temp_vcf(path, vcf)
person = Person('fam_id', 'sample', 'dad', 'mom', 'F', '2', path)
var1 = SNV(chrom="1", position=1, id=".", ref="G", alts="T",
filter="PASS", info="CQ=missense_variant;HGNC=TEST;MAX_AF=0.0001",
format="DP:GT", sample="50:0/1", gender="female", mnv_code=None)
var2 = SNV(chrom="1", position=2, id=".", ref="G", alts="T",
filter="PASS", info="CQ=missense_variant;HGNC=ATRX;MAX_AF=0.0001",
format="DP:GT", sample="50:0/1", gender="female", mnv_code=None)
self.assertEqual(self.vcf_loader.open_individual(person), [var2])
# define a set of variants to automatically pass, and check that these
# variants pass.
self.vcf_loader.child_keys = set([('1', 1), ('1', 2)])
self.assertEqual(self.vcf_loader.open_individual(person,
child_variants=True), [var1, var2])
def test_open_individual_with_mnvs(self):
''' test that open_individual works with MNVs
'''
vcf = make_vcf_header()
vcf.append(make_vcf_line(pos=1, cq='splice_region_variant',
extra='HGNC=ATRX;MAX_AF=0.0001'))
vcf.append(make_vcf_line(pos=2, cq='missense_variant',
extra='HGNC=ATRX;MAX_AF=0.0001'))
path = os.path.join(self.temp_dir, "temp.vcf.gz")
write_gzipped_vcf(path, vcf)
person = Person('fam_id', 'sample', 'dad', 'mom', 'F', '2', path)
args = {'chrom': "1", 'position': 1, 'id': ".", 'ref': "G", 'alts': "T",
'filter': "PASS", 'info': "CQ=splice_region_variant;HGNC=ATRX;MAX_AF=0.0001",
'format': "DP:GT", 'sample': "50:0/1", 'gender': "female",
'mnv_code': 'modified_protein_altering_mnv', 'qual': '1000'}
var1 = SNV(**args)
args['position'] = 2
args['mnv_code'] = None
args['info'] = "CQ=missense_variant;HGNC=ATRX;MAX_AF=0.0001"
var2 = SNV(**args)
# by default only one variant passes
self.assertEqual(open_individual(person), [var2])
# if we include MNVs, then the passing variants swap
self.assertEqual(open_individual(person,
mnvs={('1', 1): 'modified_protein_altering_mnv',
('1', 2): 'modified_synonymous_mnv'}), [var1])
def make_vcf(person):
# make a VCF, where one line would pass the default filtering
vcf = make_vcf_header()
vcf.append(make_vcf_line(pos=1, extra='HGNC=TEST;MAX_AF=0.0001'))
vcf.append(make_vcf_line(pos=2, extra='HGNC=ATRX;MAX_AF=0.0001'))
path = os.path.join(self.temp_dir, "{}.vcf.gz".format(person))
self.write_gzipped_vcf(path, vcf)
return path
def make_vcf(person):
# make a VCF, where one line would pass the default filtering
vcf = make_vcf_header()
vcf.append(make_vcf_line(pos=1, extra='HGNC=TEST;MAX_AF=0.0001'))
vcf.append(make_vcf_line(pos=2, extra='HGNC=ATRX;MAX_AF=0.0001'))
path = os.path.join(self.temp_dir, "{}.vcf.gz".format(person))
write_gzipped_vcf(path, vcf)
return path
def test_get_mnv_candidates_catch_assertion_error(self):
''' check that get_mnv_candidates works correctly
'''
lines = make_vcf_header()
lines.append(make_vcf_line(chrom='1', pos=1, extra='Protein_position=1;Codons=aaT/aaG'))
lines.append(make_vcf_line(chrom='1', pos=2, extra='Protein_position=2;Codons=Att/Ctt'))
self.write_vcf(lines)
self.assertEqual(get_mnv_candidates(self.path), {})
def test_get_mnv_candidates(self):
''' check that get_mnv_candidates works correctly
'''
lines = make_vcf_header()
lines.append(make_vcf_line(chrom='1', pos=1, extra='Protein_position=1;Codons=aaT/aaG'))
lines.append(make_vcf_line(chrom='1', pos=2, extra='Protein_position=1;Codons=Aat/Cat'))
self.write_vcf(lines)
self.assertEqual(get_mnv_candidates(self.path), {
('1', 1): 'alternate_residue_mnv', ('1', 2): 'alternate_residue_mnv'})
def test_find_nearby_variants_separated(self):
''' test that find_nearby_variants() doesn't include vars far apart
'''
lines = make_vcf_header()
lines.append(make_vcf_line(pos=1))
lines.append(make_vcf_line(pos=4))
self.write_vcf(lines)
vcf = open_vcf(self.path)
exclude_header(vcf)
self.assertEqual(find_nearby_variants(vcf), [])
def test_find_nearby_variants(self):
''' test that find_nearby_variants() works correctly
'''
lines = make_vcf_header()
lines.append(make_vcf_line(pos=1))
lines.append(make_vcf_line(pos=2))
self.write_vcf(lines)
vcf = open_vcf(self.path)
exclude_header(vcf)
self.assertEqual(find_nearby_variants(vcf), [[('1', 1), ('1', 2)]])
def test_check_mnv_consequence_alternate_residue(self):
''' test that get_mnv_consequence() works correctly
'''
var1 = make_vcf_line(extra='Codons=aaT/aaG').split('\t')
var2 = make_vcf_line(extra='Codons=Aat/Cat').split('\t')
var1 = parse_vcf_line(var1, self.Variant)
var2 = parse_vcf_line(var2, self.Variant)
self.assertEqual(check_mnv_consequence(var1, var2, self.pattern),
'alternate_residue_mnv')
def test_check_mnv_consequence_modified_altering(self):
''' test that get_mnv_consequence() works correctly
'''
var1 = make_vcf_line(extra='Codons=Cta/Tta').split('\t')
var2 = make_vcf_line(extra='Codons=ctA/ctT').split('\t')
var1 = parse_vcf_line(var1, self.Variant)
var2 = parse_vcf_line(var2, self.Variant)
self.assertEqual(check_mnv_consequence(var1, var2, self.pattern),
'modified_protein_altering_mnv')
def test_get_codons_duplicate_codons(self):
''' test that get_codons() works when variants duplicate codons
'''
var1 = make_vcf_line(extra='Codons=aGt/aTt|aGt/aTt').split('\t')
var2 = make_vcf_line(extra='Codons=agT/agC|agT/agC').split('\t')
var1 = parse_vcf_line(var1, self.Variant)
var2 = parse_vcf_line(var2, self.Variant)
self.assertEqual(get_codons(var1, var2, self.pattern),
{'reference': 'aGt', 'snv1': 'aTt', 'snv2': 'agC', 'mnv': 'aTC'})
def test_get_codons_short_codon(self):
''' test that get_codons() raises an error the codons are not 3bp long.
'''
var1 = make_vcf_line(extra='Codons=aG/aT').split('\t')
var2 = make_vcf_line(extra='Codons=Ag/Gg').split('\t')
var1 = parse_vcf_line(var1, self.Variant)
var2 = parse_vcf_line(var2, self.Variant)
with self.assertRaises(AssertionError):
get_codons(var1, var2, self.pattern)
def test_check_minv_consequence_unmodified_synonymous(self):
''' test that get_mnv_consequence() works correctly
'''
var1 = make_vcf_line(extra='Codons=Cga/Aga').split('\t')
var2 = make_vcf_line(extra='Codons=cgA/cgG').split('\t')
var1 = parse_vcf_line(var1, self.Variant)
var2 = parse_vcf_line(var2, self.Variant)
self.assertEqual(check_mnv_consequence(var1, var2, self.pattern),
'unmodified_synonymous_mnv')
def test_check_mnv_consequence_masked_stop_gained(self):
''' test that get_mnv_consequence() works correctly
'''
var1 = make_vcf_line(extra='Codons=taT/taG').split('\t')
var2 = make_vcf_line(extra='Codons=Tat/Cat').split('\t')
var1 = parse_vcf_line(var1, self.Variant)
var2 = parse_vcf_line(var2, self.Variant)
self.assertEqual(check_mnv_consequence(var1, var2, self.pattern),
'masked_stop_gain_mnv')
def test_get_codons_null_value(self):
''' test that get_codons() works correctly when some genes have null values
'''
var1 = make_vcf_line(extra='Codons=aGt/aTt|.').split('\t')
var2 = make_vcf_line(extra='Codons=agT/agC|.').split('\t')
var1 = parse_vcf_line(var1, self.Variant)
var2 = parse_vcf_line(var2, self.Variant)
self.assertEqual(get_codons(var1, var2, self.pattern),
{'reference': 'aGt', 'snv1': 'aTt', 'snv2': 'agC', 'mnv': 'aTC'})
def test_get_codons_without_uppercase_base(self):
''' test that get_codons() raises an error when the variant position is
not un upper case.
'''
var1 = make_vcf_line(extra='Codons=agt/att').split('\t')
var2 = make_vcf_line(extra='Codons=agt/agc').split('\t')
var1 = parse_vcf_line(var1, self.Variant)
var2 = parse_vcf_line(var2, self.Variant)
with self.assertRaises(AttributeError):
get_codons(var1, var2, self.pattern)
def test_find_nearby_variants_different_chroms(self):
''' test that find_nearby_variants() works correctly with successive
variants on different chroms, but at the same position.
'''
# get the default two variants
lines = make_vcf_header()
lines.append(make_vcf_line(chrom='1', pos=1))
lines.append(make_vcf_line(chrom='2', pos=1))
vcf = open_vcf(self.path)
exclude_header(vcf)
self.assertEqual(find_nearby_variants(vcf), [])
def test_get_codons_with_different_codons(self):
''' test that get_codons() raises an error when different transcripts
have different codons
'''
var1 = make_vcf_line(extra='Codons=aGt/aTt|Gta/Tta').split('\t')
var2 = make_vcf_line(extra='Codons=agT/agC|gTa/gCa').split('\t')
var1 = parse_vcf_line(var1, self.Variant)
var2 = parse_vcf_line(var2, self.Variant)
with self.assertRaises(AssertionError):
get_codons(var1, var2, self.pattern)
def test_same_aa_different_positions(self):
''' check that same_aa() works correctly for different amino acids
'''
lines = make_vcf_header()
lines.append(make_vcf_line(pos=5, extra='Protein_position=2'))
lines.append(make_vcf_line(pos=7, extra='Protein_position=3'))
lines.append(make_vcf_line(pos=8, extra='Protein_position=4'))
self.write_vcf(lines)
vcf = tabix.open(self.path)
pairs = [[('1', 7), ('1', 8)]]
self.assertEqual(same_aa(vcf, pairs), [])
def test_find_nearby_variants_different_threshold(self):
''' test that find_nearby_variants() works correctly when we change the threshold distance.
'''
# get the default two variants
lines = make_vcf_header()
lines.append(make_vcf_line(pos=1))
lines.append(make_vcf_line(pos=2))
vcf = open_vcf(self.path)
exclude_header(vcf)
# using a lower threshold shouldn't allow any of the variants to pass
self.assertEqual(find_nearby_variants(vcf, threshold=0), [])
def test_same_aa(self):
''' check that same_aa() works correctly
'''
# get the VCF lines
lines = make_vcf_header()
lines.append(make_vcf_line(pos=2, extra='Protein_position=1'))
lines.append(make_vcf_line(pos=4, extra='Protein_position=1'))
self.write_vcf(lines)
vcf = tabix.open(self.path)
pairs = [[('1', 2), ('1', 4)]]
self.assertEqual(same_aa(vcf, pairs), [[('1', 2), ('1', 4)]])
def test_check_mnv_consequence_modified_synonymous(self):
''' test that get_mnv_consequence() works correctly
This should only be true for Serine residues, such as TCT -> AGT.
'''
var1 = make_vcf_line(extra='Codons=tCt/tGt').split('\t')
var2 = make_vcf_line(extra='Codons=Tct/Act').split('\t')
var1 = parse_vcf_line(var1, self.Variant)
var2 = parse_vcf_line(var2, self.Variant)
self.assertEqual(check_mnv_consequence(var1, var2, self.pattern),
'modified_synonymous_mnv')
def test_find_nearby_variants_duplicate_position(self):
''' test that find_nearby_variants() works correctly with a duplicate var
'''
# get the default two variants
lines = make_vcf_header()
lines.append(make_vcf_line(pos=1))
lines.append(make_vcf_line(pos=2))
# make a third variant, but at the same position as the second
lines.append(make_vcf_line(pos=2))
self.write_vcf(lines)
vcf = open_vcf(self.path)
exclude_header(vcf)
self.assertEqual(find_nearby_variants(vcf), [[('1', 1), ('1', 2)]])
def test_same_aa_missing_protein_positions(self):
''' check that same_aa() works correctly when the vars aren't in the CDS
'''
# if one of the variants in the pair does not have a protein position
# listed (i.e. residue number), that indicates the variant could be
# affecting the splice site, so we can't use the pair.
lines = make_vcf_header()
lines.append(make_vcf_line(pos=5))
lines.append(make_vcf_line(pos=7))
lines.append(make_vcf_line(pos=8, extra='Protein_position=4'))
self.write_vcf(lines)
vcf = tabix.open(self.path)
pairs = [[('1', 7), ('1', 8)]]
self.assertEqual(same_aa(vcf, pairs), [])
def test_screen_pairs_nonstandard_pair(self):
''' test that screen_pairs() works correctly
'''
# get the VCF lines
lines = make_vcf_header()
lines.append(make_vcf_line(pos=2))
lines.append(make_vcf_line(pos=4))
lines.append(make_vcf_line(pos=5))
lines.append(make_vcf_line(pos=7))
lines.append(make_vcf_line(pos=8))
self.write_vcf(lines)
vcf = tabix.open(self.path)
# set up a list of 'pairs', where one 'pair' has three variants in it.
# we exclude 'pairs' where n != 2.
pairs = [[('1', 2), ('1', 4), ('1', 5)], [('1', 7), ('1', 8)]]
self.assertEqual(screen_pairs(vcf, pairs, is_not_indel), [[('1', 7), ('1', 8)]])
def test_parse_vcf_line_multi_alts(self):
''' check that parse_vcf_line() works when we have multiple alts
'''
line = make_vcf_line(alts='C,CT').split('\t')
var = parse_vcf_line(line, self.Variant)
parsed = self.Variant(chrom='1', pos=1, id='.', ref='G', alts=['C', 'CT'],
qual='1000', filter='PASS', info={'CQ': 'missense_variant'})
self.assertEqual(var, parsed)
def test_is_not_indel(self):
''' check that is_not_indel() works correctly
'''
# check a deletion indel (from ref allele)
line = make_vcf_line(ref='AA').split('\t')
var = parse_vcf_line(line, self.Variant)
self.assertFalse(is_not_indel(var))
# check a SNV, should pass
line = make_vcf_line(ref='A').split('\t')
var = parse_vcf_line(line, self.Variant)
self.assertTrue(is_not_indel(var))
# check a SNV with multiple alts
line = make_vcf_line(ref='A', alts='T,G').split('\t')
var = parse_vcf_line(line, self.Variant)
self.assertTrue(is_not_indel(var))
# check a variant with multiple alts, only one of which is for a SNV
line = make_vcf_line(ref='A', alts='TT,G').split('\t')
var = parse_vcf_line(line, self.Variant)
self.assertTrue(is_not_indel(var))
# check an indel with multiple alts, none of which are for a SNV
line = make_vcf_line(ref='A', alts='TT,*').split('\t')
var = parse_vcf_line(line, self.Variant)
self.assertFalse(is_not_indel(var))
# check a deletion indel
line = make_vcf_line(ref='A', alts='TT').split('\t')
var = parse_vcf_line(line, self.Variant)
self.assertFalse(is_not_indel(var))
def test_parse_vcf_line(self):
''' test that parse_vcf_line() works correctly
'''
line = make_vcf_line(extra='Protein_position=1;Codons=aGt/aTt').split('\t')
var = parse_vcf_line(line, self.Variant)
parsed = self.Variant(chrom='1', pos=1, id='.', ref='G', alts=['T'],
qual='1000', filter='PASS', info={'Protein_position': '1',
'CQ': 'missense_variant', 'Codons': 'aGt/aTt'})
self.assertEqual(var, parsed)
# check that passing in an unsplit string raises an error
with self.assertRaises(ValueError):
line = self.make_vcf_line()
parse_vcf_line(line, self.Variant)
def test_open_individual_male_het_chrx(self):
""" test that open_individual() passes over hets in males on chrX
"""
# the sub-functions are all tested elsewhere, this test merely checks
# that valid variants are added to the variants list, and invalid
# variants are passed over without being added to the variants list
vcf = make_vcf_header()
vcf.append(make_vcf_line(chrom='X', pos=1, genotype='0/1',
extra='HGNC=TEST;MAX_AF=0.0001'))
path = os.path.join(self.temp_dir, "temp.vcf")
write_temp_vcf(path, vcf)
person = Person('fam_id', 'sample', 'dad', 'mom', 'M', '2', path)
self.assertEqual(open_individual(person), [])
def test_open_individual_male_het_chrx(self):
""" test that open_individual() passes over hets in males on chrX
"""
# the sub-functions are all tested elsewhere, this test merely checks
# that valid variants are added to the variants list, and invalid
# variants are passed over without being added to the variants list
vcf = make_vcf_header()
vcf.append(make_vcf_line(chrom='X', pos=1, genotype='0/1',
extra='HGNC=TEST;MAX_AF=0.0001'))
path = os.path.join(self.temp_dir, "temp.vcf")
write_temp_vcf(path, vcf)
person = Person('fam_id', 'sample', 'dad', 'mom', 'M', '2', path)
self.assertEqual(open_individual(person), [])
def test_analyse_trio(self):
''' test that analyse_trio() works correctly
'''
# construct the VCFs for the trio members
paths = {}
for member in ['child', 'mom', 'dad']:
vcf = make_vcf_header()
geno, pp_dnm = '0/0', ''
if member == 'child':
geno, pp_dnm = '0/1', ';DENOVO-SNP;PP_DNM=1'
vcf.append(make_vcf_line(genotype=geno, extra='HGNC=ARID1B' + pp_dnm))
# write the VCF data to a file
handle = tempfile.NamedTemporaryFile(dir=self.temp_dir, delete=False,
suffix='.vcf')
for x in vcf:
handle.write(x.encode('utf8'))
handle.flush()
paths[member] = handle.name
# create a Family object, so we can load the data from the trio's VCFs
fam_id = 'fam01'
child = Person(fam_id, 'child', 'dad', 'mom', 'female', '2', paths['child'])
mom = Person(fam_id, 'mom', '0', '0', 'female', '1', paths['mom'])
dad = Person(fam_id, 'dad', '0', '0', 'male', '1', paths['dad'])
family = Family(fam_id, [child], mom, dad)
self.assertEqual(self.finder.analyse_trio(family),
[(TrioGenotypes(chrom="1", pos=1,
child=SNV(chrom="1", position=1, id=".", ref="G", alts="T",
filter="PASS",
info="CQ=missense_variant;DENOVO-SNP;HGNC=ARID1B;PP_DNM=1",
format="DP:GT", sample="50:0/1", gender="female", mnv_code=None),
mother=SNV(chrom="1", position=1, id=".", ref="G", alts="T",
filter="PASS", info="CQ=missense_variant;HGNC=ARID1B",
format="DP:GT", sample="50:0/0", gender="female", mnv_code=None),
father=SNV(chrom="1", position=1, id=".", ref="G", alts="T",
filter="PASS", info="CQ=missense_variant;HGNC=ARID1B",
format="DP:GT", sample="50:0/0", gender="male", mnv_code=None)),
['single_variant'], ['Monoallelic'], ['ARID1B'])])
def test_get_matches_extra(self):
''' check that get_matches works correctly with > 2 in the 'pair'
'''
# get the VCF lines
lines = make_vcf_header()
lines.append(make_vcf_line(pos=1))
lines.append(make_vcf_line(pos=2))
lines.append(make_vcf_line(pos=4))
lines.append(make_vcf_line(pos=5))
self.write_vcf(lines)
vcf = tabix.open(self.path)
pair = [('1', 2), ('1', 4), ('1', 5)]
# define the expected lines
var1 = parse_vcf_line(make_vcf_line(pos=2).split('\t'), self.Variant)
var2 = parse_vcf_line(make_vcf_line(pos=4).split('\t'), self.Variant)
var3 = parse_vcf_line(make_vcf_line(pos=5).split('\t'), self.Variant)
self.assertEqual(list(get_matches(vcf, pair)), [var1, var2, var3])
def test_is_coding(self):
''' check that is_coding() works correctly
'''
# check for a single transcript and variant in CDS
line = make_vcf_line(cq='missense_variant').split('\t')
var = parse_vcf_line(line, self.Variant)
self.assertTrue(is_coding(var))
# check for a single transcript and synonymous variant
line = make_vcf_line(cq='synonymous_variant').split('\t')
var = parse_vcf_line(line, self.Variant)
self.assertTrue(is_coding(var))
# check for a single transcript and coding variant
line = make_vcf_line(cq='intergenic_variant').split('\t')
var = parse_vcf_line(line, self.Variant)
self.assertFalse(is_coding(var))
# check for a single transcript and coding variant
line = make_vcf_line(cq='intergenic_variant|missense_variant').split('\t')
var = parse_vcf_line(line, self.Variant)
self.assertTrue(is_coding(var))
# check for a single transcript and coding variant
line = make_vcf_line(cq='intergenic_variant,missense_variant').split('\t')
var = parse_vcf_line(line, self.Variant)
self.assertTrue(is_coding(var))
# check for a single transcript and coding variant
line = make_vcf_line(cq='intergenic_variant,'
'intergenic_variant|missense_variant').split('\t')
var = parse_vcf_line(line, self.Variant)
self.assertTrue(is_coding(var))
# check for a single transcript and coding variant
line = make_vcf_line(cq='intergenic_variant,'
'intergenic_variant|intergenic_variant').split('\t')
var = parse_vcf_line(line, self.Variant)
self.assertFalse(is_coding(var))