def test_gt_call_no_header():
"""Test to get the raw chromosome"""
plugin = Plugin(name='gt_call', field='sample_id', gt_key='GT')
variant_line = get_variant_line()
with pytest.raises(IOError):
plugin.get_raw_entry(variant_line=variant_line, individual_id='ADM1003A3')
def test_gt_call_no_individual():
"""Test to get the raw chromosome"""
plugin = Plugin(name='gt_call', field='sample_id', gt_key='GT')
vcf_header = ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT', 'ADM1003A3']
variant_line = get_variant_line()
variant_dict = get_variant_dict()
with pytest.raises(IOError):
plugin.get_raw_entry(variant_line=variant_line, vcf_header=vcf_header)
with pytest.raises(IOError):
plugin.get_raw_entry(variant_dict=variant_dict, vcf_header=vcf_header)
def test_id():
"""Test to get the raw chromosome"""
plugin = Plugin(name='ID', field='ID')
db_id = 'rs001'
variant_line = get_variant_line(db_id=db_id)
variant_dict = get_variant_dict(db_id=db_id)
assert plugin.get_raw_entry(variant_line=variant_line) == db_id
assert plugin.get_raw_entry(variant_dict=variant_dict) == db_id
def test_pos():
"""Test to get the raw chromosome"""
plugin = Plugin(name='Pos', field='POS')
test_pos = '1000'
variant_line = get_variant_line(pos=test_pos)
variant_dict = get_variant_dict(pos=test_pos)
assert plugin.get_raw_entry(variant_line=variant_line) == test_pos
assert plugin.get_raw_entry(variant_dict=variant_dict) == test_pos
def test_chrom():
"""Test to get the raw chromosome"""
plugin = Plugin(name='Chrom', field='CHROM')
test_chrom = '10'
variant_line = get_variant_line(chrom=test_chrom)
variant_dict = get_variant_dict(chrom=test_chrom)
assert plugin.get_raw_entry(variant_line=variant_line) == test_chrom
assert plugin.get_raw_entry(variant_dict=variant_dict) == test_chrom
def test_gt_call():
"""Test to get the raw chromosome"""
plugin = Plugin(name='gt_call', field='sample_id', gt_key='GT')
vcf_header = ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO', 'FORMAT', 'ADM1003A3']
variant_line = get_variant_line()
variant_dict = get_variant_dict()
assert plugin.get_raw_entry(
variant_line=variant_line,
vcf_header=vcf_header,
individual_id='ADM1003A3') == '1/1'
assert plugin.get_raw_entry(
variant_dict=variant_dict,
vcf_header=vcf_header,
individual_id='ADM1003A3') == '1/1'
def test_CLNSIG():
"""Test to get the raw chromosome"""
plugin = Plugin(name='Clnsig', field='INFO', info_key="CLNSIG")
test_value = '255,10'
variant_line = get_variant_line()
variant_dict = get_variant_dict()
assert plugin.get_raw_entry(variant_line=variant_line) == test_value
assert plugin.get_raw_entry(variant_dict=variant_dict) == test_value
def test_format():
"""Test to get the raw chromosome"""
plugin = Plugin(name='Format', field='FORMAT')
form = 'GT:AD:GQ:PL'
variant_line = get_variant_line(form=form)
variant_dict = get_variant_dict(form=form)
assert plugin.get_raw_entry(variant_line=variant_line) == form
assert plugin.get_raw_entry(variant_dict=variant_dict) == form
def test_filter():
"""Test to get the raw chromosome"""
plugin = Plugin(name='Filter', field='FILTER')
filt = 'PASS'
variant_line = get_variant_line(filt=filt)
variant_dict = get_variant_dict(filt=filt)
assert plugin.get_raw_entry(variant_line=variant_line) == filt
assert plugin.get_raw_entry(variant_dict=variant_dict) == filt
def test_qual():
"""Test to get the raw chromosome"""
plugin = Plugin(name='QUAL', field='QUAL')
qual = '1234.5'
variant_line = get_variant_line(qual=qual)
variant_dict = get_variant_dict(qual=qual)
assert plugin.get_raw_entry(variant_line=variant_line) == qual
assert plugin.get_raw_entry(variant_dict=variant_dict) == qual
def test_alt():
"""Test to get the raw chromosome"""
plugin = Plugin(name='alt', field='ALT')
alt = 'A'
variant_line = get_variant_line(alt=alt)
variant_dict = get_variant_dict(alt=alt)
assert plugin.get_raw_entry(variant_line=variant_line) == alt
assert plugin.get_raw_entry(variant_dict=variant_dict) == alt
def test_ref():
"""Test to get the raw chromosome"""
plugin = Plugin(name='ref', field='REF')
ref = 'rs001'
variant_line = get_variant_line(ref=ref)
variant_dict = get_variant_dict(ref=ref)
assert plugin.get_raw_entry(variant_line=variant_line) == ref
assert plugin.get_raw_entry(variant_dict=variant_dict) == ref
def test_1000G():
"""Test to get the raw chromosome"""
plugin = Plugin(name='thousand_g', field='INFO', info_key="1000GAF")
variant_line = get_variant_line()
variant_dict = get_variant_dict()
test_value = '0.744609'
assert plugin.get_raw_entry(variant_line=variant_line) == test_value
assert plugin.get_raw_entry(variant_dict=variant_dict) == test_value
def test_dict_two_separators_with_key():
"""Test to get the raw chromosome"""
variant_dict = get_variant_dict(info="RankScore=1:12,2:11")
variant_line = get_variant_line(info="RankScore=1:12,2:11")
plugin = Plugin(
name='rank_score',
field='INFO',
info_key="RankScore",
separators=[',', ':'],
dict_entry=True
)
dict_entry = plugin.get_raw_entry(
variant_dict=variant_dict,
dict_key='1'
)
line_entry = plugin.get_raw_entry(
variant_line=variant_line,
dict_key='1'
)
assert dict_entry == '12'
assert line_entry == '12'
def test_dict_three_separators_with_key():
"""Test to get the raw chromosome"""
variant_dict = get_variant_dict(info="GeneticModels=1:AD|AD_dn,2:AR_hom")
variant_line = get_variant_line(info="GeneticModels=1:AD|AD_dn,2:AR_hom")
plugin = Plugin(
name='genetic_models',
field='INFO',
info_key="GeneticModels",
separators=[',', ':', '|'],
dict_entry=True
)
dict_entry = plugin.get_raw_entry(
variant_dict=variant_dict,
dict_key='1'
)
line_entry = plugin.get_raw_entry(
variant_line=variant_line,
dict_key='1'
)
assert dict_entry == 'AD|AD_dn'
assert line_entry == 'AD|AD_dn'
def test_gt_call_no_header_dict():
"""Test to get the raw chromosome"""
plugin = Plugin(name='gt_call', field='sample_id', gt_key='GT')
variant_dict = get_variant_dict()
assert plugin.get_raw_entry(variant_dict=variant_dict, individual_id='ADM1003A3') == '1/1'
