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_rank_models():
"""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',
data_type='string',
info_key="GeneticModels",
separators=[',', ':', '|'],
dict_entry=True,
string_rules={
'AD_dn':1,
'AD':2
}
)
dict_entry = plugin.get_value(
variant_dict=variant_dict,
dict_key='1'
)
line_entry = plugin.get_value(
variant_line=variant_line,
dict_key='1'
)
assert dict_entry == 'AD'
assert line_entry == 'AD'
def test_non_existing():
"""Test to get the raw chromosome"""
plugin = Plugin(name='non_existing', field='INFO', info_key="non", separators=[','])
variant_line = get_variant_line()
variant_dict = get_variant_dict()
assert plugin.get_entry(variant_line=variant_line) == []
assert plugin.get_entry(variant_dict=variant_dict) == []
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_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_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_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_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_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_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_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_1000G():
"""Test to get the raw chromosome"""
plugin = Plugin(name='thousand_g', field='INFO', info_key="1000GAF", separators=[','])
test_value = '0.744609'
variant_line = get_variant_line()
variant_dict = get_variant_dict()
assert plugin.get_entry(variant_line=variant_line) == [test_value]
assert plugin.get_entry(variant_dict=variant_dict) == [test_value]
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_CLNSIG():
"""Test to get the raw chromosome"""
plugin = Plugin(name='Clnsig', field='INFO', info_key="CLNSIG", separators=[','])
test_value = ['255','10']
variant_line = get_variant_line()
variant_dict = get_variant_dict()
assert plugin.get_entry(variant_line=variant_line) == test_value
assert plugin.get_entry(variant_dict=variant_dict) == test_value
def test_multiple_id_no_rule():
"""Test to get the raw chromosome"""
plugin = Plugin(name='ID', field='ID', data_type='flag')
db_id_1 = 'rs001'
db_id_2 = 'rs002'
db_id = "{0};{1}".format(db_id_1, db_id_2)
variant_line = get_variant_line(db_id=db_id)
variant_dict = get_variant_dict(db_id=db_id)
assert plugin.get_value(variant_line=variant_line) == True
assert plugin.get_value(variant_dict=variant_dict) == True
def test_multiple_alt():
"""Test to get the raw chromosome"""
plugin = Plugin(name='alt', field='ALT')
alt_1 = 'A'
alt_2 = 'T'
alt = "{0},{1}".format(alt_1, alt_2)
variant_line = get_variant_line(alt=alt)
variant_dict = get_variant_dict(alt=alt)
assert plugin.get_entry(variant_line=variant_line) == [alt_1, alt_2]
assert plugin.get_entry(variant_dict=variant_dict) == [alt_1, alt_2]
def test_multiple_filter():
"""Test to get the raw chromosome"""
plugin = Plugin(name='Filter', field='FILTER')
filt_1 = 'PASS'
filt_2 = 'low_qual'
filt = "{0};{1}".format(filt_1, filt_2)
variant_line = get_variant_line(filt=filt)
variant_dict = get_variant_dict(filt=filt)
assert plugin.get_entry(variant_line=variant_line) == [filt_1, filt_2]
assert plugin.get_entry(variant_dict=variant_dict) == [filt_1, filt_2]
def test_multiple_alt():
"""Test to get the raw chromosome"""
plugin = Plugin(name='alt', field='ALT')
alt_1 = 'A'
alt_2 = 'T'
alt = "{0},{1}".format(alt_1, alt_2)
variant_line = get_variant_line(alt=alt)
variant_dict = get_variant_dict(alt=alt)
assert plugin.get_entry(variant_line=variant_line) == [alt_1, alt_2]
assert plugin.get_entry(variant_dict=variant_dict) == [alt_1, alt_2]
def test_multiple_id():
"""Test to get the raw chromosome"""
plugin = Plugin(name='ID', field='ID')
db_id_1 = 'rs001'
db_id_2 = 'rs002'
db_id = "{0};{1}".format(db_id_1, db_id_2)
variant_line = get_variant_line(db_id=db_id)
variant_dict = get_variant_dict(db_id=db_id)
assert plugin.get_entry(variant_line=variant_line) == [db_id_1, db_id_2]
assert plugin.get_entry(variant_dict=variant_dict) == [db_id_1, db_id_2]
def test_multiple_filter():
"""Test to get the raw chromosome"""
plugin = Plugin(name='Filter', field='FILTER')
filt_1 = 'PASS'
filt_2 = 'low_qual'
filt = "{0};{1}".format(filt_1, filt_2)
variant_line = get_variant_line(filt=filt)
variant_dict = get_variant_dict(filt=filt)
assert plugin.get_entry(variant_line=variant_line) == [filt_1, filt_2]
assert plugin.get_entry(variant_dict=variant_dict) == [filt_1, filt_2]
def test_multiple_id():
"""Test to get the raw chromosome"""
plugin = Plugin(name='ID', field='ID')
db_id_1 = 'rs001'
db_id_2 = 'rs002'
db_id = "{0};{1}".format(db_id_1, db_id_2)
variant_line = get_variant_line(db_id=db_id)
variant_dict = get_variant_dict(db_id=db_id)
assert plugin.get_entry(variant_line=variant_line) == [db_id_1, db_id_2]
assert plugin.get_entry(variant_dict=variant_dict) == [db_id_1, db_id_2]
def test_non_existing():
"""Test to get the raw chromosome"""
plugin = Plugin(name='non_existing',
field='INFO',
info_key="non",
separators=[','])
variant_line = get_variant_line()
variant_dict = get_variant_dict()
assert plugin.get_entry(variant_line=variant_line) == []
assert plugin.get_entry(variant_dict=variant_dict) == []
def test_CLNSIG():
"""Test to get the raw chromosome"""
plugin = Plugin(name='Clnsig',
field='INFO',
info_key="CLNSIG",
separators=[','])
test_value = ['255', '10']
variant_line = get_variant_line()
variant_dict = get_variant_dict()
assert plugin.get_entry(variant_line=variant_line) == test_value
assert plugin.get_entry(variant_dict=variant_dict) == test_value
def test_1000G():
"""Test to get the raw chromosome"""
plugin = Plugin(name='thousand_g',
field='INFO',
info_key="1000GAF",
separators=[','])
test_value = '0.744609'
variant_line = get_variant_line()
variant_dict = get_variant_dict()
assert plugin.get_entry(variant_line=variant_line) == [test_value]
assert plugin.get_entry(variant_dict=variant_dict) == [test_value]
def test_CSQ():
"""Test to get the raw chromosome"""
plugin = Plugin(name='CSQ', field='INFO', info_key="CSQ", csq_key="Gene", separators=['&'])
variant_line = get_variant_line()
variant_dict = get_variant_dict()
test_value = [
'ENSG00000138378',
'ENSG00000138378'
]
assert plugin.get_entry(variant_line=variant_line, csq_format=csq_format) == test_value
assert plugin.get_entry(variant_dict=variant_dict, csq_format=csq_format) == test_value
def test_dict_two_separators_no_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_entry(variant_dict=variant_dict)
line_entry = plugin.get_entry(variant_line=variant_line)
assert dict_entry == ['11']
assert line_entry == ['11']
def test_flag():
"""Test to get the raw chromosome"""
plugin = Plugin(
name='DB',
field='INFO',
info_key="DB",
data_type='flag',
)
variant_line = get_variant_line()
variant_dict = get_variant_dict()
assert plugin.get_value(variant_line=variant_line) == True
assert plugin.get_value(variant_dict=variant_dict) == True
def test_1000G_float():
"""Test to get the raw chromosome"""
plugin = Plugin(
name='thousand_g',
field='INFO',
info_key="1000GAF",
separators=[','],
data_type='float',
)
test_value = 0.744609
variant_line = get_variant_line()
variant_dict = get_variant_dict()
assert plugin.get_value(variant_line=variant_line) == test_value
assert plugin.get_value(variant_dict=variant_dict) == test_value
def test_dict_two_separators_no_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)
line_entry = plugin.get_raw_entry(variant_line=variant_line)
assert dict_entry == '11'
assert line_entry == '11'
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_entry(variant_dict=variant_dict, dict_key='1')
line_entry = plugin.get_entry(variant_line=variant_line, dict_key='1')
assert dict_entry == ['AD', 'AD_dn']
assert line_entry == ['AD', 'AD_dn']
def test_1000G_record_rule():
"""Test to get the raw chromosome"""
plugin = Plugin(
name='thousand_g',
field='INFO',
info_key="1000GAF",
separators=[','],
data_type='float',
record_rule='min',
)
info = "1000GAF=0.744609,0.02;AC=2;AF=1.00;AN=2"
variant_line = get_variant_line(info=info)
variant_dict = get_variant_dict(info=info)
assert plugin.get_value(variant_line=variant_line) == 0.02
assert plugin.get_value(variant_dict=variant_dict) == 0.02
def test_CSQ():
"""Test to get the raw chromosome"""
plugin = Plugin(name='CSQ',
field='INFO',
info_key="CSQ",
csq_key="Gene",
separators=['&'])
variant_line = get_variant_line()
variant_dict = get_variant_dict()
test_value = ['ENSG00000138378', 'ENSG00000138378']
assert plugin.get_entry(variant_line=variant_line,
csq_format=csq_format) == test_value
assert plugin.get_entry(variant_dict=variant_dict,
csq_format=csq_format) == test_value
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_dict_three_separators_no_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)
line_entry = plugin.get_raw_entry(variant_line=variant_line)
assert dict_entry == 'AR_hom'
assert line_entry == 'AR_hom'
def test_filter_min_rule():
"""Test to get the raw chromosome"""
plugin = Plugin(
name='Filter',
field='FILTER',
data_type='string',
string_rules={
'PASS':2,
'NOT_PASS':1
},
record_rule='min'
)
filt = "PASS;NOT_PASS"
variant_line = get_variant_line(filt=filt)
variant_dict = get_variant_dict(filt=filt)
assert plugin.get_value(variant_line=variant_line) == 'NOT_PASS'
assert plugin.get_value(variant_dict=variant_dict) == 'NOT_PASS'
def test_rank_score_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',
data_type='integer',
field='INFO',
info_key="RankScore",
separators=[',', ':'],
dict_entry=True
)
dict_entry = plugin.get_value(
variant_dict=variant_dict,
dict_key='1'
)
line_entry = plugin.get_value(
variant_line=variant_line,
dict_key='1'
)
assert dict_entry == 12
assert line_entry == 12
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_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'