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_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_entry(variant_line=variant_line) == [ref]
assert plugin.get_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_entry(variant_line=variant_line) == [alt]
assert plugin.get_entry(variant_dict=variant_dict) == [alt]
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_entry(variant_line=variant_line) == [db_id]
assert plugin.get_entry(variant_dict=variant_dict) == [db_id]
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_entry(variant_line=variant_line) == [db_id]
assert plugin.get_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_entry(variant_line=variant_line) == [test_pos]
assert plugin.get_entry(variant_dict=variant_dict) == [test_pos]
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_entry(variant_line=variant_line) == [filt]
assert plugin.get_entry(variant_dict=variant_dict) == [filt]
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_entry(variant_line=variant_line) == [alt]
assert plugin.get_entry(variant_dict=variant_dict) == [alt]
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_entry(variant_line=variant_line) == [test_chrom]
assert plugin.get_entry(variant_dict=variant_dict) == [test_chrom]
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_entry(variant_line=variant_line) == [filt]
assert plugin.get_entry(variant_dict=variant_dict) == [filt]
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_entry(variant_line=variant_line) == [ref]
assert plugin.get_entry(variant_dict=variant_dict) == [ref]
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_entry(variant_line=variant_line) == [qual]
assert plugin.get_entry(variant_dict=variant_dict) == [qual]
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_entry(variant_line=variant_line) == [test_pos]
assert plugin.get_entry(variant_dict=variant_dict) == [test_pos]
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_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_entry(variant_line=variant_line) == [test_chrom]
assert plugin.get_entry(variant_dict=variant_dict) == [test_chrom]
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_entry(variant_line=variant_line) == [qual]
assert plugin.get_entry(variant_dict=variant_dict) == [qual]
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_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():
"""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_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_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_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_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_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_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_entry(
variant_dict=variant_dict,
dict_key='1'
)
line_entry = plugin.get_entry(
variant_line=variant_line,
dict_key='1'
)
assert dict_entry == ['12']
assert line_entry == ['12']
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_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_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']