def test_parse_coordinates_indel():
variant = CyvcfVariant(alt="ACCC", end=80003)
coordinates = parse_coordinates(variant, "snv")
assert coordinates["position"] == variant.POS
assert coordinates["end"] == variant.end
def test_parse_coordinates_indel():
variant = CyvcfVariant(alt='ACCC', end=80003)
coordinates = parse_coordinates(variant, 'snv')
assert coordinates['position'] == variant.POS
assert coordinates['end'] == variant.end
def test_parse_coordinates_indel():
variant = CyvcfVariant(alt='ACCC', end=80003)
coordinates = parse_coordinates(variant, 'snv')
assert coordinates['position'] == variant.POS
assert coordinates['end'] == variant.end
def _is_managed(
self,
variant,
category="snv",
build="37",
):
"""Check if variant is on the managaged list.
All variants on the list will be loaded regardless of the kind of relevance.
Arguments:
variant(cyvcf2.Variant)
category(str): snv, sv, str, cancer, cancer_sv
build(str): "37" or "38"
Returns:
is_managed(boolean)
"""
coordinates = parse_coordinates(variant, category, build)
return (self.find_managed_variant(
parse_managed_variant_id(
coordinates["chrom"],
coordinates["position"],
coordinates["ref"],
coordinates["alt"],
category,
coordinates["sub_category"],
build,
)) is not None)
def test_parse_coordinates_indel(mock_variant):
"""Test to parse the coordinates for an indel"""
mock_variant.ALT = "ACCC"
mock_variant.end = 80003
variant = mock_variant
coordinates = parse_coordinates(variant, "snv")
assert coordinates["position"] == variant.POS
assert coordinates["end"] == variant.end
assert coordinates["sub_category"] == "indel"
assert coordinates["length"] == len(variant.ALT[0])
def test_parse_coordinates_translocation(mock_variant):
"""Test to parse the coordinates for a translocation"""
mock_variant.INFO = {"SVTYPE": "BND"}
mock_variant.REF = "N"
mock_variant.ALT = "N[hs37d5:12060532["
mock_variant.POS = 724779
mock_variant.end = 724779
mock_variant.var_type = "sv"
variant = mock_variant
coordinates = parse_coordinates(variant, "sv")
assert coordinates["position"] == variant.POS
assert coordinates["end"] == 12060532
assert coordinates["end_chrom"] == "hs37d5"
assert coordinates["length"] == 10e10
assert coordinates["sub_category"] == "bnd"
def test_parse_coordinates_snv(mock_variant):
"""Test to parse the coordinates for a simple snv"""
# GIVEN a cyvcf2 variant
variant = mock_variant
# WHEN parsing the coordinate info
coordinates = parse_coordinates(variant, "snv")
# THEN assert that they are correctly parsed
assert coordinates["position"] == variant.POS
assert coordinates["end"] == variant.end
assert coordinates["length"] == len(variant.ALT)
assert coordinates["sub_category"] == "snv"
assert coordinates["mate_id"] is None
assert (coordinates["cytoband_start"] == coordinates["cytoband_end"] ==
get_cytoband_coordinates(variant.CHROM, variant.POS, "37"))
assert coordinates["end_chrom"] == variant.CHROM
def test_parse_coordinates_translocation_2():
info_dict = {"SVTYPE": "BND"}
variant = CyvcfVariant(
ref="N",
alt="N[GL000232.1:25141[",
pos=724779,
end=724779,
var_type="sv",
info_dict=info_dict,
)
coordinates = parse_coordinates(variant, "sv")
assert coordinates["position"] == variant.POS
assert coordinates["end"] == 25141
assert coordinates["end_chrom"] == "GL000232.1"
assert coordinates["length"] == 10e10
assert coordinates["sub_category"] == "bnd"
def test_parse_coordinates_translocation():
info_dict = {"SVTYPE": "BND"}
variant = CyvcfVariant(
ref="N",
alt="N[hs37d5:12060532[",
pos=724779,
end=724779,
var_type="sv",
info_dict=info_dict,
)
coordinates = parse_coordinates(variant, "sv")
assert coordinates["position"] == variant.POS
assert coordinates["end"] == 12060532
assert coordinates["end_chrom"] == "hs37d5"
assert coordinates["length"] == 10e10
assert coordinates["sub_category"] == "bnd"
def test_parse_coordinates_translocation_2():
info_dict = {
'SVTYPE': 'BND',
}
variant = CyvcfVariant(
ref='N',
alt='N[GL000232.1:25141[',
pos=724779,
end=724779,
var_type='sv',
info_dict=info_dict,
)
coordinates = parse_coordinates(variant, 'sv')
assert coordinates['position'] == variant.POS
assert coordinates['end'] == 25141
assert coordinates['end_chrom'] == 'GL000232.1'
assert coordinates['length'] == 10e10
assert coordinates['sub_category'] == 'bnd'
def test_parse_coordinates_translocation():
info_dict = {
'SVTYPE': 'BND',
}
variant = CyvcfVariant(
ref='N',
alt='N[hs37d5:12060532[',
pos=724779,
end=724779,
var_type='sv',
info_dict=info_dict,
)
coordinates = parse_coordinates(variant, 'sv')
assert coordinates['position'] == variant.POS
assert coordinates['end'] == 12060532
assert coordinates['end_chrom'] == 'hs37d5'
assert coordinates['length'] == 10e10
assert coordinates['sub_category'] == 'bnd'
def test_parse_coordinates_translocation_2():
info_dict = {
'SVTYPE': 'BND',
}
variant = CyvcfVariant(
ref='N',
alt='N[GL000232.1:25141[',
pos=724779,
end=724779,
var_type='sv',
info_dict=info_dict,
)
coordinates = parse_coordinates(variant, 'sv')
assert coordinates['position'] == variant.POS
assert coordinates['end'] == 25141
assert coordinates['end_chrom'] == 'GL000232.1'
assert coordinates['length'] == 10e10
assert coordinates['sub_category'] == 'bnd'
def test_parse_coordinates_translocation():
info_dict = {
'SVTYPE': 'BND',
}
variant = CyvcfVariant(
ref='N',
alt='N[hs37d5:12060532[',
pos=724779,
end=724779,
var_type='sv',
info_dict=info_dict,
)
coordinates = parse_coordinates(variant, 'sv')
assert coordinates['position'] == variant.POS
assert coordinates['end'] == 12060532
assert coordinates['end_chrom'] == 'hs37d5'
assert coordinates['length'] == 10e10
assert coordinates['sub_category'] == 'bnd'
def test_parse_coordinates_snv():
variant = CyvcfVariant()
coordinates = parse_coordinates(variant, "snv")
assert coordinates["position"] == variant.POS
def test_parse_coordinates_snv():
variant = CyvcfVariant()
coordinates = parse_coordinates(variant, 'snv')
assert coordinates['position'] == variant.POS
def test_parse_coordinates_snv():
variant = CyvcfVariant()
coordinates = parse_coordinates(variant, 'snv')
assert coordinates['position'] == variant.POS