def passes_filters(self):
"""Checks whether a VCF variant passes user defined criteria.
Returns:
boolean value for whether the variant passes the filters
"""
# some CNVs are on female Y chrom, which give errors, fail those CNVs
try:
self.set_genotype()
except ValueError:
return False
# we rely on the CALLSOURCE field to inform us what the CNV has been
# called by. Raise an error if this is not present.
assert "CALLSOURCE" in self.info
track_variant = False
if self.get_chrom() == self.debug_chrom and self.get_position() == self.debug_pos:
track_variant = True
passes = True
if "aCGH" in self.info["CALLSOURCE"]:
filt = ACGH_CNV(self)
passes = filt.filter_cnv(track_variant)
elif "EXOME" in self.info["CALLSOURCE"]:
# currently return false for all exome-only CNVs, undergoing testing
filt = ExomeCNV(self)
passes = filt.filter_cnv(track_variant)
else:
if track_variant:
print("CNV is not an aCGH or exome CNV")
passes = False
return passes
def setUp(self):
""" define a default VcfInfo object
"""
extra = "HGNC=OR5A1;CQ=missense_variant;CONVEX;RC50INTERNALFREQ=0.005;COMMONFORWARDS=0.000;MEANLR2=0.5;MADL2R=0.02"
cnv = create_cnv('F', 'deNovo', extra_info=extra)
self.var = ExomeCNV(cnv)
def setUp(self):
""" define a default VcfInfo object
"""
chrom = "1"
pos = "15000000"
snp_id = "."
ref = "A"
alt = "<DUP>"
filt = "PASS"
# set up a SNV object, since SNV inherits VcfInfo
cnv = CNV(chrom, pos, snp_id, ref, alt, filt)
self.var = ExomeCNV(cnv)
info = "HGNC=TEST;HGNC_ALL=TEST,OR5A1;CQ=missense_variant;CONVEX;RC50INTERNALFREQ=0.005;COMMONFORWARDS=0.000;MEANLR2=0.5;MADL2R=0.02"
format_keys = "inheritance:DP"
sample_values = "deNovo:50"
self.var.cnv.add_info(info)
self.var.cnv.add_format(format_keys, sample_values)
self.var.cnv.set_gender("F")
def passes_filters(self):
"""Checks whether a VCF variant passes user defined criteria.
Returns:
boolean value for whether the variant passes the filters
"""
# some CNVs are on female Y chrom, which give errors, fail those CNVs
try:
self.set_genotype()
except ValueError:
return False
track_variant = False
if self.get_chrom() == self.debug_chrom and self.get_position(
) == self.debug_pos:
track_variant = True
passes = True
if "CONVEX" in self.info and "CNSOLIDATE" not in self.info:
# currently return false for all exome-only CNVs, undergoing testing
filt = ExomeCNV(self)
# passes = filt.filter_cnv(track_variant)
passes = False
elif "CNSOLIDATE" in self.info:
filt = ACGH_CNV(self)
passes = filt.filter_cnv(track_variant)
elif "BREAKDANCER" in self.info:
filt = BreakdancerCNV(self)
passes = filt.filter_cnv(track_variant)
else:
if track_variant:
print("CNV is not an aCGH or exome CNV")
passes = False
return passes
