def test_debug_option(self):
""" test whether we can set up the class with the debug option
"""
counter = 0
total_trios = 1
known_genes = {}
self.vcf_loader = LoadVCFs(total_trios, known_genes, "1", "10000")
# check that the debug filter function got set correctly
self.assertEqual(SNV.passes_filters, SNV.passes_filters_with_debug)
def setUp(self):
""" define a default LoadVCFs object
"""
total_trios = 1
known_genes = {"ATRX": {"inheritance": {"Hemizygous": \
{"Loss of function"}}, "start": 1, "chrom": "1", \
"confirmed_status": {"Confirmed DD Gene"}, "end": 20000000}}
self.vcf_loader = LoadVCFs(total_trios, known_genes, None, None)
# make a temp directory for the cache file
self.temp_dir = tempfile.mkdtemp()
def filter_trios(self):
""" loads trio variants, and screens for candidate variants
"""
self.vcf_loader = LoadVCFs(len(self.families), self.known_genes, \
self.debug_chrom, self.debug_pos)
# load the trio paths into the current path setup
for family_ID in sorted(self.families):
self.family = self.families[family_ID]
# some families have more than one child in the family, so run
# through each child.
self.family.set_child()
while self.family.child is not None:
if self.family.child.is_affected():
variants = self.vcf_loader.get_trio_variants(
self.family, self.pp_filter)
self.vcf_provenance = self.vcf_loader.get_trio_provenance()
self.analyse_trio(variants)
self.family.set_child_examined()
sys.exit(0)
