def test_get_consequence_last_base(self):
'''check get_consequence() works with last base of exon changes
'''
chrom, pos = '1', 1000
alts = ('C', )
info = Info('CQ=missense_variant;HGNC=TEST')
info.set_genes_and_consequence(chrom, pos, alts, [])
# Now check that if the variant is at a position where it is a final
# base in an exon with a conserved base, the consequence gets converted.
info.last_base = set([("1", 1000)])
self.assertEqual(info.get_consequences(chrom, pos, alts, []),
[["conserved_exon_terminus_variant"]])
# If we have a variant in multiple genes, check that it only alters the
# missense/splice_region variants, and doesn't alter synonymous variants
# (since these will be in transcripts where the variant is distant from
# an exon boundary.)
info = Info('CQ=missense_variant|synonymous_variant;HGNC=TEST|TEST1')
info.set_genes_and_consequence(chrom, pos, alts, [])
info.last_base = set([("1", 1000)])
self.assertEqual(
info.get_consequences(chrom, pos, alts, []),
[["conserved_exon_terminus_variant", "synonymous_variant"]])
def test_get_consequence(self):
""" test that get_consequence works correctly
"""
chrom, pos = '1', 1000
info = Info('CQ=missense_variant;HGNC=TEST')
alts = ('C', )
# check that in the absence of any known conserved final exon positions,
# the consequence is unchanged.
self.assertEqual(info.get_consequences(chrom, pos, alts, []),
[['missense_variant']])
info = Info('CQ=missense_variant|stop_gained;HGNC=TEST|TEST2')
self.assertEqual(info.get_consequences(chrom, pos, alts, []),
[['missense_variant', 'stop_gained']])
def test_get_consequence(self):
""" test that get_consequence works correctly
"""
chrom, pos = '1', 1000
info = Info('CQ=missense_variant;HGNC=TEST')
alts = ('C',)
# check that in the absence of any known conserved final exon positions,
# the consequence is unchanged.
self.assertEqual(info.get_consequences(chrom, pos, alts, []),
[['missense_variant']])
info = Info('CQ=missense_variant|stop_gained;HGNC=TEST|TEST2')
self.assertEqual(info.get_consequences(chrom, pos, alts, []),
[['missense_variant', 'stop_gained']])
def test_get_consequence_multiallelic(self):
''' test that get_consequence works correctly with multiple alleles
'''
chrom, pos = '1', 1000
info = Info('CQ=missense_variant,synonymous_variant')
alts = ('C', 'G')
self.assertEqual(info.get_consequences(chrom, pos, alts, []),
[['missense_variant'], ['synonymous_variant']])
def test_get_consequence_multiallelic_with_masked(self):
''' test that get_consequence works correctly with multiple alleles
'''
chrom, pos = '1', 1000
info = Info('CQ=missense_variant,synonymous_variant')
alts = ('C', 'G')
self.assertEqual(info.get_consequences(chrom, pos, alts, ['G']),
[['missense_variant']])
def test_get_consequence_last_base(self):
'''check get_consequence() works with last base of exon changes
'''
chrom, pos = '1', 1000
alts = ('C',)
info = Info('CQ=missense_variant;HGNC=TEST')
info.set_genes_and_consequence(chrom, pos, alts, [])
# Now check that if the variant is at a position where it is a final
# base in an exon with a conserved base, the consequence gets converted.
info.last_base = set([("1", 1000)])
self.assertEqual(info.get_consequences(chrom, pos, alts, []),
[["conserved_exon_terminus_variant"]])
# If we have a variant in multiple genes, check that it only alters the
# missense/splice_region variants, and doesn't alter synonymous variants
# (since these will be in transcripts where the variant is distant from
# an exon boundary.)
info = Info('CQ=missense_variant|synonymous_variant;HGNC=TEST|TEST1')
info.set_genes_and_consequence(chrom, pos, alts, [])
info.last_base = set([("1", 1000)])
self.assertEqual(info.get_consequences(chrom, pos, alts, []),
[["conserved_exon_terminus_variant", "synonymous_variant"]])
