def test_dbsnp_snp_mapping(self):
"""
unit test for _get_rs_id()
Test that we can resolve snps in dbsnp
to rsids
"""
udp = UDP('rdf_graph', True)
rs_map = udp._parse_rs_map_file(udp.map_files['dbsnp_map'])
variant_type = 'snp'
variant = {
'build': 'hg19',
'chromosome': 'chr15',
'reference_allele': 'A',
'variant_allele': 'C',
'position': '54624219'
}
rsid = udp._get_rs_id(variant, rs_map, variant_type)
self.assertEqual(rsid, '755532609')
def test_dbsnp_snp_mapping(self):
"""
unit test for _get_rs_id()
Test that we can resolve snps in dbsnp
to rsids
"""
udp = UDP('rdf_graph', True)
rs_map = udp._parse_rs_map_file(udp.map_files['dbsnp_map'])
variant_type = 'snp'
variant = {
'build': 'hg19',
'chromosome': 'chr15',
'reference_allele': 'A',
'variant_allele': 'C',
'position': '54624219'
}
rsid = udp._get_rs_id(variant, rs_map, variant_type)
self.assertEqual(rsid, '755532609')
def test_dbsnp_indel_resolution(self):
"""
unit test for _get_rs_id()
Test that we can resolve indels that
have different insertion sequence(s)
for one rsid
15 51766637 374313651 in-del -/A/AA/AAA/AAAA/CAAA/TAAA
"""
udp = UDP('rdf_graph', True)
rs_map = udp._parse_rs_map_file(udp.map_files['dbsnp_map'])
variant_type = 'indel'
variant = {
'build': 'hg19',
'chromosome': 'chr15',
'reference_allele': '-',
'variant_allele': 'AAAA',
'position': '51766637'
}
rsid = udp._get_rs_id(variant, rs_map, variant_type)
self.assertEqual(rsid, '374313651')
def test_dbsnp_indel_resolution(self):
"""
unit test for _get_rs_id()
Test that we can resolve indels that
have different insertion sequence(s)
for one rsid
15 51766637 374313651 in-del -/A/AA/AAA/AAAA/CAAA/TAAA
"""
udp = UDP('rdf_graph', True)
rs_map = udp._parse_rs_map_file(udp.map_files['dbsnp_map'])
variant_type = 'indel'
variant = {
'build': 'hg19',
'chromosome': 'chr15',
'reference_allele': '-',
'variant_allele': 'AAAA',
'position': '51766637'
}
rsid = udp._get_rs_id(variant, rs_map, variant_type)
self.assertEqual(rsid, '374313651')