def test_alignmentmapper_failures(self):
with self.assertRaises(HGVSDataNotAvailableError):
AlignmentMapper(self.hdp,
tx_ac="bogus",
alt_ac="NM_033089.6",
alt_aln_method="splign")
with self.assertRaises(HGVSDataNotAvailableError):
AlignmentMapper(self.hdp,
tx_ac="bogus",
alt_ac="NM_033089.6",
alt_aln_method="transcript")
with self.assertRaises(HGVSDataNotAvailableError):
AlignmentMapper(self.hdp,
tx_ac="NM_033089.6",
alt_ac="bogus",
alt_aln_method="splign")
with self.assertRaises(HGVSDataNotAvailableError):
AlignmentMapper(self.hdp,
tx_ac="NM_000051.3",
alt_ac="NC_000011.9",
alt_aln_method="bogus")
with self.assertRaises(HGVSInvalidIntervalError):
AlignmentMapper(self.hdp, 'NM_000348.3',
'NC_000002.11', 'splign').n_to_g(
self.parser.parse_n_interval("-1"))
with self.assertRaises(HGVSInvalidIntervalError):
AlignmentMapper(self.hdp, 'NM_000348.3',
'NC_000002.11', 'splign').n_to_c(
self.parser.parse_n_interval("-1"))
with self.assertRaises(HGVSInvalidIntervalError):
AlignmentMapper(self.hdp, 'NM_000348.3', 'NC_000002.11',
'splign').c_to_n(
self.parser.parse_c_interval("99999"))
def test_alignmentmapper_AlignmentMapper_LCE3C_uncertain(self):
"""Use NM_178434.2 tests to test mapping with uncertain positions"""
tx_ac = "NM_178434.2"
alt_ac = "NC_000001.10"
tm = AlignmentMapper(self.hdp, tx_ac, alt_ac, alt_aln_method="splign")
parser = hgvs.parser.Parser()
test_cases = [
# ? is not yet supported
# {"g": parser.parse_g_interval("(?_152573139)"), "n": parser.parse_n_interval("(?_2)"), "c": parser.parse_c_interval("(?_-69)")},
# {"g": parser.parse_g_interval("(152573138_?)"), "n": parser.parse_n_interval("(1_?)"), "c": parser.parse_c_interval("(-70_?)")},
]
self.run_cases(tm, test_cases)
def test_alignmentmapper_AlignmentMapper_LCE3C(self):
"""NM_178434.2: LCE3C single exon, strand = +1, all coordinate input/output are in HGVS"""
tx_ac = "NM_178434.2"
alt_ac = "NC_000001.10"
tm = AlignmentMapper(self.hdp, tx_ac, alt_ac, alt_aln_method="splign")
parser = hgvs.parser.Parser()
test_cases = [
# 5'
{
"g": parser.parse_g_interval("152573138"),
"n": parser.parse_n_interval("1"),
"c": parser.parse_c_interval("-70")
},
{
"g": parser.parse_g_interval("152573140"),
"n": parser.parse_n_interval("3"),
"c": parser.parse_c_interval("-68")
},
# cds
{
"g": parser.parse_g_interval("152573207"),
"n": parser.parse_n_interval("70"),
"c": parser.parse_c_interval("-1")
},
{
"g": parser.parse_g_interval("152573208"),
"n": parser.parse_n_interval("71"),
"c": parser.parse_c_interval("1")
},
# 3'
{
"g": parser.parse_g_interval("152573492"),
"n": parser.parse_n_interval("355"),
"c": parser.parse_c_interval("285")
},
{
"g": parser.parse_g_interval("152573493"),
"n": parser.parse_n_interval("356"),
"c": parser.parse_c_interval("*1")
},
{
"g": parser.parse_g_interval("152573560"),
"n": parser.parse_n_interval("423"),
"c": parser.parse_c_interval("*68")
},
{
"g": parser.parse_g_interval("152573562"),
"n": parser.parse_n_interval("425"),
"c": parser.parse_c_interval("*70")
},
]
self.run_cases(tm, test_cases)
def test_alignmentmapper_AlignmentMapper_HIST3H2A(self):
"""NM_033445.2: LCE3C single exon, strand = -1, all coordinate input/output are in HGVS"""
tx_ac = "NM_033445.2"
alt_ac = "NC_000001.10"
tm = AlignmentMapper(self.hdp, tx_ac, alt_ac, alt_aln_method="splign")
parser = hgvs.parser.Parser()
test_cases = [
# 3'
{
"g": parser.parse_g_interval("228645560"),
"n": parser.parse_n_interval("1"),
"c": parser.parse_c_interval("-42")
},
{
"g": parser.parse_g_interval("228645558"),
"n": parser.parse_n_interval("3"),
"c": parser.parse_c_interval("-40")
},
# cds
{
"g": parser.parse_g_interval("228645519"),
"n": parser.parse_n_interval("42"),
"c": parser.parse_c_interval("-1")
},
{
"g": parser.parse_g_interval("228645518"),
"n": parser.parse_n_interval("43"),
"c": parser.parse_c_interval("1")
},
# 5'
{
"g": parser.parse_g_interval("228645126"),
"n": parser.parse_n_interval("435"),
"c": parser.parse_c_interval("393")
},
{
"g": parser.parse_g_interval("228645125"),
"n": parser.parse_n_interval("436"),
"c": parser.parse_c_interval("*1")
},
{
"g": parser.parse_g_interval("228645124"),
"n": parser.parse_n_interval("437"),
"c": parser.parse_c_interval("*2")
},
{
"g": parser.parse_g_interval("228645065"),
"n": parser.parse_n_interval("496"),
"c": parser.parse_c_interval("*61")
},
]
self.run_cases(tm, test_cases)
def test_alignmentmapper_AlignmentMapper_PTH2(self):
"""NM_178449.3: PTH2, two exons, strand = -1, all coordinate input/output are in HGVS"""
tx_ac = "NM_178449.3"
alt_ac = "NC_000019.9"
tm = AlignmentMapper(self.hdp, tx_ac, alt_ac, alt_aln_method="splign")
parser = hgvs.parser.Parser()
test_cases = [
# 3'
{
"g": parser.parse_g_interval("49926698"),
"n": parser.parse_n_interval("1"),
"c": parser.parse_c_interval("-102")
},
# cds
{
"g": parser.parse_g_interval("49926597"),
"n": parser.parse_n_interval("102"),
"c": parser.parse_c_interval("-1")
},
{
"g": parser.parse_g_interval("49926596"),
"n": parser.parse_n_interval("103"),
"c": parser.parse_c_interval("1")
},
# around end of exon 1
{
"g": parser.parse_g_interval("49926469"),
"n": parser.parse_n_interval("230"),
"c": parser.parse_c_interval("128")
},
{
"g": parser.parse_g_interval("49926468"),
"n": parser.parse_n_interval("230+1"),
"c": parser.parse_c_interval("128+1")
},
# span
{
"g": parser.parse_g_interval("49925901_49926467"),
"n": parser.parse_n_interval("230+2_231-2"),
"c": parser.parse_c_interval("128+2_129-2")
},
# around beginning of exon 2
{
"g": parser.parse_g_interval("49925900"),
"n": parser.parse_n_interval("231-1"),
"c": parser.parse_c_interval("129-1")
},
{
"g": parser.parse_g_interval("49925899"),
"n": parser.parse_n_interval("231"),
"c": parser.parse_c_interval("129")
},
# around end of exon 2
{
"g": parser.parse_g_interval("49925725"),
"n": parser.parse_n_interval("405"),
"c": parser.parse_c_interval("303")
},
{
"g": parser.parse_g_interval("49925724"),
"n": parser.parse_n_interval("406"),
"c": parser.parse_c_interval("*1")
},
{
"g": parser.parse_g_interval("49925671"),
"n": parser.parse_n_interval("459"),
"c": parser.parse_c_interval("*54")
},
]
self.run_cases(tm, test_cases)
def test_alignmentmapper_AlignmentMapper_LCE2B(self):
"""NM_014357.4: LCE2B, two exons, strand = +1, all coordinate input/output are in HGVS"""
tx_ac = "NM_014357.4"
alt_ac = "NC_000001.10"
tm = AlignmentMapper(self.hdp, tx_ac, alt_ac, alt_aln_method="splign")
parser = hgvs.parser.Parser()
test_cases = [
# 5'
{
"g": parser.parse_g_interval("152658599"),
"n": parser.parse_n_interval("1"),
"c": parser.parse_c_interval("-54")
},
{
"g": parser.parse_g_interval("152658601"),
"n": parser.parse_n_interval("3"),
"c": parser.parse_c_interval("-52")
},
# cds
{
"g": parser.parse_g_interval("152659319"),
"n": parser.parse_n_interval("54"),
"c": parser.parse_c_interval("-1")
},
{
"g": parser.parse_g_interval("152659320"),
"n": parser.parse_n_interval("55"),
"c": parser.parse_c_interval("1")
},
# around end of exon 1
{
"g": parser.parse_g_interval("152658632"),
"n": parser.parse_n_interval("34"),
"c": parser.parse_c_interval("-21")
},
{
"g": parser.parse_g_interval("152658633"),
"n": parser.parse_n_interval("34+1"),
"c": parser.parse_c_interval("-21+1")
},
# span
{
"g": parser.parse_g_interval("152658633_152659299"),
"n": parser.parse_n_interval("34+1_35-1"),
"c": parser.parse_c_interval("-21+1_-20-1")
},
# around beginning of exon 2
{
"g": parser.parse_g_interval("152659300"),
"n": parser.parse_n_interval("35"),
"c": parser.parse_c_interval("-20")
},
{
"g": parser.parse_g_interval("152659299"),
"n": parser.parse_n_interval("35-1"),
"c": parser.parse_c_interval("-20-1")
},
# around end of exon 2
{
"g": parser.parse_g_interval("152659652"),
"n": parser.parse_n_interval("387"),
"c": parser.parse_c_interval("333")
},
{
"g": parser.parse_g_interval("152659653"),
"n": parser.parse_n_interval("388"),
"c": parser.parse_c_interval("*1")
},
# span
{
"g": parser.parse_g_interval("152659651_152659654"),
"n": parser.parse_n_interval("386_389"),
"c": parser.parse_c_interval("332_*2")
},
# 3'
{
"g": parser.parse_g_interval("152659877"),
"n": parser.parse_n_interval("612"),
"c": parser.parse_c_interval("*225")
},
]
self.run_cases(tm, test_cases)