def from_hgvs(self, hgvs_expr):
"""parse hgvs into a VR object (typically an Allele)
#>>> a = tlr.from_hgvs("NM_012345.6:c.22A>T")
#>>> a.as_dict()
{
'location': {
'interval': {'end': 22, 'start': 21, 'type': 'SimpleInterval'},
'sequence_id': 'refseq:NM_012345.6',
'type': 'SequenceLocation'
},
'state': {'sequence': 'T', 'type': 'SequenceState'},
'type': 'Allele'
}
"""
sv = self._hgvs_parser.parse_hgvs_variant(hgvs_expr)
# prefix accession with namespace
sequence_id = coerce_namespace(sv.ac)
if isinstance(sv.posedit.pos, hgvs.location.BaseOffsetInterval):
if sv.posedit.pos.start.is_intronic or sv.posedit.pos.end.is_intronic:
raise ValueError(
"Intronic HGVS variants are not supported ({sv.posedit})")
if sv.posedit.edit.type == 'ins':
interval = models.SimpleInterval(start=sv.posedit.pos.start.base,
end=sv.posedit.pos.start.base)
state = sv.posedit.edit.alt
elif sv.posedit.edit.type in ('sub', 'del', 'delins', 'identity'):
interval = models.SimpleInterval(start=sv.posedit.pos.start.base -
1,
end=sv.posedit.pos.end.base)
if sv.posedit.edit.type == 'identity':
state = self.data_proxy.get_sequence(
sv.ac, sv.posedit.pos.start.base - 1,
sv.posedit.pos.end.base)
else:
state = sv.posedit.edit.alt or ''
else:
raise ValueError(
f"HGVS variant type {sv.posedit.edit.type} is unsupported")
location = models.Location(sequence_id=sequence_id, interval=interval)
sstate = models.SequenceState(sequence=state)
allele = models.Allele(location=location, state=sstate)
allele = self._post_process_imported_allele(allele)
return allele
def from_beacon(self, beacon_expr, assembly_name=None):
"""Parse beacon expression into VR Allele
#>>> a = tlr.from_beacon("13 : 32936732 G > C")
#>>> a.as_dict()
{'location': {'interval': {'end': 32936732,
'start': 32936731,
'type': 'SimpleInterval'},
'sequence_id': 'GRCh38:13 ',
'type': 'SequenceLocation'},
'state': {'sequence': 'C', 'type': 'SequenceState'},
'type': 'Allele'}
"""
m = beacon_re.match(beacon_expr.replace(" ", ""))
if not m:
raise ValueError(f"Not a Beacon expression: {beacon_expr}")
g = m.groupdict()
if assembly_name is None:
assembly_name = self.default_assembly_name
sequence_id = assembly_name + ":" + g["chr"]
start = int(g["pos"]) - 1
ref = g["ref"]
alt = g["alt"]
end = start + len(ref)
ins_seq = alt
interval = models.SimpleInterval(start=start, end=end)
location = models.Location(sequence_id=sequence_id, interval=interval)
sstate = models.SequenceState(sequence=ins_seq)
allele = models.Allele(location=location, state=sstate)
allele = self._post_process_imported_allele(allele)
return allele
def from_vcf(self, vcf_expr, assembly_name=None):
"""Parse gnomAD-style VCF expression into VR Allele
#>>> a = tlr.from_vcf("1-55516888-G-GA")
#>>> a.as_dict()
{'location': {'interval': {'end': 55516888,
'start': 55516887,
'type': 'SimpleInterval'},
'sequence_id': 'GRCh38:1',
'type': 'SequenceLocation'},
'state': {'sequence': 'GA', 'type': 'SequenceState'},
'type': 'Allele'}
"""
m = vcf_re.match(vcf_expr)
if not m:
raise ValueError(f"Not a vcf/gnomAD expression: {vcf_expr}")
g = m.groupdict()
if assembly_name is None:
assembly_name = self.default_assembly_name
sequence_id = assembly_name + ":" + g["chr"]
start = int(g["pos"]) - 1
ref = g["ref"]
alt = g["alt"]
end = start + len(ref)
ins_seq = alt
interval = models.SimpleInterval(start=start, end=end)
location = models.Location(sequence_id=sequence_id, interval=interval)
sstate = models.SequenceState(sequence=ins_seq)
allele = models.Allele(location=location, state=sstate)
allele = self._post_process_imported_allele(allele)
return allele
def from_spdi(self, spdi_expr):
"""Parse SPDI expression in to a GA4GH Allele
#>>> a = tlr.from_spdi("NM_012345.6:21:1:T")
#>>> a.as_dict()
{
'location': {
'interval': {'end': 22, 'start': 21, 'type': 'SimpleInterval'},
'sequence_id': 'refseq:NM_012345.6',
'type': 'SequenceLocation'
},
'state': {'sequence': 'T', 'type': 'SequenceState'},
'type': 'Allele'
}
"""
m = spdi_re.match(spdi_expr)
if not m:
raise ValueError(f"Not a SPDI expression: {spdi_expr}")
g = m.groupdict()
sequence_id = coerce_namespace(g["ac"])
start = int(g["pos"])
try:
del_len = int(g["del_len_or_seq"])
except ValueError:
del_len = len(g["del_len_or_seq"])
end = start + del_len
ins_seq = g["ins_seq"]
interval = models.SimpleInterval(start=start, end=end)
location = models.Location(sequence_id=sequence_id, interval=interval)
sstate = models.SequenceState(sequence=ins_seq)
allele = models.Allele(location=location, state=sstate)
allele = self._post_process_imported_allele(allele)
return allele
def test_SimpleInterval(test):
o = models.SimpleInterval(**test["in"])
assert test["out"]["ga4gh_serialize"] == ga4gh_serialize(o).decode()