def add_location(self, seqid, gene, params, sr):
"""Get a gene's Sequence Location.
:param str seqid: The sequence ID.
:param Feature gene: A gene from the source file.
:param dict params: The transformed gene record.
:param SeqRepo sr: Access to the SeqRepo
:return: A dictionary of a GA4GH VRS SequenceLocation.
"""
location = dict()
aliases = self.get_aliases(sr, seqid)
if not aliases:
return location
sequence_id = [a for a in aliases if a.startswith('ga4gh')][0]
if gene.start != '.' and gene.end != '.' and sequence_id:
if 0 <= gene.start <= gene.end:
seq_location = models.SequenceLocation(
sequence_id=sequence_id,
start=models.Number(value=gene.start - 1, type="Number"),
end=models.Number(value=gene.end, type="Number"),
type="SequenceLocation"
)
seq_location.id = ga4gh_identify(seq_location)
location = seq_location.as_dict()
else:
logger.info(f"{params['concept_id']} has invalid interval:"
f"start={gene.start - 1} end={gene.end}")
return location
def add_location(self, location):
"""Get a gene's Chromosome Location.
:param dict location: A gene's location.
:return: A dictionary of a GA4GH VRS ChromosomeLocation.
"""
chr_location = models.ChromosomeLocation(species_id="taxonomy:9606",
chr=location['chr'],
start=location['start'],
end=location['end'],
type="ChromosomeLocation")
chr_location.id = ga4gh_identify(chr_location)
return chr_location.as_dict()
def test_vr():
assert a.as_dict() == allele_dict
assert ga4gh_serialize(
a.location.interval
) == b'{"end":55181320,"start":55181319,"type":"SimpleInterval"}'
assert ga4gh_serialize(
a.location
) == b'{"interval":{"end":55181320,"start":55181319,"type":"SimpleInterval"},"sequence_id":"F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul","type":"SequenceLocation"}'
assert sha512t24u(ga4gh_serialize(
a.location)) == '5D9eG-ev4fA7mYIpOpDEe-4Am1lzPZlQ'
assert ga4gh_digest(a.location) == '5D9eG-ev4fA7mYIpOpDEe-4Am1lzPZlQ'
assert ga4gh_identify(
a.location) == 'ga4gh:VSL.5D9eG-ev4fA7mYIpOpDEe-4Am1lzPZlQ'
assert ga4gh_serialize(
a
) == b'{"location":"5D9eG-ev4fA7mYIpOpDEe-4Am1lzPZlQ","state":{"sequence":"T","type":"SequenceState"},"type":"Allele"}'
assert ga4gh_digest(a) == 'vU0meY5wGjpyRLCjSxCfb2Jlruyn2adL'
assert ga4gh_identify(a) == 'ga4gh:VA.vU0meY5wGjpyRLCjSxCfb2Jlruyn2adL'
assert a.as_dict() == {
'location': {
'interval': {
'end': 55181320,
'start': 55181319,
'type': 'SimpleInterval'
},
'sequence_id': 'ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul',
'type': 'SequenceLocation'
},
'state': {
'sequence': 'T',
'type': 'SequenceState'
},
'type': 'Allele'
}
def _post_process_imported_allele(self, allele):
"""Provide common post-processing for imported Alleles IN-PLACE.
"""
if self.translate_sequence_identifiers:
seq_id = self.data_proxy.translate_sequence_identifier(
allele.location.sequence_id._value, "ga4gh")[0]
allele.location.sequence_id = seq_id
if self.normalize:
self._normalize_allele(allele)
if self.identify:
allele._id = ga4gh_identify(allele)
return allele
def put(body):
request = body
defn = request.pop("definition")
av = get_anyvar()
messages = []
if "members" in defn:
return {"messages": ["unsupported"]}, 400
if "member_ids" in defn:
vo = models.VariationSet(members=defn["member_ids"])
vo._id = ga4gh_identify(vo)
av.put_object(vo)
result = {
"messages": messages,
"data": vo.as_dict(),
}
return result, 200
a0_dict = {
'location': {
'interval': {'end': 44908822, 'start': 44908821, 'type': 'SimpleInterval'},
'sequence_id': 'ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl',
'type': 'SequenceLocation'
},
'state': {
'sequence': 'T',
'type': 'SequenceState'
},
'type': 'Allele'
}
a0 = models.Allele(**a0_dict)
a0id = ga4gh_identify(a0)
assert a0id == "ga4gh:VA.EgHPXXhULTwoP4-ACfs-YCXaeUQJBjH_"
a0._id = a0id
a0l = a0.location
a0lid = ga4gh_identify(a0l)
assert a0lid == "ga4gh:VSL.u5fspwVbQ79QkX6GHLF8tXPCAXFJqRPx"
ros.redis.flushdb() # Danger!
# db looks empty?
assert len(ros) == 0
assert list(ros.keys()) == []
# add Allele
def create_text(self, defn):
vo = models.Text(definition=defn)
vo._id = ga4gh_identify(vo)
return vo
def put_object(self, vo):
v = vrs_enref(vo, self.object_store)
_id = ga4gh_identify(v)
return _id
