def test_serialization():
variants = [
Variant(1, start=10, ref="AA", alt="AAT", ensembl=ensembl77),
Variant(10, start=15, ref="A", alt="G"),
Variant(20, start=150, ref="", alt="G"),
]
for original in variants:
# This causes the variant's ensembl object to make a SQL connection,
# which makes the ensembl object non-serializable. By calling this
# method, we are checking that we don't attempt to directly serialize
# the ensembl object.
original.effects()
# Test pickling.
serialized = pickle.dumps(original)
reconstituted = pickle.loads(serialized)
assert original == reconstituted
assert original.contig == reconstituted.contig
assert original.ref == reconstituted.ref
assert original.alt == reconstituted.alt
assert original.start == reconstituted.start
assert original.end == reconstituted.end
# Test json.
serialized = original.to_json()
reconstituted = Variant.from_json(serialized)
assert original == reconstituted
def test_serialization():
variants = [
Variant(
1, start=10, ref="AA", alt="AAT", ensembl=ensembl_grch38),
Variant(10, start=15, ref="A", alt="G"),
Variant(20, start=150, ref="", alt="G"),
]
for original in variants:
# This causes the variant's ensembl object to make a SQL connection,
# which makes the ensembl object non-serializable. By calling this
# method, we are checking that we don't attempt to directly serialize
# the ensembl object.
original.effects()
# Test pickling.
serialized = pickle.dumps(original)
reconstituted = pickle.loads(serialized)
eq_(original, reconstituted)
eq_(original.contig, reconstituted.contig)
eq_(original.ref, reconstituted.ref)
eq_(original.alt, reconstituted.alt)
eq_(original.start, reconstituted.start)
eq_(original.end, reconstituted.end)
eq_(original.original_ref, reconstituted.original_ref)
eq_(original.original_alt, reconstituted.original_alt)
eq_(original.original_start, reconstituted.original_start)
# Test json.
serialized = original.to_json()
reconstituted = Variant.from_json(serialized)
eq_(original, reconstituted)
def test_serialization():
variants = [
Variant(
1, start=10, ref="AA", alt="AAT", genome=ensembl_grch38),
Variant(10, start=15, ref="A", alt="G"),
Variant(20, start=150, ref="", alt="G"),
]
for original in variants:
# This causes the variant's ensembl object to make a SQL connection,
# which makes the ensembl object non-serializable. By calling this
# method, we are checking that we don't attempt to directly serialize
# the ensembl object.
original.effects()
# Test pickling.
serialized = pickle.dumps(original)
reconstituted = pickle.loads(serialized)
eq_(original, reconstituted)
eq_(original.contig, reconstituted.contig)
eq_(original.ref, reconstituted.ref)
eq_(original.alt, reconstituted.alt)
eq_(original.start, reconstituted.start)
eq_(original.end, reconstituted.end)
eq_(original.original_ref, reconstituted.original_ref)
eq_(original.original_alt, reconstituted.original_alt)
eq_(original.original_start, reconstituted.original_start)
# Test json.
serialized = original.to_json()
reconstituted = Variant.from_json(serialized)
eq_(original, reconstituted)
def test_deserialization_old_keywords():
old_variant_representation_json = """
{
"ref": "T",
"contig": "22",
"start": 23230319,
"__class__": {
"__name__": "Variant",
"__module__": "varcode.variant"
},
"normalize_contig_name": true,
"alt": "G",
"allow_extended_nucleotides": false,
"ensembl": {
"__class__": {
"__name__": "EnsemblRelease",
"__module__": "pyensembl.ensembl_release"
},
"release": 75,
"server": "ftp://ftp.ensembl.org",
"species": {
"__class__": {
"__name__": "Species",
"__module__": "pyensembl.species"
},
"latin_name": "homo_sapiens"
}
}
}
"""
variant = Variant.from_json(old_variant_representation_json)
eq_(variant.contig, "22")
eq_(variant.ref, "T")
eq_(variant.alt, "G")
eq_(variant.reference_name, "GRCh37")
eq_(variant.normalize_contig_names, True)
eq_(variant.allow_extended_nucleotides, False)
