def test_serialization():
original = VariantCollection([
Variant(
1, start=10, ref="AA", alt="AAT", ensembl=77),
Variant(10, start=15, ref="A", alt="G"),
Variant(20, start=150, ref="", alt="G"),
])
original.metadata[original[0]] = {"a": "b"}
original.metadata[original[2]] = {"bar": 2}
# This causes the variants' ensembl objects 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_(reconstituted[0], original[0])
eq_(reconstituted.metadata[original[0]], original.metadata[original[0]])
# Test json.
serialized = original.to_json()
reconstituted = VariantCollection.from_json(serialized)
eq_(original, reconstituted)
eq_(reconstituted[0], original[0])
eq_(reconstituted.metadata[original[0]], original.metadata[original[0]])
def variant_collection_from_args(args):
variant_collections = []
if args.reference_name:
genome = genome_for_reference_name(args.reference_name)
else:
# no genome specified, assume it can be inferred from the file(s)
# we're loading
genome = None
for vcf_path in args.vcf:
vcf_variants = load_vcf(vcf_path, genome=genome)
variant_collections.append(vcf_variants)
for maf_path in args.maf:
maf_variants = load_maf(maf_path)
variant_collections.append(maf_variants)
if args.variant:
if not genome:
raise ValueError(
"--reference-name must be specified when using --variant")
variants = [
Variant(
chromosome,
start=position,
ref=ref,
alt=alt,
ensembl=genome)
for (chromosome, position, ref, alt)
in args.variant
]
variant_collection = VariantCollection(variants)
variant_collections.append(variant_collection)
if len(variant_collections) == 0:
raise ValueError(
"No variants loaded (use --maf, --vcf, or --variant options)")
for json_path in args.json_variant_files:
with open(json_path, 'r') as f:
json_string = f.read()
variant_collections.append(
VariantCollection.from_json(json_string))
if len(variant_collections) == 0:
raise ValueError(
"No variants loaded (use --maf, --vcf, --json-variants options)")
elif len(variant_collections) == 1:
return variant_collections[0]
else:
combined_variants = []
for variant_collection in variant_collections:
combined_variants.extend(list(variant_collection))
return VariantCollection(combined_variants)
def variant_collection_from_args(args):
variant_collections = []
if args.reference_name:
genome = genome_for_reference_name(args.reference_name)
else:
# no genome specified, assume it can be inferred from the file(s)
# we're loading
genome = None
for vcf_path in args.vcf:
vcf_variants = load_vcf(vcf_path, genome=genome)
variant_collections.append(vcf_variants)
for maf_path in args.maf:
maf_variants = load_maf(maf_path)
variant_collections.append(maf_variants)
if args.variant:
if not genome:
raise ValueError(
"--reference-name must be specified when using --variant")
variants = [
Variant(chromosome,
start=position,
ref=ref,
alt=alt,
ensembl=genome)
for (chromosome, position, ref, alt) in args.variant
]
variant_collection = VariantCollection(variants)
variant_collections.append(variant_collection)
if len(variant_collections) == 0:
raise ValueError(
"No variants loaded (use --maf, --vcf, or --variant options)")
for json_path in args.json_variant_files:
with open(json_path, 'r') as f:
json_string = f.read()
variant_collections.append(
VariantCollection.from_json(json_string))
if len(variant_collections) == 0:
raise ValueError(
"No variants loaded (use --maf, --vcf, --json-variants options)")
elif len(variant_collections) == 1:
return variant_collections[0]
else:
combined_variants = []
for variant_collection in variant_collections:
combined_variants.extend(list(variant_collection))
return VariantCollection(combined_variants)
def test_variant_collection_serialization():
variant_list = [
Variant(1, start=10, ref="AA", alt="AAT"),
Variant(10, start=15, ref="A", alt="G"),
Variant(20, start=150, ref="", alt="G"),
]
original = VariantCollection(
variant_list,
source_to_metadata_dict={
"test_data":
{variant: {
"a": "b",
"bar": 2
}
for variant in variant_list}
})
# This causes the variants' ensembl objects 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()
original_first_variant = original[0]
original_metadata = original.metadata
# Test pickling
reconstructed = pickle.loads(pickle.dumps(original))
eq_(original, reconstructed)
eq_(reconstructed[0], original_first_variant)
eq_(reconstructed.metadata[original_first_variant],
original_metadata[original_first_variant])
merged = original.intersection(original)
merged_reconstructed = pickle.loads(pickle.dumps(merged))
eq_(merged, merged_reconstructed)
# Test JSON serialization
variants_from_json = VariantCollection.from_json(original.to_json())
eq_(original, variants_from_json)
eq_(variants_from_json[0], original_first_variant)
# pylint: disable=no-member
eq_(variants_from_json.metadata[original_first_variant],
original_metadata[original_first_variant])
def test_variant_collection_serialization():
variant_list = [
Variant(
1, start=10, ref="AA", alt="AAT"),
Variant(10, start=15, ref="A", alt="G"),
Variant(20, start=150, ref="", alt="G"),
]
original = VariantCollection(
variant_list,
source_to_metadata_dict={
"test_data":
{variant: {"a": "b", "bar": 2} for variant in variant_list}})
# This causes the variants' ensembl objects 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()
original_first_variant = original[0]
original_metadata = original.metadata
# Test pickling
reconstructed = pickle.loads(pickle.dumps(original))
eq_(original, reconstructed)
eq_(reconstructed[0], original_first_variant)
eq_(reconstructed.metadata[original_first_variant],
original_metadata[original_first_variant])
merged = original.intersection(original)
merged_reconstructed = pickle.loads(pickle.dumps(merged))
eq_(merged, merged_reconstructed)
# Test JSON serialization
variants_from_json = VariantCollection.from_json(original.to_json())
eq_(original, variants_from_json)
eq_(variants_from_json[0], original_first_variant)
# pylint: disable=no-member
eq_(variants_from_json.metadata[original_first_variant],
original_metadata[original_first_variant])
