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# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import pickle
from nose.tools import eq_, with_setup
from pyensembl import Genome, Transcript, Gene, Exon
from pyensembl.species import Species, human
from .common import test_ensembl_releases
from .data import (
TP53_gene_id,
custom_mouse_genome_grcm38_subset,
setup_init_custom_mouse_genome
)
@test_ensembl_releases()
def test_pickle_ensembl_gene(ensembl_genome):
gene = ensembl_genome.gene_by_id(TP53_gene_id)
gene_new = pickle.loads(pickle.dumps(gene))
eq_(gene, gene_new)
@test_ensembl_releases()
def test_pickle_ensembl_transcript(ensembl_genome):
gene = ensembl_genome.gene_by_id(TP53_gene_id)
transcript = gene.transcripts[0]
transcript_reconstructed = pickle.loads(pickle.dumps(transcript))
eq_(transcript, transcript_reconstructed)
@test_ensembl_releases()
def test_pickle_ensembl_exon(ensembl_genome):
gene = ensembl_genome.gene_by_id(TP53_gene_id)
transcript = gene.transcripts[0]
exon = transcript.exons[0]
exon_reconstructed = pickle.loads(pickle.dumps(exon))
eq_(exon, exon_reconstructed)
@test_ensembl_releases()
def test_json_ensembl_gene(ensembl_genome):
gene = ensembl_genome.gene_by_id(TP53_gene_id)
gene_reconstructed = Gene.from_json(gene.to_json())
eq_(gene, gene_reconstructed)
@test_ensembl_releases()
def test_json_ensembl_transcript(ensembl_genome):
gene = ensembl_genome.gene_by_id(TP53_gene_id)
transcript = gene.transcripts[0]
transcript_reconstructed = Transcript.from_json(transcript.to_json())
eq_(transcript, transcript_reconstructed)
@test_ensembl_releases()
def test_json_ensembl_exon(ensembl_genome):
gene = ensembl_genome.gene_by_id(TP53_gene_id)
transcript = gene.transcripts[0]
exon = transcript.exons[0]
exon_reconstructed = Exon.from_json(exon.to_json())
eq_(exon, exon_reconstructed)
@test_ensembl_releases()
def test_pickle_ensembl_genome(ensembl_genome):
genome_pickled = pickle.dumps(ensembl_genome)
genome_reconstructed = pickle.loads(genome_pickled)
eq_(ensembl_genome, genome_reconstructed)
# This Genome happens to be an EnsemblRelease; test that too.
eq_(ensembl_genome.release, genome_reconstructed.release)
eq_(ensembl_genome.species, genome_reconstructed.species)
@test_ensembl_releases()
def test_ensembl_genome_to_dict(ensembl_genome):
genome_dict = ensembl_genome.to_dict()
genome_reconstructed = ensembl_genome.__class__.from_dict(genome_dict)
eq_(ensembl_genome, genome_reconstructed)
@test_ensembl_releases()
def test_ensembl_genome_to_json(ensembl_genome):
genome_json = ensembl_genome.to_json()
genome_class = ensembl_genome.__class__
genome_reconstructed = genome_class.from_json(genome_json)
eq_(ensembl_genome, genome_reconstructed)
@with_setup(setup=setup_init_custom_mouse_genome)
def test_custom_genome_to_json():
json = custom_mouse_genome_grcm38_subset.to_json()
reconstructed = Genome.from_json(json)
eq_(custom_mouse_genome_grcm38_subset, reconstructed)
@with_setup(setup=setup_init_custom_mouse_genome)
def test_custom_genome_to_dict():
reconstructed = Genome.from_dict(custom_mouse_genome_grcm38_subset.to_dict())
eq_(custom_mouse_genome_grcm38_subset, reconstructed)
def test_species_to_dict():
eq_(human, Species.from_dict(human.to_dict()))
def test_species_to_json():
eq_(human, Species.from_json(human.to_json()))
def test_species_to_pickle():
eq_(human, pickle.loads(pickle.dumps(human)))
@test_ensembl_releases()
def test_unique_memory_address_of_unpickled_genomes(ensembl_genome):
unpickled = pickle.loads(pickle.dumps(ensembl_genome))
assert ensembl_genome is unpickled, \
"Expected same object for %s but got two different instances" % (unpickled,)
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