def test_store_biopython_seq_record_DOI(self):
"""Tests - __init__ and store_biopython_seq_record with DOI."""
# DOI TESTING
db2 = BibDatabase()
db2.entries = [{
"journal": "Nice Journal",
"comments": "A comment",
"pages": "12--23",
"month": "jan",
"abstract": "This is an abstract. This line should be "
"long enough to test multilines...",
"title": "An amazing title",
"year": "2013",
"doi": "10.1186/s12864-016-2535-300002",
"volume": "12",
"ID": "Teste2018",
"author": "Foo, b. and Foo1, b. and Foo b.",
"keyword": "keyword1, keyword2",
"ENTRYTYPE": "article",
}]
for entry in db2.entries:
bibtest3 = PublicationLoader()
bibtest3.store_bibtex_entry(entry)
test_bibtex3 = Pub.objects.get(uniquename="Teste2018")
test_bibtex3_pubdbxref = PubDbxref.objects.get(pub=test_bibtex3)
test_bibtex3_dbxref = Dbxref.objects.get(
dbxref_id=test_bibtex3_pubdbxref.dbxref_id)
self.assertEqual("10.1186/s12864-016-2535-300002",
test_bibtex3_dbxref.accession)
Organism.objects.create(genus="Mus", species="musculus")
test_seq_file_pub = SequenceLoader(
filename="sequence_doi.fasta",
doi="10.1186/s12864-016-2535-300002")
test_seq_obj_pub = SeqRecord(Seq("acgtgtgtgcatgctagatcgatgcatgca"),
id="chr2",
description="chromosome 2")
test_seq_file_pub.store_biopython_seq_record(test_seq_obj_pub,
"assembly",
"Mus musculus")
test_feature_doi = Feature.objects.get(name="chromosome 2")
self.assertEqual("chr2", test_feature_doi.uniquename)
test_feature_pub_doi = FeaturePub.objects.get(
pub_id=test_bibtex3.pub_id)
test_pub_dbxref_doi = PubDbxref.objects.get(
pub_id=test_feature_pub_doi.pub_id)
test_dbxref_doi = Dbxref.objects.get(
dbxref_id=test_pub_dbxref_doi.dbxref_id)
self.assertEqual("10.1186/s12864-016-2535-300002",
test_dbxref_doi.accession)
# test remove_file
self.assertTrue(
Dbxrefprop.objects.filter(value="sequence_doi.fasta").exists())
call_command("remove_file", "--name=sequence_doi.fasta",
"--verbosity=0")
self.assertFalse(
Dbxrefprop.objects.filter(value="sequence_doi.fasta").exists())
def handle(
self, file: str, soterm: str, verbosity: int = 1, cpu: int = 1, **options
):
"""Execute the main function."""
try:
FileValidator().validate(file)
except ImportingError as e:
raise CommandError(e)
# retrieve only the file name
filename = os.path.basename(file)
try:
sequence_file = SequenceLoader(filename=filename)
except ImportingError as e:
raise CommandError(e)
if verbosity > 0:
self.stdout.write("Processing file: {}".format(filename))
fasta_sequences = SeqIO.parse(open(file), "fasta")
pool = ThreadPoolExecutor(max_workers=cpu)
tasks = list()
for fasta in fasta_sequences:
tasks.append(
pool.submit(sequence_file.add_sequence_to_feature, fasta, soterm)
)
if verbosity > 0:
self.stdout.write("Loading")
for task in tqdm(as_completed(tasks), total=len(tasks)):
if task.result():
raise (task.result())
pool.shutdown()
if verbosity > 0:
self.stdout.write(self.style.SUCCESS("Done with {}".format(filename)))
def test_store_biopython_seq_record(self):
"""Tests - __init__ and store_biopython_seq_record."""
# test insert sequence
Organism.objects.create(genus="Mus", species="musculus")
test_seq_file = SequenceLoader(filename="sequence.fasta")
test_seq_obj = SeqRecord(Seq("acgtgtgtgcatgctagatcgatgcatgca"),
id="chr1",
description="chromosome 1")
test_seq_file.store_biopython_seq_record(test_seq_obj, "assembly",
"Mus musculus")
test_feature = Feature.objects.get(uniquename="chr1",
organism__genus="Mus",
organism__species="musculus")
self.assertEqual("chr1", test_feature.uniquename)
self.assertEqual("chromosome 1", test_feature.name)
self.assertEqual("acgtgtgtgcatgctagatcgatgcatgca",
test_feature.residues)
# test insert no sequence
test_seq_obj = SeqRecord(Seq("acgtgtgtgcatgctagatcgatgcatgca"),
id="chr2")
test_seq_file.store_biopython_seq_record(test_seq_obj,
"assembly",
"Mus musculus",
ignore_residues=True)
test_feature = Feature.objects.get(uniquename="chr2")
self.assertEqual("chr2", test_feature.uniquename)
self.assertEqual("", test_feature.residues)
# test fail insert same id, different organism
# dbxref.accession must be unique
Organism.objects.create(genus="H**o", species="sapiens")
test_seq_file = SequenceLoader(filename="sequence2.fasta")
test_seq_obj = SeqRecord(
Seq("atgctagctagcatgactgactggtgcagtgcatgca"),
id="chr1",
description="chromosome 1",
)
with self.assertRaises(IntegrityError):
test_seq_file.store_biopython_seq_record(test_seq_obj, "assembly",
"H**o sapiens")
def handle(self,
file: str,
organism: str,
soterm: str,
nosequence: bool = False,
cpu: int = 1,
description: str = None,
url: str = None,
doi: str = None,
verbosity: int = 1,
**options) -> None:
"""Execute the main function."""
if verbosity > 0:
self.stdout.write("Preprocessing")
try:
FileValidator().validate(file)
except ImportingError as e:
raise CommandError(e)
# retrieve only the file name
filename = os.path.basename(file)
try:
sequence_file = SequenceLoader(filename=filename,
description=description,
url=url,
doi=doi)
except ImportingError as e:
raise CommandError(e)
fasta_sequences = SeqIO.parse(open(file), "fasta")
pool = ThreadPoolExecutor(max_workers=cpu)
tasks = list()
for fasta in fasta_sequences:
tasks.append(
pool.submit(
sequence_file.store_biopython_seq_record,
fasta,
soterm,
organism,
nosequence,
))
if verbosity > 0:
self.stdout.write("Loading")
for task in tqdm(as_completed(tasks), total=len(tasks)):
if task.result():
raise (task.result())
pool.shutdown()
if verbosity > 0:
self.stdout.write(self.style.SUCCESS("Done"))
def test_add_sequence_to_feature(self):
"""Tests - add_sequence_to_feature."""
# test insert sequence
Organism.objects.create(genus="Mus", species="musculus")
test_seq_file = SequenceLoader(filename="sequence.fasta")
test_seq_obj = SeqRecord(Seq("acgtgtgtgcatgctagatcgatgcatgca"),
id="chr1",
description="chromosome 1")
test_seq_file.store_biopython_seq_record(test_seq_obj, "assembly",
"Mus musculus")
# test add_sequence_to_feature
test_seq_obj = SeqRecord(Seq("aaaaaaaaaaaaaaaaaaaa"),
id="chr1",
description="chromosome 1")
test_seq_file.add_sequence_to_feature(test_seq_obj, "assembly")
test_feature_seq = Feature.objects.get(uniquename="chr1")
self.assertEqual("aaaaaaaaaaaaaaaaaaaa", test_feature_seq.residues)
def test_fail_biopython_seq_record(self):
"""Tests fail __init__ and store_biopython_seq_record."""
# sequence already registered
Organism.objects.create(genus="Mus", species="musculus")
with self.assertRaises(ImportingError):
test_seq_file = SequenceLoader(filename="sequence.fasta")
test_seq_obj = SeqRecord(
Seq("acgtgtgtgcatgctagatcgatgcatgca"),
id="chr1",
description="chromosome 1",
)
test_seq_file.store_biopython_seq_record(test_seq_obj, "assembly",
"Mus musculus")
test_seq_obj = SeqRecord(
Seq("acgtgtgtgcatgctagatcgatgcatgca"),
id="chr1",
description="chromosome 1",
)
test_seq_file.store_biopython_seq_record(test_seq_obj, "assembly",
"Mus musculus")