def maybe_make_db(self):
"""Get GFFutils database from file or create from a gtf"""
if self.gffutils_db is not None:
copied_db = os.path.join(self.gtf_folder,
os.path.basename(self.gffutils_db))
util.progress('Copying gffutils database from {} to {} '
'...'.format(self.gffutils_db, copied_db))
shutil.copyfile(self.gffutils_db, copied_db)
util.done()
util.progress('Reading gffutils database from {} ...'.format(
copied_db))
db = gffutils.FeatureDB(copied_db)
util.done()
else:
basename = os.path.basename(self.gtf_filename)
db_filename = os.path.join(self.gtf_folder,
'{}.db'.format(basename))
util.progress("Found GTF file in {}".format(self.gtf_filename))
try:
db = gffutils.FeatureDB(db_filename)
util.progress(
"Found existing built outrigger-built gffutils database "
"file in {}".format(db_filename))
except (ValueError, TypeError):
util.progress(
'Creating a "gffutils" '
'database {} ...'.format(db_filename))
db = gtf.create_db(self.gtf_filename, db_filename)
util.done()
return db
def test_create_db(gtf_filename, db, snap25_exon_id):
from outrigger.io import gtf
true = db
test = gtf.create_db(gtf_filename, 'test.gtf.db')
# Check that all the true db features are in the test database
for featuretype in true.featuretypes():
for feature in true.features_of_type(featuretype=featuretype):
try:
test[feature.id]
except gffutils.FeatureNotFoundError:
pytest.fail('Feature in true database not found in test '
'database')
# Check that all the test db features are in the true database
for featuretype in test.featuretypes():
for feature in test.features_of_type(featuretype=featuretype):
try:
true[feature.id]
except gffutils.FeatureNotFoundError:
pytest.fail('Feature in test database not found in true '
'database')
# SNAP25 should be in both the true and test databases
assert true[snap25_exon_id] is not None
assert test[snap25_exon_id] is not None