def run(self):
ReadPairImporter._check_database(self.db, self.seqrep_id,
self.isolate_id,
self.sequence_replicate_number)
for filename in self.reads_file_1, self.reads_file_2:
if not os.path.exists(filename):
raise Error('Error! Reads file ' + filename +
' not found, Cannot continue.')
iso_dir = isolate_dir.IsolateDir(self.pipeline_root_dir,
self.sample_id, self.isolate_id)
iso_dir.make_essential_dirs()
lock_file = os.path.join(iso_dir.reads_dir,
'import_lock.' + str(self.seqrep_id))
if os.path.exists(lock_file):
raise Error('Error! Lock file ' + lock_file +
' found. Cannot continue')
utils.make_empty_file(lock_file)
try:
fqtools.validate([self.reads_file_1, self.reads_file_2])
ReadPairImporter._copy_reads_file(
self.reads_file_1,
iso_dir.reads_filename('original',
self.sequence_replicate_number, 1),
self.reads_file_md5_1)
ReadPairImporter._copy_reads_file(
self.reads_file_2,
iso_dir.reads_filename('original',
self.sequence_replicate_number, 2),
self.reads_file_md5_2)
ReadPairImporter._update_database(self.db,
self.seqrep_id,
self.isolate_id,
self.sequence_replicate_number,
import_status=1)
os.unlink(self.reads_file_1)
os.unlink(self.reads_file_2)
for filename in (self.reads_file_1 + '.md5',
self.reads_file_2 + '.md5'):
if os.path.exists(filename):
os.unlink(filename)
self.db.commit_and_close()
os.unlink(lock_file)
except:
ReadPairImporter._update_database(self.db,
self.seqrep_id,
self.isolate_id,
self.sequence_replicate_number,
import_status=-1)
self.db.commit_and_close()
if os.path.exists(lock_file):
os.unlink(lock_file)
def test_validate(self):
"""test validate"""
bad_file = os.path.join(data_dir, "validate.bad.fq")
with self.assertRaises(Exception):
fqtools.validate([bad_file])
bad_pair_1 = os.path.join(data_dir, "validate.bad.pair.1.fq")
bad_pair_2 = os.path.join(data_dir, "validate.bad.pair.2.fq")
with self.assertRaises(Exception):
fqtools.validate([bad_pair_1, bad_pair_2])
ok_pair_1 = os.path.join(data_dir, "validate.ok.pair.1.fq")
ok_pair_2 = os.path.join(data_dir, "validate.ok.pair.2.fq")
fqtools.validate([ok_pair_1, ok_pair_2])
def test_validate(self):
'''test validate'''
bad_file = os.path.join(data_dir, 'validate.bad.fq')
with self.assertRaises(fqtools.Error):
fqtools.validate([bad_file])
bad_pair_1 = os.path.join(data_dir, 'validate.bad.pair.1.fq')
bad_pair_2 = os.path.join(data_dir, 'validate.bad.pair.2.fq')
with self.assertRaises(fqtools.Error):
fqtools.validate([bad_pair_1, bad_pair_2])
ok_pair_1 = os.path.join(data_dir, 'validate.ok.pair.1.fq')
ok_pair_2 = os.path.join(data_dir, 'validate.ok.pair.2.fq')
fqtools.validate([ok_pair_1, ok_pair_2])