def test_genome(db):
session = Session(db, from_id='testid')
assert session.genome == {}
genome = {
'locus':
'NC_003888',
'definition':
'Streptomyces coelicolor A3(2) chromosome, complete genome.',
'source':
'Streptomyces coelicolor A3(2)',
'orfs': [
{
'id': 'SCO4711',
'start': 5132708,
'end': 5132995,
'strand': 1,
'gene': 'rpsQ'
},
],
'clusters': [
{
'start':
235986,
'end':
271084,
'name':
"Cluster 3",
'type':
"Lantipeptide",
'description':
"Sanglifehrin_A_biosynthetic_gene_cluster (4% of genes show similarity)"
},
],
}
session.genome = genome
assert session.genome == genome
def main():
parser = argparse.ArgumentParser(
description='CRISPy sequence preparation service')
parser.add_argument('-d',
'--debug',
dest='debug',
action='store_true',
default=False,
help='print diagnostic messages while running')
parser.add_argument('-q',
'--queue',
dest='queue',
default='redis://127.0.0.1:6379/0',
help='URI of the Queue server')
parser.add_argument(
'-u',
'--upload-dir',
dest='upload_dir',
default='../uploads',
help='Path to directory where the session files are stored')
parser.add_argument('-V',
'--version',
action="version",
version=version.__version__)
args = parser.parse_args()
if args.debug:
logging.basicConfig(format='%(levelname)s %(asctime)s: %(message)s',
level=logging.INFO)
UPLOAD_PATH = path.abspath(args.upload_dir)
db = redis.Redis.from_url(args.queue, decode_responses=True)
queue = Queue(db, 'prepare')
while True:
job_key = queue.next()
if job_key is None:
time.sleep(1)
continue
logging.info('processing {}'.format(job_key))
job_id = int(job_key.split(':')[-1])
job = Session(db, session_id=job_id)
dirname = path.join(UPLOAD_PATH, str(job_id))
if job.asid != 'None':
logging.info('grabbing file for id {}'.format(job.asid))
try:
json_rec, filename = fetch(job.asid, dirname)
job.filename = filename
except requests.HTTPError:
job.state = 'error'
job.error = 'Downloading sequence file failed. Is the ID spelled correctly?'
continue
except Exception:
job.state = 'error'
job.error = 'Failed to load the sequence'
continue
else:
logging.info('parsing uploaded file {}'.format(job.filename))
full_path = path.join(dirname, job.filename)
if job.filename.endswith('.gbk') or job.filename.endswith('.gb'):
try:
rec = list(SeqIO.parse(full_path, 'genbank'))[0]
except (IndexError, ValueError, AssertionError, AttributeError,
UnicodeDecodeError):
job.state = 'error'
job.error = 'Parsing the uploaded file failed. Please check it is a valid GenBank file'
continue
try:
json_rec = genome_json(rec)
except (TypeError):
job.state = 'error'
job.error = 'Invalid input file. Please check the file contains a nucleotide sequence.'
continue
elif job.filename.endswith('.json'):
with open(full_path, 'r') as handle:
as_json = json.load(handle)
json_rec = convert_json(as_json)
gbk_record = json_to_gbk(as_json)
job.filename = 'input.gbk'
SeqIO.write([gbk_record], path.join(dirname, job.filename),
'genbank')
else:
job.state = 'error'
job.error = 'Invalid input file'
continue
job.genome = json_rec
job.state = 'loaded'
logging.info('done with {}'.format(job_key))