def post(self):
parser = reqparse.RequestParser()
parser.add_argument('forward',
type=str,
help='The sequence of the forward primer')
parser.add_argument('reverse',
type=str,
help='The sequence of the reverse primer')
args = parser.parse_args()
args['sequence'] = args['forward'] + '_' + args['reverse']
job = BlastJob()
job_id = job.get_job_id()
cmd = (
"INSERT INTO jobs VALUES ('{}', '{}', '{}', '{}', '{}', '{}', '{}')"
.format(job_id, args['sequence'], 0000, time.time(), 'submitted',
'', '', ''))
conn = sqlite3.connect(job.result_db)
c = conn.cursor()
c.execute(cmd)
conn.commit()
conn.close()
args['job_id'] = job_id
print(args, file=sys.stderr)
args = job.set_arguments_for_primer_blast(args)
print(str(args) + '#' * 20, file=sys.stderr)
job.future = executor.submit(
functools.partial(job.run, parameters=args))
jobs[job_id] = job
return job_id
def get(self):
args = parser.parse_args()
args['accession'] = args['accession'][0]
if args['format'] == 'txt':
return RestNucleotideMinimal().get(args['accession'])
else:
job = BlastJob()
acc = job.get_accession(args['accession'])
return jsonify({'response': acc})
def post(self):
args = parser.parse_args()
job = BlastJob()
resp = {}
for acc in args['accession']:
resp[acc] = job.get_accession(acc)
if args['format'] == 'txt':
return resp
else:
return jsonify(resp)
def post(self):
parser = reqparse.RequestParser()
parser.add_argument('sequence', type=str, help='Sequence')
parser.add_argument('number_of_pairs',
type=int,
required=False,
default=5,
help='Number of pairs to design')
args = parser.parse_args()
# TODO default
filename = os.path.join(os.getcwd(), '..', 'input',
BlastJob.get_job_id() + '.fa')
resp = {'error': False, 'primers': [], 'message': ''}
with open(filename, 'w') as f:
f.write(args['sequence'])
try:
primers = design_primers(filename, args['number_of_pairs'])
except ValueError as e:
resp['error'] = True
resp['message'] = str(e)
return jsonify(resp)
for p, primer in enumerate(primers):
primers[p] = str(primer)
resp['primers'] = primers
if len(primers) == 0:
resp[
'message'] = 'Failed to design primers for the target sequence'
else:
resp['message'] = 'Successfully designed primers'
return jsonify(resp)
def post(self):
parser = reqparse.RequestParser()
parser.add_argument('sequence', type=str, help='Sequence')
args = parser.parse_args()
job = BlastJob()
job_id = job.get_job_id()
cmd = (
"INSERT INTO jobs VALUES ('{}', '{}', '{}', '{}', '{}', '{}', '{}')"
.format(job_id, args['sequence'], 0000, time.time(), 'submitted',
'', ''))
conn = sqlite3.connect(job.result_db)
c = conn.cursor()
c.execute(cmd)
conn.commit()
conn.close()
args['job_id'] = job_id
job.future = executor.submit(
functools.partial(job.run, parameters=args))
jobs[job_id] = job
return job_id
def get(self, accession):
job = BlastJob()
acc = job.get_accession(accession)
return flask.Response(acc, mimetype='txt')
def get(self, blast_id):
if blast_id is None or len(blast_id) == 0 or blast_id not in jobs:
return flask.abort(404)
if not jobs[blast_id].finished:
return flask.abort(404)
return BlastJob.extract_hits_from_blast(jobs[blast_id].stdout)
def design_primers(filename, number_of_primers, database='nt', primer_pairs_to_screen=3200):
make_directories()
# get target sequence
if filename.startswith('>') and not os.path.isfile(filename):
filename = write_sequence_to_file(filename)
try:
record = SeqIO.read(filename, 'fasta')
except ValueError as e:
raise e
# run BLAST in the background
blast = BlastJob(blast_db=database)
blast.run(parameters={'sequence': record.format('fasta')})
while not blast.finished:
time.sleep(0.1)
if blast.stderr is None or blast.stderr != '':
raise RuntimeError('BLAST failed with error: {}'.format(blast.stderr))
# get BLAST sequences
executor = concurrent.futures.ThreadPoolExecutor(4)
future_blast = executor.submit(functools.partial(blast.extract_hits_from_blast, blast.stdout))
acc_hits = future_blast.result(timeout=120)
# TODO default
filename_hits = os.path.join(os.path.dirname(__file__), 'data', 'input', blast.get_job_id() + '.fa')
with open(filename_hits, 'w') as f:
f.write(blast.get_accession(acc_hits))
primer_pairs = []
valid_pairs = []
primers = {}
while len(valid_pairs) < number_of_primers:
old_len = primers.get('PRIMER_LEFT_NUM_RETURNED', 0)
future_primers = executor.submit(functools.partial(create_primers, record,
number_of_primers=primer_pairs_to_screen))
primers = future_primers.result(timeout=120)
for i in range(old_len, primers['PRIMER_LEFT_NUM_RETURNED']):
pp = PrimerPair.parse_primer3(primers, index=i)
primer_pairs.append(pp)
valid_pairs = list(set(validate_primerpairs(primer_pairs, filename=filename_hits)))
primer_pairs_to_screen = primer_pairs_to_screen * 2
with open('optimal_pairs.txt', 'a') as f:
f.write(str(primer_pairs_to_screen))
f.write('\n')
blast_outputs = []
for v, valid in enumerate(valid_pairs):
# run against all nucleotides
for orientation in ('forward', 'reverse'):
sequence = '>{}_{}\n{}'.format(orientation, v, valid.__getattribute__(orientation).seq)
blast.run(parameters={'sequence': sequence})
while not blast.finished:
time.sleep(0.1)
blast_outputs.extend(blast.extract_hits_from_blast(blast.stdout))
# collect new sequences
# print(blast_outputs, file=sys.stderr)
# add new sequences to initial
pass
#acc_hits = blast.get_accessions_from_list(blast_outputs)
#print(acc_hits, file=sys.stderr)
return valid_pairs[0:number_of_primers]