def data():
args = request.form
length = int(args['length'])
match_type = args['matches']
refs = json.loads(args['ref'])
queries = json.loads(args['query'])
m = []
# pairwise mode:
if len(queries) == len(refs):
for ref, query in zip(refs, queries):
with NamedTemporaryFile(delete=False) as f_ref, \
NamedTemporaryFile(delete=False) as f_query:
fn_ref = f_ref.name
print('>{}'.format(ref['name']), file=f_ref)
print(ref['seq'], file=f_ref)
fn_query = f_query.name
print('>{}'.format(query['name']), file=f_query)
print(query['seq'], file=f_query)
# close file. Otherwise an error occurs from time to time
matches = maze.mummer_matches(fn_ref,
fn_query,
length,
match_type,
cfg['debug'])
m.append(matches)
os.remove(fn_query)
os.remove(fn_ref)
# classical mode
else:
with NamedTemporaryFile(delete=False) as f_ref:
fn_ref = f_ref.name
print('>{}'.format(refs[0]['name']), file=f_ref)
print(refs[0]['seq'], file=f_ref)
for query in queries:
with NamedTemporaryFile(delete=False) as f_query:
fn_query = f_query.name
print('>{}'.format(query['name']), file=f_query)
print(query['seq'], file=f_query)
matches = maze.mummer_matches(fn_ref,
fn_query,
length,
match_type,
cfg['debug'])
m.append(matches)
os.remove(fn_query)
os.remove(fn_ref)
return json.dumps(m)
def data():
args = request.form
length = int(args['length'])
match_type = args['matches']
ref = json.loads(args['ref'])
queries = json.loads(args['query'])
m = []
with NamedTemporaryFile(delete=False) as f_ref:
fn_ref = f_ref.name
print('>{}'.format(ref['name']), file=f_ref)
print(ref['seq'], file=f_ref)
for query in queries:
with NamedTemporaryFile(delete=False) as f_query:
fn_query = f_query.name
print('>{}'.format(query['name']), file=f_query)
print(query['seq'], file=f_query)
matches = maze.mummer_matches(fn_ref,
fn_query,
length,
match_type,
cfg['debug'])
m.append(matches)
os.remove(fn_query)
os.remove(fn_ref)
return json.dumps(m)
def data():
args = request.form
length = int(args['length'])
match_type = args['matches']
refs = json.loads(args['ref'])
queries = json.loads(args['query'])
m = []
# pairwise mode:
if len(queries) == len(refs):
for ref, query in zip(refs, queries):
with NamedTemporaryFile(delete=False) as f_ref, \
NamedTemporaryFile(delete=False) as f_query:
fn_ref = f_ref.name
print('>{}'.format(ref['name']), file=f_ref)
print(ref['seq'], file=f_ref)
fn_query = f_query.name
print('>{}'.format(query['name']), file=f_query)
print(query['seq'], file=f_query)
# close file. Otherwise an error occurs from time to time
matches = maze.mummer_matches(fn_ref, fn_query, length, match_type,
cfg['debug'])
m.append(matches)
os.remove(fn_query)
os.remove(fn_ref)
# classical mode
else:
with NamedTemporaryFile(delete=False) as f_ref:
fn_ref = f_ref.name
print('>{}'.format(refs[0]['name']), file=f_ref)
print(refs[0]['seq'], file=f_ref)
for query in queries:
with NamedTemporaryFile(delete=False) as f_query:
fn_query = f_query.name
print('>{}'.format(query['name']), file=f_query)
print(query['seq'], file=f_query)
matches = maze.mummer_matches(fn_ref, fn_query, length, match_type,
cfg['debug'])
m.append(matches)
os.remove(fn_query)
os.remove(fn_ref)
return json.dumps(m)