def fold(self, shmiR, prefix=None):
task_id = self.request.id
if prefix is not None:
task_id = "{}/{}".format(prefix, task_id)
pdf, ss = execute(
task_id, shmiR, to_zip=False
)
with mfold_path(task_id) as tmp_dirname:
zip_file(self.request.id, [pdf, ss], tmp_dirname)
return {
'path_id': task_id,
'ss': ss,
}
def fold_and_score(
self, seq1, seq2, frame_tuple, original, score_fun, args_fun, prefix=None
):
"""Function for scoring and folding sequnces.
Args:
seq1(str): First RNA sequence.
seq2(str): Second RNA sequence.
frame_tuple(tuple): Tuple with frame and inserts.
orginal(Backbone): orginal Backbone model.
score_fun(function): Scoring function.
args_fun(tuple): Arguments for scoring function.
Kwargs:
prefix(str): prefix for mfold path (default None)
Returns:
tuple with score, sh-miR, name of Backbone, task id and sequences.
"""
if prefix:
path_id = "%s/%s" % (prefix, self.request.id)
else:
path_id = self.request.id
frame, insert1, insert2 = frame_tuple
mfold_data = execute_mfold(
path_id, frame.template(insert1, insert2), zip_file=False
)
pdf, ss = mfold_data
score = score_fun(frame_tuple, original, ss, *args_fun)
with mfold_path(path_id) as tmp_dirname:
zipped_mfold(self.request.id, [pdf, ss], tmp_dirname)
return [
score,
frame.template(insert1, insert2),
frame.name,
path_id,
(seq1, seq2),
]
def execute(directory, sequence, to_zip=True):
"""Function which executes mfold
Args:
directory: directory in which mfold is executed & output files are stored
sequence(str): sequence to be folded via mfold
to_zip(bool): tells if files should be zipped (default: True)
Returns:
Path of foleded files
"""
with mfold_path(directory) as tmp_dirname:
with open('sequence', "w") as f:
f.write(sequence)
pid = os.fork()
if pid == 0:
os.execl(MFOLD_PATH, 'mfold', 'SEQ=sequence')
process_id, status = os.waitpid(pid, 0)
# Status in 0 - 255
status = (status & 0xff00) >> 8
if status == 0:
result = map(
lambda mfold_path: os.path.join(
tmp_dirname, mfold_path.format('sequence')
),
["{}_1.pdf", "{}_1.ss"]
)
if to_zip:
result = zip_file(directory, result, tmp_dirname)
if status != 0:
remove_error_folding(directory)
raise NoResultError("No foldings for %s" % sequence)
return result
def execute_mfold(path_id, sequence, zip_file=True):
"""Function which executes mfold
Args:
path_id: path where is mfold
sequence(str): sequence to be folded via mfold
zip_file(bool): tells if files should be zipped (default: True)
Returns:
Path of foleded files
"""
with mfold_path(path_id) as tmp_dirname:
with open('sequence', "w") as f:
f.write(sequence)
pid = fork()
if pid == 0:
execl(MFOLD_PATH, 'mfold', 'SEQ=sequence')
process_id, status = waitpid(pid, 0)
# Status in 0 - 255
status = (status & 0xff00) >> 8
if status == 0:
result = map(
lambda mfold_path: path.join(
tmp_dirname, mfold_path.format('sequence')
),
["{}_1.pdf", "{}_1.ss"]
)
if zip_file:
result = zipped_mfold(path_id, result, tmp_dirname)
if status != 0:
remove_error_folding(path_id)
raise NoResultError("No foldings for %s" % sequence)
return result
def execute_mfold(path_id, sequence, zip_file=True):
"""Function which executes mfold
Args:
path_id: path where is mfold
sequence(str): sequence to be folded via mfold
zip_file(bool): tells if files should be zipped (default: True)
Returns:
Path of foleded files
"""
with mfold_path(path_id) as tmp_dirname:
with open('sequence', "w") as f:
f.write(sequence)
pid = fork()
if pid == 0:
execl(MFOLD_PATH, 'mfold', 'SEQ=sequence')
process_id, status = waitpid(pid, 0)
# Status in 0 - 255
status = (status & 0xff00) >> 8
if status == 0:
result = map(
lambda mfold_path: path.join(tmp_dirname,
mfold_path.format('sequence')),
["{}_1.pdf", "{}_1.ss"])
if zip_file:
result = zipped_mfold(path_id, result, tmp_dirname)
if status != 0:
remove_error_folding(path_id)
raise NoResultError("No foldings for %s" % sequence)
return result