def extract_file(input_file):
try:
(raw_data, raw_label, raw_start,
raw_length) = labelop.get_label_raw(input_file, FLAGS.basecall_group,
FLAGS.basecall_subgroup)
except IOError:
return False, (None, None)
except:
return False, (None, None)
raw_data_array = []
for index, start in enumerate(raw_start):
raw_data_array.append(
[start, start + raw_length[index],
str(raw_label['base'][index])])
if FLAGS.mode == 'rna':
raw_data = raw_data[::-1]
return True, (raw_data, np.array(raw_data_array, dtype='S5'))
def extract_file(input_file):
try:
(raw_data, raw_label, raw_start,
raw_length) = labelop.get_label_raw(input_file, FLAGS.basecall_group,
FLAGS.basecall_subgroup)
except Exception as e:
print(str(e))
return False, (None, None)
raw_data_array = []
for index, start in enumerate(raw_start):
# if raw_length[index]==0:
# print("input_file:" + input_file)
# raise ValueError("catch a label with length 0")
raw_data_array.append(
[start, start + raw_length[index],
str(raw_label['base'][index])])
if FLAGS.mode == 'rna':
raw_data = raw_data[::-1]
return True, (raw_data, np.array(raw_data_array, dtype='S8'))
def extract_file(input_file):
try:
raw_info,channel_info = labelop.get_label_raw(
input_file, FLAGS.basecall_group,
FLAGS.basecall_subgroup)
raw_data, raw_label, raw_start, raw_length = raw_info
offset,range_s,digitisation = channel_info
except Exception as e:
return str(e), (None, None) ,(None, None,None)
raw_data_array = []
for index, start in enumerate(raw_start):
# if raw_length[index]==0:
# print("input_file:" + input_file)
# raise ValueError("catch a label with length 0")
raw_data_array.append(
[start, start + raw_length[index], raw_label['base'][index].decode()])
if FLAGS.mode=='rna':
raw_data = raw_data[::-1]
if len(raw_data_array)>FLAGS.min_bps:
return SUCCEED_TAG, (raw_data, raw_data_array) , (offset,digitisation,range_s)
else:
return "Read has too few nucleotides output", (None, None) ,(None, None,None)