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from argparse import ArgumentParser
from multiprocessing import Pool
import logging
import os
from ont_fast5_api import __version__
from ont_fast5_api.conversion_tools.conversion_utils import get_fast5_file_list, get_progress_bar
from ont_fast5_api.fast5_file import EmptyFast5, Fast5FileTypeError
from ont_fast5_api.fast5_interface import check_file_type, MULTI_READ
from ont_fast5_api.multi_fast5 import MultiFast5File
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)
exc_info = False
def batch_convert_multi_files_to_single(input_path, output_folder, threads, recursive, follow_symlinks):
pool = Pool(threads)
file_list = get_fast5_file_list(input_path, recursive, follow_symlinks=follow_symlinks)
pbar = get_progress_bar(len(file_list))
def update(result):
input_file = result[0]
with open(os.path.join(output_folder, "filename_mapping.txt"), 'a') as output_table:
for filename in result[1]:
output_table.write("{}\t{}\n".format(input_file, filename))
pbar.update(pbar.currval + 1)
if not os.path.exists(output_folder):
os.makedirs(output_folder)
results_array = []
for batch_num, filename in enumerate(file_list):
results_array.append(pool.apply_async(convert_multi_to_single,
args=(filename, output_folder,
str(batch_num)),
callback=update))
pool.close()
pool.join()
pbar.finish()
def convert_multi_to_single(input_file, output_folder, subfolder):
output_files = ()
try:
output_files = try_multi_to_single_conversion(input_file, output_folder, subfolder)
except Exception as e:
logger.error("{}\n\tFailed to copy files from: {}"
"".format(e, input_file), exc_info=exc_info)
return input_file, output_files
def try_multi_to_single_conversion(input_file, output_folder, subfolder):
output_files = []
with MultiFast5File(input_file, 'r') as multi_f5:
file_type = check_file_type(multi_f5)
if file_type != MULTI_READ:
raise Fast5FileTypeError("Could not convert Multi->Single for file type '{}' with path '{}'"
"".format(file_type, input_file))
for read in multi_f5.get_reads():
try:
output_file = os.path.join(output_folder, subfolder, "{}.fast5".format(read.read_id))
create_single_f5(output_file, read)
output_files.append(os.path.basename(output_file))
except Exception as e:
logger.error("{}\n\tFailed to copy read '{}' from {}"
"".format(str(e), read.read_id, input_file), exc_info=exc_info)
return output_files
def create_single_f5(output_file, read):
if not os.path.exists(os.path.dirname(output_file)):
os.makedirs(os.path.dirname(output_file))
with EmptyFast5(output_file, 'w') as single_f5:
for group in read.handle:
if group == "Raw":
read_number = read.handle["Raw"].attrs["read_number"]
single_f5.handle.copy(read.handle[group], "Raw/Reads/Read_{}".format(read_number))
elif group in ("channel_id", "context_tags", "tracking_id"):
if "UniqueGlobalKey" not in single_f5.handle:
single_f5.handle.create_group("UniqueGlobalKey")
single_f5.handle.copy(read.handle[group], "UniqueGlobalKey/{}".format(group))
else:
single_f5.handle.copy(read.handle[group], group)
def main():
parser = ArgumentParser("")
parser.add_argument('-i', '--input_path', required=True,
help="MultiRead fast5 file or path to directory of MultiRead files")
parser.add_argument('-s', '--save_path', required=True,
help="Folder to output SingleRead fast5 files to")
parser.add_argument('--recursive', action='store_true',
help="Search recursively through folders for MultiRead fast5 files")
parser.add_argument('--ignore_symlinks', action='store_true',
help="Ignore symlinks when searching recursively for fast5 files")
parser.add_argument('-t', '--threads', type=int, default=1, required=False,
help="Number of threads to use")
parser.add_argument('-v', '--version', action='version', version=__version__)
args = parser.parse_args()
batch_convert_multi_files_to_single(args.input_path, args.save_path, args.threads,
args.recursive, follow_symlinks=not args.ignore_symlinks)
if __name__ == '__main__':
main()
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