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from argparse import ArgumentParser
from ont_fast5_api.compression_settings import COMPRESSION_MAP
from ont_fast5_api.conversion_tools.conversion_utils import yield_fast5_files
from ont_fast5_api.fast5_interface import get_fast5_file
def check_read_compression(read):
"""
Check the compresion type on the raw data of a read
:param read: Fast5Read object
:return: AbstractCompression object
"""
detected_compression = read.raw_compression_filters
for compression in COMPRESSION_MAP.values():
if compression.filter_settings == detected_compression:
return compression
return detected_compression
def check_compression(input_path, recursive, follow_symlinks, check_all_reads):
"""
Check the compression type of the raw data in files in a folder
:param input_path:
:param recursive:
:param follow_symlinks:
:param check_all_reads: bool - check all reads in a file or just the first
:return: (Compression, read_id, file_path)
"""
for input_file in yield_fast5_files(input_path, recursive, follow_symlinks):
with get_fast5_file(input_file, 'r') as f5:
for read in f5.get_reads():
compression = check_read_compression(read)
yield (compression, read.read_id, input_file)
if not check_all_reads:
break
def main():
parser = ArgumentParser("Tool for checking the compression type of raw data in fast5 files")
parser.add_argument('-i', '--input_path', required=True,
help="Path to Fast5 file or directory of Fast5 files")
parser.add_argument('--check_all_reads', action='store_true', required=False, default=False,
help="Check all reads in a file individually (default: check only the first read)")
parser.add_argument('-r', '--recursive', action='store_true', required=False, default=False,
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('--file_list', required=False,
help="File containing names of files to search in")
args = parser.parse_args()
compression_results = check_compression(args.input_path, args.recursive, not args.ignore_symlinks,
args.check_all_reads)
for result in compression_results:
print(result)
if __name__ == '__main__':
main()
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