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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Fast5 compression filter for demonstrating vbz compression
"""
import os
import h5py
import argparse
from shutil import copy2
__version__ = "0.1.1"
def compress_fast5(filename, output_suffix, vbz_version=0, decompress=False):
"""
(De)compress the raw signal in the fast5
"""
# create a copy of the input file for compressing
filename = os.path.abspath(filename)
out_filename = filename + output_suffix
copy2(filename, out_filename)
# open the copy and compress the signal datasets only
with h5py.File(out_filename, 'r+') as fast5:
if decompress:
compression_opts = {
"compression": "gzip", "compression_opts": 1
}
else:
compression_opts = {
"compression": 32020,
# 2 byte integers with zig zag + level 1 zstd
"compression_opts": (vbz_version, 2, 1, 1)
}
# multi read files
for read in fast5:
if not read.startswith("read_"):
continue
# read the signal dataset
group = '%s/Raw/' % read
raw = fast5[group]["Signal"][:]
# remove the dataset
del fast5[group]["Signal"]
# store the dataset with the new compression
fast5[group].create_dataset(
"Signal",
data=raw,
**compression_opts,
chunks=(len(raw),)
)
return out_filename
def main(args, print_help):
for filename in args.files:
print(compress_fast5(filename, args.output_suffix, args.vbz_version, args.decompress))
if __name__ == "__main__":
parser = argparse.ArgumentParser("fast5compress")
parser.add_argument('files', nargs='*', help='input files')
parser.add_argument("-d", "--decompress", action="store_true", default=False)
parser.add_argument("-s", "--output-suffix", default=".tmp")
parser.add_argument('-v', '--version', action='version', version=__version__)
parser.add_argument('--vbz-version', type=int, default=1)
main(parser.parse_args(), parser.print_help)
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