A common use case in Bioinformatics is having to temporarily decompress a file in
order to run it through some tool. For instance, blastn can only read uncompressed
FASTA files. This library provides a simple way to do this. The library will automatically
detect the compression format of the file and decompress it to a temporary file. The
temporary file will be automatically deleted when the program exits. The library
currently supports the following compression formats: gzip, bzip2, xz, lz4, and lzma.
from dcompressee import unpack
# A list of file paths as pathlib.Path objects with various compression formats,
# and some are not compressed
files = ["/path/to/file1.fasta.gz", "/path/to/file2.fasta.bz2", "/path/to/file3.fasta.xz", "/path/to/file4.fasta"]
# Generate a list of paths as pathlib.Path objects to temporarily decompressed
# files (these will be created in $TMPDIR) if necessary. For files that are not
# compressed, the function will return the original path.
# The created temporary files will be automaicallly deleted when the program exits.
paths = [unpack(f) for f in files]pip install dcompresseeTwo examples are provided in the examples directory. The first example shows how to
use dcompressee in a simple Python script. The second example shows how to use
dcompressee in a asynchronous manner.
Anders Goncalves da Silva (@andersgs)