dcompressee: a small Python library to generate temporarirly decompressed files

Background

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.

Usage

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]

Installation

pip install dcompressee

Examples

Two 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.

Author

Anders Goncalves da Silva (@andersgs)