dnazip

Compress all your DNA (multi-FASTA) files in my project! It's very easy to use :)

It uses 2 bits per base, couldn't get any more efficient than that!

This algorithm is not entirely lossless, it converts lowercase actg to uppercase ACTG, and also adds newlines in decompression.

Installation

Install it using pip

$ pip install dnazip
$ dnazip -h
usage: dnazip [-h] [-l LINELENGTH] [-d] [-c] [--debug] [FILE]

Compress FASTA files, using 2 bits per base. If no input file is given, standard input is used

positional arguments:
  FILE                  Input file name

optional arguments:
  -h, --help            show this help message and exit
  -l LINELENGTH, --linelength LINELENGTH
                        Characters per line
  -d, --decompress      Decompress file
  -c, --stdout          Write to standard output
  --debug               Show debugging statements

Or to install it from source:

$ git clone https://github.com/Bartvelp/dnazip
$ cd dnazip
$ pip install .

Testing

To run the tests run:

$ cd dnazip
$ python tests.py