BITS: miscellaneous BioInformatics ToolS

Basically bioinformatics-related, reusable Python3 codes as a package.

Requirements

• Python packages listed in setup.cfg (automatically installed)
• Seqkit (if you use bits.seq.load_fast[a|q] with range= option)
• Edlib (if you use bits.seq.EdlibRunner)
• Gepard (if you use bits.seq.DotPlot)
• DAZZ_DB (if you use bits.seq.load_db etc)

How to install

git clone https://github.com/yoshihikosuzuki/bits
cd bits
pip install .

To run unit tests:

python -m unittest

How to use

BITS has two submodules:

• bits.seq for DNA sequence manipulations, and
• bits.util for other, general purposes in Python programming.

Import and use any function/class as follows:

import bits.seq as bs
print(bs.revcomp_seq('aactg'))

> cagtt