BITS: miscellaneous BioInformatics ToolS

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

How to install

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

To run unit tests,

python -m unittest

Optional requirements

If you use bits.seq.load_fast[a|q] with range= option,

• Seqkit

If you use bits.seq.DotPlot,

• Gepard, or
• modified Gepard (recommended)

If you use bits.seq.load_db etc.,

• DAZZ_DB

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