bits-yoshi 0.1.0

miscellaneous BioInformatics ToolS

BITS: miscellaneous BioInformatics ToolS

Basically bioinformatics-related, reusable Python codes as a package. Developed in Python 3.7, but most of the codes should work with any Python >= 3.

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
$ python3 setup.py install

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:

from bits.seq import revcomp_seq
print(revcomp_seq('aactg'))

> cagtt

List of functions

If you are using IPython or Jupyter, you can look at the list of functions and classes with the completion function they provide, by typing from bits.seq import + TAB:

and from bits.util import + TAB: