miscellaneous BioInformatics ToolS
Project description
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]
withrange=
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, andbits.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
:
Project details
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