molbiox

Utilities for bioinformatics

Experimental stage. Interfaces are unstable yet. Versions before 1.0.0 will be experimental and not ready for use.

Install from PyPI

mkdir try-molbiox && cd try-molbiox
virtualenv venv
source venv/bin/activate
pip install molbiox --upgrade

Install from GitHub

mkdir try-molbiox && cd try-molbiox 
virtualenv venv   
source venv/bin/activate
pip install https://github.com/frozflame/molbiox/archive/master.zip

General form of commandline interfaces

$ mbx SUBCOMMAND INPUT1 INPUT2 ... -o OUTPUT OTHER_OPTIONS

Generate random sequences

$ mbx rs
$ mbx rs -h
$ mbx rs -l 900 -o randseq.fa

Generate reverse complement of randseq.fa

$ mbx rc randseq.fa -o randseq.rc.fa

Translate DNA to protein

$ mbx tl randseq.fa -o randseq.faa

Read a fasta file (output like fastalength)

>>> from molbiox.io import fasta
>>> for rec in fasta.read('sample.fa'):
...     print(len(rec.seq), rec.cmt)