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)