Biobrary

Introduction

Biobrary is a python library, which contain data and methods for biological computation.

Requirement

• ete3 pyqt5 is needed by ete3. you maybe need install it manually.

Install

• using pip
  pip install biobrary --user

• manally install
  git clone https://github.com/benjaminfang/biobrary.git
cd biobrary
mv biobrary PYTHONPATH
  where PYTHONPATH is python library searching path.

Usage

import biobrary  
dir(biobrary)  

Data and Method

• biopaser

  • Fasta_parser
    class for fasta file.
  • Gff_parser
    class for gff file.

• biocondon

  • CODON_AA
    python dictionary of codon and amino acids.
  • base_complement
  • start_codon
  • stop_codon

• amino_acids_mw

• CircleNode
  class for phylogenic tree traverse and operations. And divide tree to circle node according to phylogenic distance.