Install biopython

From Shiu Lab

Contents 1 Install egenix 2 Install Numeric Python 3 Install ReportLab 4 Install MySQL-python 5 Install BioPython

Install egenix

wget http://www.egenix.com/files/python/egenix-mx-base-2.0.6.tar.gz
gunzip egenix-mx-base-2.0.6.tar.gz
tar -xvf egenix-mx-base-2.0.6.tar
cd egenix-mx-base-2.0.6/
python setup.py build
python setup.py install
python
>>> from mx import TextTools

Install Numeric Python

wget http://downloads.sourceforge.net/numpy/Numeric-24.2.tar.gz?modtime=1131825262&big_mirror=0
gunzip Numeric-24.2.tar.gz
tar -xvf Numeric-24.2.tar
cd Numeric-24.2
python setup.py build
python setup.py install
python
>>> from Numeric import *

Install ReportLab

wget http://www.reportlab.org/ftp/ReportLab_2_0.tgz
gunzip ReportLab_2_0.tgz
tar -xvf ReportLab_2_0.tar
cd reportlab_2_0/reportlab
python setup.py build
python setup.py install
python
>>> from reportlab.graphics import renderPDF

Install MySQL-python

• Official nstruction

Install BioPython

wget http://biopython.org/DIST/biopython-1.42.tar.gz
gunzip biopython-1.42.tar.gz
tar -xvf biopython-1.42.tar
python setup.py build
python setup.py install

• For verification

from Bio.Seq import Seq
from Bio.Alphabet.IUPAC import unambiguous_dna
new_seq = Seq('GATCAGAAG', unambiguous_dna)
new_seq[0:2]
from Bio import Translate
translator = Translate.unambiguous_dna_by_name["Standard"]
translator.translate(new_seq)