Getting Started

Revision as of 20:04, 16 August 2008

Download and Installation

See our downloads page for details including the prerequisites. For Windows we provide click-and-run installers. Most Linux distributions will include an optional Biopython package. Otherwise you typically install from source by downloading and uncompressing the archive, then running the command:

sudo python setup.py install

You can check your installation has worked at the python prompt:

>>> import Bio

If that gives no error, you should be done. If you get something like "ImportError: No module named Bio" something has gone wrong.

Tutorial

The Biopython Tutorial and Cookbook (HTML, PDF) contains the bulk of our documentation. See Documentation for more links.

Quick example

Executing this:

from Bio.Seq import Seq,translate
 
#create a sequence object of some DNA
my_seq = Seq('CATGTAGATAG')
 
#print out some details about it
print 'seq is %i bases long' % len(my_seq)
print 'reverse complement is %s' % my_seq.reverse_complement().tostring()
 
#or see the whole record
print 'sequence record:', my_seq
 
#translate the sequence into a protein
my_protein = translate(my_seq)
 
print 'protein translation is %s' % my_protein.tostring()
print 'protein record:', my_protein

Produces:

seq is 11 bases long
reverse complement is CTATCTACATG
sequence record: Seq('CATGTAGATAG', Alphabet())
protein translation is HVD
protein record: Seq('HVD', HasStopCodon(IUPACProtein(), '*'))

Reading and writing Sequence Files

If you are using Biopython 1.43 or later, try out the new SeqIO module.

Beginners

• Learn how to program in Python
  • A Byte of Python
  • Dive Into Python
  • Python Quick Reference
• Browse the Biopython Tutorial
• Examine the Class Diagram if you'd like to know more about the relationships between the modules.

Further reading

• Use the Wiki Search tools to find more information on specific topics.