Getting Started

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(Reading and writing Sequence Files: Bio.SeqIO isn't really new anymore. Also link to AlignIO page)
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** [http://rgruet.free.fr/PQR25/PQR2.5.html Python Quick Reference]
 
** [http://rgruet.free.fr/PQR25/PQR2.5.html Python Quick Reference]
 
* Browse the [http://biopython.org/DIST/docs/tutorial/Tutorial.html Biopython Tutorial]
 
* Browse the [http://biopython.org/DIST/docs/tutorial/Tutorial.html Biopython Tutorial]
 +
* Read this paper <biblio>Bassi2007 pmid=18052533</biblio>
 
* Examine the [http://biopython.org/DIST/docs/api Class Diagram] if you'd like to know more about the relationships between the modules.
 
* Examine the [http://biopython.org/DIST/docs/api Class Diagram] if you'd like to know more about the relationships between the modules.
  

Latest revision as of 07:58, 24 February 2014

Contents

Download and Installation

For Windows we provide click-and-run installers. Most Linux distributions will include an optional Biopython package (although this may be out of date). Otherwise you typically download and uncompress the archive, and install from source. See our downloads page for details including the prerequisites.

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

Try executing this in python:

from Bio.Seq import Seq
 
#create a sequence object
my_seq = Seq('CATGTAGACTAG')
 
#print out some details about it
print 'seq %s is %i bases long' % (my_seq, len(my_seq))
print 'reverse complement is %s' % my_seq.reverse_complement()
print 'protein translation is %s' % my_seq.translate()

You should get the following output:

seq CATGTAGACTAG is 12 bases long
reverse complement is CTAGTCTACATG
protein translation is HVD*

This was a very quick demonstration of Biopython's Seq (sequence) object and some of its methods.

Reading and writing Sequence Files

Use the SeqIO module for reading or writing sequences as SeqRecord objects. For multiple sequence alignment files, you can alternatively use the AlignIO module.

Beginners

  • 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.
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