Getting Started

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==Download==
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==Download and Installation==
  
See [[Download|Getting BioPython]]
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See our [[Download|downloads page]] for details including the prerequisites.  For Windows we provide click-and-run installers.  Most Linux distributions will include an optional Biopython package.
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Otherwise you typically install from source by downloading and uncompressing the archive, then running the command:
  
==Installation==
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sudo python setup.py install
  
See [http://biopython.org/DIST/docs/install/Installation.html Installing BioPython]
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You can check your installation has worked at the python prompt:
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<python>
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>>> import Bio
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</python>
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If that gives no error, you should be done. If you get something like "ImportError: No module named Bio" something has gone wrong.
  
 
==Tutorial==
 
==Tutorial==

Revision as of 20:04, 16 August 2008

Contents

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

Further reading

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