Getting Started

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(Download and Installation)
(Quick example: Don't need tostring() any more, also I wanted to include a stop codon)
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#create a sequence object of some DNA
 
#create a sequence object of some DNA
my_seq = Seq('CATGTAGATAG')
+
my_seq = Seq('CATGTAGACTAG')
  
 
#print out some details about it
 
#print out some details about it
print 'seq is %i bases long' % len(my_seq)
+
print 'seq %s is %i bases long' % (my_seq, len(my_seq))
print 'reverse complement is %s' % my_seq.reverse_complement().tostring()
+
print 'reverse complement is %s' % my_seq.reverse_complement()
 
+
#or see the whole record
+
print 'sequence record:', my_seq
+
  
 
#translate the sequence into a protein
 
#translate the sequence into a protein
 
my_protein = translate(my_seq)
 
my_protein = translate(my_seq)
  
print 'protein translation is %s' % my_protein.tostring()
+
print 'protein translation is %s' % my_protein
print 'protein record:', my_protein
+
 
+
 
</python>
 
</python>
  
 
You should get the following output:
 
You should get the following output:
 
<pre>
 
<pre>
seq is 11 bases long
+
seq CATGTAGACTAG is 12 bases long
reverse complement is CTATCTACATG
+
reverse complement is CTAGTCTACATG
sequence record: Seq('CATGTAGATAG', Alphabet())
+
protein translation is HVD*
protein translation is HVD
+
protein record: Seq('HVD', HasStopCodon(IUPACProtein(), '*'))
+
 
</pre>
 
</pre>
  

Revision as of 16:47, 9 October 2008

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 Most Linux distributions will include an optional Biopython package (although this may be out of date).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,translate
 
#create a sequence object of some DNA
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()
 
#translate the sequence into a protein
my_protein = translate(my_seq)
 
print 'protein translation is %s' % my_protein

You should get the following output:

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

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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