Getting Started
(→Quick example: Don't need tostring() any more, also I wanted to include a stop codon) |
m (→Quick example: Use translate method) |
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| Line 19: | Line 19: | ||
Try executing this in python: | Try executing this in python: | ||
<python> | <python> | ||
| − | from Bio.Seq import Seq | + | from Bio.Seq import Seq |
#create a sequence object of some DNA | #create a sequence object of some DNA | ||
| Line 27: | Line 27: | ||
print 'seq %s is %i bases long' % (my_seq, len(my_seq)) | print 'seq %s is %i bases long' % (my_seq, len(my_seq)) | ||
print 'reverse complement is %s' % my_seq.reverse_complement() | print 'reverse complement is %s' % my_seq.reverse_complement() | ||
| − | + | print 'protein translation is %s' % my_protein.translate() | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | print 'protein translation is %s' % my_protein | + | |
</python> | </python> | ||
Revision as of 22:21, 15 January 2009
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 Most Linux distributions will include an optional Biopython package (although this may be out of date).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 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() print 'protein translation is %s' % my_protein.translate()
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
- Learn how to program in Python
- 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.
