(→Beginners: Added educational PLoS paper on Biopython.)
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Revision as of 12:24, 2 July 2010
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 Most Linux distributions will include an optional Biopython package (although this may be out of date).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.
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
- Learn how to program in Python
- Browse the Biopython Tutorial
- Read this paper
- Bassi S. A primer on python for life science researchers. PLoS Comput Biol 2007 Nov; 3(11) e199. doi:10.1371/journal.pcbi.0030199 pmid:18052533.
- Examine the Class Diagram if you'd like to know more about the relationships between the modules.
- Use the Wiki Search tools to find more information on specific topics.