Getting Started

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(Initial page creation modeled off of equivalent page for bioperl)
 
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==Quick example==
 
==Quick example==
  
 +
Executing this:
 
<python>
 
<python>
 
from Bio.Seq import Seq,translate
 
from Bio.Seq import Seq,translate
import Bio.SeqIO
 
  
 
#create a sequence object of some DNA
 
#create a sequence object of some DNA
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#or see the whole record
 
#or see the whole record
print my_seq
+
print 'sequence record:', my_seq
  
 
#translate the sequence into a protein
 
#translate the sequence into a protein
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print 'protein translation is %s' % my_protein.tostring()
 
print 'protein translation is %s' % my_protein.tostring()
print my_protein
+
print 'protein record:', my_protein
  
 
</python>
 
</python>
 +
 +
Produces:
 +
<pre>
 +
seq is 11 bases long
 +
reverse complement is CTATCTACATG
 +
sequence record: Seq('CATGTAGATAG', Alphabet())
 +
protein translation is HVD
 +
protein record: Seq('HVD', HasStopCodon(IUPACProtein(), '*'))
 +
</pre>
  
 
==Beginners==
 
==Beginners==

Revision as of 21:39, 19 January 2007

--Jblucks 16:36, 19 January 2007 (EST): This page modeled after the one for bioperl

Contents

Download

See Getting BioPerl

Installation

See Installing BioPerl

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(), '*'))

Beginners

Further reading

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