compositioncalc1.py from Practical Computing for Biologists by Steven H. D. Haddock and Casey W. Dunn. Posted as a Gist by Wayne Decatur (fomightez) with full credit and reference to the original authors and specifying where they freely share the code online. You can see a static IPython Notebook version at http://nbviewer.ipython.org/6077226

compositioncalc1.py

# code by Steven H. D. Haddock and Casey W. Dunn as described in:
# Practical Computing for Biologists
# Steven H. D. Haddock and Casey W. Dunn
# Published in 2011 by Sinauer Associates.
# ISBN 978-0-87893-391-4
# http://www.sinauer.com/practical-computing-for-biologists.html
# see practicalcomputing.org
#
#scripts freely available by the original authors at practicalcomputing.org
#DIRECT LINK: http://practicalcomputing.org/files/pcfb_examples.zip
#
#! /usr/bin/env python
DNASeq = "ATGTCTCATTCAAAGCA"
SeqLength = float(len(DNASeq))

BaseList = "ACGT"
for Base in BaseList:
  Percent = 100 * DNASeq.count(Base) / SeqLength
  print "%s: %4.1f" % (Base,Percent)









#--------------------------------------------------------#
#****ALL BELOW ADDED BY WAYNE DECATUR TO HELP  *********#
#****WITH UNDERSTANDING THIS SCRIPT AND EXPLORING******#
#****FURTHER USING THE INTERACTIVE CONSOLE.    ********#
#--------------------------------------------------------#
print "\n\n\n\n---------------------------------------------------------------------------"
print "Following added by Wayne Decatur beyond Haddock and Dunn code, as a starting point"
print "for understanding the script in this gist."
print "---------------------------------------------------------------------------"
print "The compositoncalc1 script calculates percent of the four bases (A,C,G,&T) in a DNA sequence."
print "Here, the DNA sequence (DNASeq) = %s" % DNASeq
for Base in BaseList:
  Percent = 100 * DNASeq.count(Base) / SeqLength
  print "%s: %4.1f%%" % (Base,Percent)
 
 
#-----defining the calculator as a function to make interaction via the interactive gist console easier 
def calc (MyDNASeq):
  SeqLength = float(len(MyDNASeq))
  BaseList = "ACGT"
  for Base in BaseList:
    Percent = 100 * MyDNASeq.count(Base) / SeqLength
    print "%s: %4.1f%%" % (Base,Percent)
    
#initialize MyDNASeq with same sequence 'calc(MyDNASeq)' works for testing purposes without necesarily needing to define
MyDNASeq = DNASeq
  

import pprint  #this is simply to allow use of the pprint command mentioned below
print "\n\nSee the raw code by clicking the blue numbers after 'Gist ID and link' in the side panel."
print "Tip: Opening the code in a separate browswer window can make it easier to follow along."
print "See a static IPython Notebook of the input and output at http://nbviewer.ipython.org/6077226"

print "\n\nTo calculate composition for your own sequence:"
print "  Define the MyDNASeq variable to what you want by typing 'MyDNASeq=\"YOUR SEQUENCE HERE\" ' where you type"
print "  your sequence in place of YOUR SEQUENCE HERE and hit return. Then type, 'calc (MyDNASeq)'"
print "  and hit return."
print "  You can also skip the MyDNASeq defining and type 'calc(\"YOUR SEQUENCE HERE\") and hit return."
print"\nHelp getting started exploring the code in the iPython interactive shell:"
print "  You can get a list of the variable and values by typing 'pprint.pprint(locals())' at the prompt."
print "  Type the name of a variable or object followed by a '?' to get information."
print "In all cases you actually type the double quotes and simply what is between the single quotes."