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An Introduction to Python – Part II Dr. Nancy Warter-Perez June 15, 2005.

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1 An Introduction to Python – Part II Dr. Nancy Warter-Perez June 15, 2005

2 6/15/05Introduction to Python – Part II2 Overview References Python Programming for the Absolute Beginner (PP) Learning Python (LP) Solution to Programming Workshop #1 If tests (PP Ch1, LP Ch 9) Loops (PP Ch1, LP Ch 10) for while Example amino acid search program Programming Workshop #2

3 6/15/05Introduction to Python – Part II3 Solution to Programming Workshop 1 Write a Python program to compute the hydrophobicity of an amino acid # Program to compute the hydrophobicity of an amino acid # (solution only includes first 3 amino acids) # Written by: Prof. Warter-Perez # Date created: April 15, 2004 # Last modified: hydro = {"A":1.8,"C":2.5,"D":-3.5} aa = raw_input ("Please enter amino acid: ") print "The hydrophobicity of %s is %f."% (aa, hydro[aa])

4 6/15/05Introduction to Python – Part II4 Make solution case insensitive # Program to compute the hydrophobicity of an amino acid # Written by: Prof. Warter-Perez # Date created: April 15, 2004 # Last modified: April 20, 2004 - made script case insensitive for # amino acids hydro = {"A":1.8,"C":2.5,"D":-3.5} aa = raw_input ("Please enter amino acid: ") aa = aa.upper() print "The hydrophobicity of %s is %f."% (aa, hydro[aa])

5 6/15/05Introduction to Python – Part II5 Python Basics – Relational and Logical Operators Relational operators ==equal !=not equal >greater than >=greater than or equal <less than <=less than or equal Logical operatorsandornot

6 6/15/05Introduction to Python – Part II6 if Statement if expression: action Example: a1 = 'A‘; a2 = 'C'; match = 0; if (a1 == a2) : match+=1;

7 6/15/05Introduction to Python – Part II7 if-elif-else Statement if expression: action 1 elif expression: action 2 else : action 3 Example: a1 = 'A‘; a2 = 'C'; match = 0; gap = 0; if (a1 == a2) : match+=1; elif (a1 > a2): else: gap+=1;

8 6/15/05Introduction to Python – Part II8 for Statement for var in list: action Sets var to each item in list and performs action range() function generates lists of numbers: range (5) -> [0,1,2,3,4] Example mylist=[“hello”,”hi”,”hey”,”!”]; for i in mylist: print i Iteration 1 prints: hello Iteration 2 prints: hi Iteration 3 prints: hey Iteration 4 prints: !

9 6/15/05Introduction to Python – Part II9 while Statement while expression: action Example x = 0; while x != 3: x = x + 1 Iteration 1: x=0+1=1 Iteration 2: x=1+1=2 Iteration 3: x=2+1=3 Iteration 4: don’t exec / 2 Infinite loop!

10 6/15/05Introduction to Python – Part II10 Example: Amino Acid Search Write a program to count the number of occurrences of an amino acid in a sequence. The program should prompt the user for A sequence of amino acids (seq) The search amino acid (aa) The program should display the number of times the search amino acid (aa) occurred in the sequence (seq)

11 6/15/05Introduction to Python – Part II11 Example: Amino Acid Search (2) #this program will calculate the number of occurrences of an amino acid in a #sequence #by Bryce Ready done=0 while (not done): sequence=raw_input("Please enter a sequence:"); aa=raw_input("Please enter the amino acid to look for:");

12 6/15/05Introduction to Python – Part II12 Example: Amino Acid Search (3) #compute the number of occurrences using for loop cnt=0 for i in sequence: if i == aa: cnt+=1 if cnt == 1: print "%s occurs in that sequence once" % aa else: print "%s occurs in that sequence %d times" % (aa, cnt) answer=raw_input("try again? [yn]") if answer == "n" or answer == "N": done = 1

13 6/15/05Introduction to Python – Part II13 Programming Workshop #2 Write a sliding window program to compute the %GC in a sequence of nucleotides. The program should prompt the user for The DNA sequence The window size (assume the window increment is 1)


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