An Introduction to Python – Part II Dr. Nancy Warter-Perez April 21, 2005

4/21/05Introduction to Python – Part II2 Overview Solution to Programming Workshop #1 If tests Loops for while Example amino acid search program Programming Workshop #2

4/21/05Introduction 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])

4/21/05Introduction 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, 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])

4/21/05Introduction 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

4/21/05Introduction to Python – Part II6 if Statement if expression: action Example: a1 = 'A‘; a2 = 'C'; match = 0; if (a1 == a2) : match+=1;

4/21/05Introduction 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;

4/21/05Introduction to Python – Part II8 String operations mystring = “Hello World!” ExpressionValuePurpose len(mystring)12 number of characters in mystring “hello”+“world”“helloworld” Concatenate strings “%s world”%“hello”“hello world” Format strings (like sprintf) “world” == “hello” “world” == “world” 0 or False 1 or True Test for equality “a” < “b” “b” < “a” 1 or True 0 or False Alphabetical ordering

4/21/05Introduction to Python – Part II9 Lists mylist=[“a”,”b”,3.58,”d”,4,0] mylist[0] mylist[2] a 3.58 Indexing mylist[-1] mylist[-2] 0404 Negative indexing (counts from end) mylist[1:4][“b”,3.58,”d”]Slicing (like strings) “b” in mylist “e” not in mylist 1 or True mylist.append(8)[“a”,”b”,3.58,”d”,4,0,8]Add to end of list

4/21/05Introduction to Python – Part II10 Dictionaries mydict={“r”:1,”g”:2,”y”:3.5,8.5:8,9:”nine”} mydict.keys()['y', 8.5, 'r', 'g', 9]List of the keys mydict.values()[3.5, 8, 1, 2, 'nine']List of the values mydict[“y”]3.5Value lookup mydict.has_key(“r”)True or 1Check for keys mydict.update({“a”:75}){8.5: 8, 'a': 75, 'r': 1, 'g': 2, 'y': 3.5, 9: 'nine'} Add pairs to dictionary

4/21/05Introduction to Python – Part II11 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: !

4/21/05Introduction to Python – Part II12 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!

4/21/05Introduction to Python – Part II13 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)

4/21/05Introduction to Python – Part II14 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:");

4/21/05Introduction to Python – Part II15 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

4/21/05Introduction to Python – Part II16 Creating a Python Program Enter your program in the editor Notice that the editor has a color coding Comments Key words Etc… Also notice that it automatically indents Don’t override!! – this is how python tells when block statements end! If doesn’t indent to proper location – indicates bug

4/21/05Introduction to Python – Part II17 Running your Program To build your program Under File->Run… Select No Debugging in the drop-down window Fix any errors, then run again

4/21/05Introduction to Python – Part II18 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) Test your program using the data for Workshop 3.