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An Introduction to Python – Part II Dr. Nancy Warter-Perez April 20, 2004 Overview Solution to Programming Workshop #1 If tests Loops for while Example amino acid search program Programming Workshop #2 4/20/04 Introduction to Python – Part II 2 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]) 4/20/04 Introduction to Python – Part II 3 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]) 4/20/04 Introduction to Python – Part II 4 Python Basics – Relational and Logical Operators Relational operators == != > >= < <= 4/20/04 equal not equal greater than greater than or equal less than less than or equal Logical operators and or not Introduction to Python – Part II and or not 5 if Statement if expression: action 4/20/04 Example: a1 = 'A‘; a2 = 'C'; match = 0; if (a1 == a2) : match+=1; Introduction to Python – Part II 6 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; 4/20/04 Introduction to Python – Part II 7 String operations mystring = “Hello World!” Expression Value Purpose 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 4/20/04 Introduction to Python – Part II 8 Lists mylist=[“a”,”b”,3.58,”d”,4,0] mylist[0] mylist[2] a 3.58 Indexing mylist[-1] mylist[-2] 0 4 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 1 or True mylist.append(8) [“a”,”b”,3.58,”d”,4,0,8] 4/20/04 Introduction to Python – Part II Add to end of list 9 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”] 3.5 Value lookup mydict.has_key(“r”) True or 1 Check for keys mydict.update({“a”:75}) {8.5: 8, 'a': 75, 'r': 1, 'g': 2, 'y': 3.5, 9: 'nine'} 4/20/04 Introduction to Python – Part II Add pairs to dictionary 10 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: ! 4/20/04 Introduction to Python – Part II 11 while Statement while expression: action Example x = 0; while x != 3: x = x + 1/ 2 Infinite loop! Iteration Iteration Iteration Iteration 4/20/04 Introduction to Python – Part II 1: 2: 3: 4: x=0+1=1 x=1+1=2 x=2+1=3 don’t exec 12 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 4/20/04 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) Introduction to Python – Part II 13 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:"); 4/20/04 Introduction to Python – Part II 14 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 4/20/04 Introduction to Python – Part II 15 Creating a Python Program Enter your program in the editor Notice that the editor has a color coding Also notice that it automatically indents 4/20/04 Comments Key words Etc… Don’t override!! – this is how python tells when block statements end! If doesn’t indent to proper location – indicates bug Introduction to Python – Part II 16 Running your Program To build your program Under File->Run… 4/20/04 Select No Debugging in the drop-down window Fix any errors, then run again Introduction to Python – Part II 17 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. 4/20/04 Introduction to Python – Part II 18 Programming Homework #1 Due April 29th Modify your sliding window program from programming workshop #2 to compute the hydrophobicity of an amino acid sequence. Use the Kyte and Doolittle scale (programming workshop 1). Obtain the SWISSPROT entry of bacteriorhodopsin and compute the hydrophobicity. Plot your result in EXCEL and compare with plot from lecture 3 4/20/04 Introduction to Python – Part II 19