An Introduction to Python

1
An Introduction to Python Part II

• Dr. Nancy Warter-Perez
• April 12, 2007

2
Overview

• Solution to Programming Workshop 1
• If tests
• Loops
• for
• while
• Example amino acid search program
• Programming Workshop 2

3
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,
  hydroaa)

4
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, hydroaa)
5
Python Basics Relational and Logical Operators

• Relational operators
• equal
• ! not equal
• gt greater than
• gt greater than or
• equal
• lt less than
• lt less than or equal

• Logical operators
• and and
• or or
• not not

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if Statement

• if expression
• action

• Example
• a1 'A a2 'C'
• match 0
• if (a1 a2)
• match1

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if-elif-else Statement

• if expression
• action 1
• elif expression action 2else
• action 3

• Example
• a1 'A a2 'C'
• match 0 gap 0
• if (a1 a2)
• match1
• elif (a1 gt a2)
• else
• gap1

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String operations
mystring Hello World! mystring Hello World! mystring Hello World!
Expression Value Purpose
len(mystring) 12 number of characters in mystring
helloworld helloworld Concatenate strings
s worldhello hello world Format strings (like sprintf)
world hello world world 0 or False 1 or True Test for equality
a lt b b lt a 1 or True 0 or False Alphabetical ordering
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Lists
mylista,b,3.58,d,4,0 mylista,b,3.58,d,4,0 mylista,b,3.58,d,4,0
mylist0 mylist2 a 3.58 Indexing
mylist-1 mylist-2 0 4 Negative indexing (counts from end)
mylist14 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 Add to end of list
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Dictionaries
mydictr1,g2,y3.5,8.58,9nine mydictr1,g2,y3.5,8.58,9nine mydictr1,g2,y3.5,8.58,9nine
mydict.keys() 'y', 8.5, 'r', 'g', 9 List of the keys
mydict.values() 3.5, 8, 1, 2, 'nine' List of the values
mydicty 3.5 Value lookup
mydict.has_key(r) True or 1 Check for keys

mydict.update(a75) 8.5 8, 'a' 75, 'r' 1, 'g' 2, 'y' 3.5, 9 'nine' Add pairs to dictionary
11
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) -gt 0,1,2,3,4

• Example
• mylisthello,hi,hey,!
• for i in mylist
• print i

Iteration 1 prints hello Iteration 2 prints
hi Iteration 3 prints hey Iteration 4 prints !
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while Statement

• Example
• x 0
• while x ! 3
• x x 1

• while expression
• action

/ 2 Infinite loop!
Iteration 1 x011 Iteration 2
x112 Iteration 3 x213 Iteration 4 dont
exec
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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)

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Example Amino Acid Search (2)
this program will calculate the number of
occurrences of an amino acid in a sequence by
Bryce Ready done0 while (not done)
sequenceraw_input("Please enter a sequence")
aaraw_input("Please enter the amino acid to
look for")
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Example Amino Acid Search (3)
compute the number of occurrences using for
loop cnt0 for i in sequence
if i aa cnt1 if cnt 1
print "s occurs in that sequence once"
aa else print "s occurs in that
sequence d times" (aa, cnt)
answerraw_input("try again? yn") if answer
"n" or answer "N" done 1
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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
• Dont override!! this is how python tells when
  block statements end!
• If doesnt indent to proper location indicates
  bug

17
Running your Program

• To build your program
• Under File-gtRun
• Select No Debugging in the drop-down window
• Fix any errors, then run again

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File I/O

• To open a file
• myfile open('pathname', ltmodegt)
• modes
• 'r' read
• 'w' write
• Ex infile open("D\\Docs\\test.txt", 'r')
• Ex outfile open("out.txt", 'w') in same
  directory

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Common input file operations
Operation Interpretation
input open ('file', 'r') open input file
S input.read() read entire file into string S
S input.read(N) Read N bytes (Ngt 1)
S input.readline() Read next line
L input.readlines() Read entire file into list of line strings
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Common output file operations
Operation Interpretation
output open('file', 'w') create output file
output.write(S) Write string S into file
output.writelines(L) Write all line strings in list L into file
output.close() Manual close (good habit)
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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.