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An Introduction to Python – Part II
Dr. Nancy Warter-Perez
June 15, 2005
Overview
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References
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Solution to Programming Workshop #1
If tests (PP Ch1, LP Ch 9)
Loops (PP Ch1, LP Ch 10)
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Python Programming for the Absolute Beginner (PP)
Learning Python (LP)
for
while
Example amino acid search program
Programming Workshop #2
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Solution to Programming Workshop 1
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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])
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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])
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Python Basics – Relational and
Logical Operators
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Relational operators
==
!=
>
>=
<
<=
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equal
not equal
greater than
greater than or
equal
less than
less than or equal
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Logical operators
and
or
not
Introduction to Python – Part II
and
or
not
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if Statement
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if expression:
action
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Example:
a1 = 'A‘; a2 = 'C';
match = 0;
if (a1 == a2) :
match+=1;
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if-elif-else Statement
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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;
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for Statement
for var in list:
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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: !
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while Statement
while expression:
action
Example
x = 0;
while x != 3:
x = x + 1/ 2
Infinite loop!
Iteration
Iteration
Iteration
Iteration
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2:
3:
4:
x=0+1=1
x=1+1=2
x=2+1=3
don’t exec
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Example: Amino Acid Search
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Write a program to count the number of
occurrences of an amino acid in a
sequence.
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The program should prompt the user for
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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
done=0
while (not done):
sequence=raw_input("Please enter a sequence:");
aa=raw_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
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
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Programming Workshop #2
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Write a sliding window program to compute
the %GC in a sequence of nucleotides.
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The program should prompt the user for
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The DNA sequence
The window size (assume the window increment is 1)
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