Transcript An Introduction to Python – Part II Dr. Nancy Warter-Perez Overview    Solution to Programming Workshop #1 If tests Loops     for while Example amino acid search program Programming Workshop.

An Introduction to Python – Part II
Dr. Nancy Warter-Perez
Overview
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Solution to Programming Workshop #1
If tests
Loops
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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
==
!=
>
>=
<
<=
equal
not equal
greater than
greater than or
equal
less than
less than or equal
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Logical operators
and
or
not
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and
or
not
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if Statement
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if expression:
action
Example:
a1 = 'A'
a2 = 'C'
match = 0
if a1 == a2 :
match = 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:
mismatch = 0
match = 0; gap = 0
if a1[i] == a2[j]:
match+=1
elif a1[i] == '-' or a2[i]] == '-' :
gap += 1
else:
mismatch += 1
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String operations
mystring = “Hello World!”
Expression
Value
Purpose
len(mystring)
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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
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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]
Introduction to Python – Part II
Add to end of list
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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”]
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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'}
Introduction to Python – Part II
Add pairs to
dictionary
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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:
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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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Creating a Python Program
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Enter your program in the editor
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Notice that the editor has a color coding
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Comments
Key words
Etc…
Also notice that it automatically indents
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Don’t override!! – this is how python tells when block
statements end!
If doesn’t indent to proper location – indicates bug
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Running your Program
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To build your program
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Under File->Run…
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Select No Debugging in the drop-down window
Fix any errors, then run again
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File I/O
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To open a file
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myfile = open('pathname', <mode>)
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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
input = open ('file', 'r')
S = input.read()
S = input.read(N)
S = input.readline()
L = input.readlines()
Interpretation
open input file
read entire file into
string S
Read N bytes (N>= 1)
Read next line
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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Homework #1P
Chapter 13 – Problem 2
Write a sliding window program that computes the %GC of DNA
sequence. The program should prompt the user for the DNA
sequence and the window size. You can assume that the
window increment is 1, that is, as the program slides the
window it will move the window over one nucleotide.
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Test your program on the following DNA sequence:
GAACTCATACGAATTCACGTCAGCCCATCGTGCCACGT
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Homework #1P
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Chapter 13 – Problem 5
Write a program to detect transmembrane regions in a protein. Your
program should input the protein file and the results.txt file generated
by the Kyte_Doolittle_v3.py program. Kyte and Doolittle found that to
detect transmembrane regions in a protein a window size of 19 is
needed. Transmembrane regions are identified by average hydropathy
scores greater than 1.6. Your program should output the following
information in tabular form:
****************** Transmembrane Regions ******************
Window
Window Sequence
Average Hydropathy (> 1.6)
Steps:
1.
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Write your program.
Run the Kyte_Doolittle_v3.py program (see exercise 3) on the
bacteriorhodopsin protein with a window size of 19.
Test your program using the bacteriorhodopsin protein file with the
result.txt file generated from step ii.
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