python tutorial ii monty python, game of life and sequence alignment feb 1, 2011
DESCRIPTION
Python Tutorial II Monty Python, Game of Life and Sequence Alignment Feb 1, 2011. Daniel Fernandez and Alejandro Quiroz [email protected] [email protected]. 1 st ACT (1 hour) Random Module Monty Hall Game of Life Sequence Alignment INTERMISSION Chillout sessions (10 min) - PowerPoint PPT PresentationTRANSCRIPT
STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology
Python Tutorial II Monty Python, Game of Life
and Sequence AlignmentFeb 1, 2011
Daniel Fernandez and Alejandro Quiroz [email protected]
STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology
1st ACT (1 hour)Random Module
Monty HallGame of Life
Sequence Alignment
INTERMISSIONChillout sessions (10 min)
2nd ACT (1 hour 50 min)Homework help Q5, Q6, Q7 and Q8.
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STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology
Important Module: random
Method Resultrandint(x,y) Integer Random numbers between integer x and y
rand() Random()
distname(a,b) Uniform, Triangular, Gaussian, Lognormal, Negative, Exponential, Gamma, Beta, Pareto, Weibull
choice(list) Choose an element from a list at random
sample(list, k) Choose k elements from a list at random – without replacement!
shuffle(list) Shuffles the element in list
seed() Change the seed to generate random numbers
STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology
Example. Simulate Flip of a Coin.import randomcoin = [‘heads’, ‘tails’]num_heads = 0num_tails = 0for i in range(0,1000):
flip = random.choice(coin)if flip == ‘heads’:
num_heads += 1else:
num_tails += 1print ‘number of heads: ‘, num_headsprint ‘number of heads: ‘, num_tails
STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology
Monty Hall Problem
Suppose you’re on a game show, and you’re given a choice of three doors: Behind one door is a car; behind the others, goats. You pick a door, say number 3, and the host, who knows what’s behind the doors, opens another door, say number 2, which has a goat. He says to you, ‘Do you want to pick door number 1?’ Is it to your advantage to switch your choice of doors?
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STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology
Monty Hall Problem• Run montyhall.py to see the results.• Read montyhall.py and try to understand what
did the program do?
Visual Simulation.Python source.
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Solution: montyhall.pyUsage: python montyhall.py
STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology
Exercise 1. Read a fasta file.
• Write a python module for reading fasta files – add it to your utils.py module – if feeling lazy read q7 code.
Solution: ex1_fasta.pyUsage: from ex1_fasta import *
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STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology
Exercise 2. Complimentary DNA sequence and palindromic sequence
• Write a program that takes as an input a DNA sequence 5’ to 3’ and returns the same sequence 3’ to 5’ end (i.e., its reverse complement).
• Also make the program to output if the sequence is a palindromic sequence or not.
• HINT: http://en.wikipedia.org/wiki/Complementarity_(molecular_biology)
Solution: ex2_complimentarydna.pyUsage: python ex2_complimentarydna.py 8
STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology 9
GAME OF LIFE
STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology
Game of Life
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Life is a "game" or cellular automaton developed by Conway.
Instructions:
Start with a board of dimensions (x,y). Populate the board with an initial pattern of occupied and empty cells. In every turn, the rules are:
(i) if an empty cell has three neighbors, fill it next turn;
(ii) if an occupied cell has zero or one neighbor, it dies of loneliness; and
(iii) if an occupied cell has four or more neighbors, it dies of overcrowding.
STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology
Game of Life• Run the game of life (in the terminal)
– First Install Jython Standard package into – Then add to your .bash_profile
# For Jythonexport JYTHON_HOME=/Users/dfernan/bin/jython2.5.2/export PATH=$JYTHON_HOME:$PATHexport CLASSPATH=$JYTHON_HOME/jython.jar:$CLASSPATH
– jython LifeGame.py
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Solution: LifeGame.py (GridMutator.py)Usage: jython LifeGame.py
STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology
HH Question 5. Melting Temp
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STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology
HH Question 5. Melting Temp
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Usage: python q5.py q5_input.txt q5.output 20 55
STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology
HH Question 6. Longest Sequence
• Any ideas for retrieving the longest exact matching sequence between two sequences?
• How to read a fasta file? Write a function that takes a file name as an input and outputs a list containing each sequence in the fasta file.– If lazy, just look at homework q7.
Solution: fasta.py, Q8_input.fastaUsage: Use it as a python module containing the fasta class and the read_fasta function
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STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology
Sequence Alignment
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How many operations? _____
STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology
Sequence Alignment
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HOMOLOGOUS
Paralogs
Orthologous
STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology
Sequence Alignment
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STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology 18
• Align the following sequences and explain it. Bellow are the sequences and the match/mismatch (sub)BLOSUM matrix (HH1 and HH7)
Sequence Alignment
STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology
Sequence Alignment
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Dynamic Programming:“The art of dividing a problem into simpler (sub)problems and then apply the sub-solutions recursively in order to obtain the
final solution”
i
j
New best alignment = Best previous alignment + align (i,j)
How many operations? _____ Memory cost? _______
STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology
Sequence Alignment
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• Strategy:
• Align the two sequences .• Read template code and think how to fill it in.