stat115 stat225 bist512 bio298 - intro to computational biology python tutorial ii monty python,...

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]

[email protected]

mailto:[email protected]

mailto:[email protected]


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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Important Module: random

Method Result

randint(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


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


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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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

http://math.ucsd.edu/~crypto/cgi-bin/MontyKnows/monty1?0

http://programmingzen.com/2009/01/01/monte-carlo-simulation-of-the-monty-hall-problem-in-ruby-and-python/


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.py

Usage: from ex1_fasta import *

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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.py

Usage: python ex2_complimentarydna.py8

STAT115 STAT225 BIST512 BIO298 - Intro to Computational Biology 9

GAME OF LIFE


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.


Game of Life

• Run the game of life (in the terminal)– First Install Jython Standard package into – Then add to your .bash_profile

# For Jython

export JYTHON_HOME=/Users/dfernan/bin/jython2.5.2/

export PATH=$JYTHON_HOME:$PATH

export CLASSPATH=$JYTHON_HOME/jython.jar:$CLASSPATH

– jython LifeGame.py

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Solution: LifeGame.py (GridMutator.py)Usage: jython LifeGame.py


HH Question 5. Melting Temp

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HH Question 5. Melting Temp

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Usage: python q5.py q5_input.txt q5.output 20 55


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.fasta

Usage: Use it as a python module containing the fasta class and the read_fasta function

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Sequence Alignment

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How many operations? _____


Sequence Alignment

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HOMOLOGOUS

Paralogs

Orthologous


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


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? _______


Sequence Alignment

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• Strategy:

• Align the two sequences .• Read template code and think how to fill it in.

stat115 stat225 bist512 bio298 - intro to computational biology python tutorial ii monty python,...

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