Difference between revisions of "Python for Biologists/C2/Introduction-to-Python-for-Biologists/English"

Learning Objectives

• Installation of Python/IPython interpreter.
• Simple Python programs using examples of DNA and Protein sequences.

System Requirements

• Ubuntu OS version 12.04
• Python 3.2.3
• IPython 0.12.1

Prerequisites

• Basic biochemistry

You can also refer to Spoken Tutorials on Python for better understanding of this tutorial.

These are available at the given link.

Why Python for biologists?

• Python has many tools to write small programs that are useful in biology.
• It has a consistent syntax.
• It has built-in-libraries for common tasks.
• We can manipulate DNA and protein sequences easily .

Why Pyhton for biologists?

• It has a large user base as it is commonly used in bioinformatics.
• Listed here are examples of few bioinformatic tools in Python:

Biopython, Modeller, chemopy, BLASTorage, Pymol

For more information, refer the given website:

http://pythonforbiologists.com

Installation

• Python comes installed, by default on Ubuntu.
• IPython is an interactive terminal for Python
• To install Python on Windows, Mac OS and Android devices, visit the given link

Python comes installed, by default on Ubuntu.

and press Enter.

sudo apt-get install ipython3 and press Enter.

Give root password if asked.

Note : Python3 does not overwrite the default Python on the system.

Type ipython3 and press Enter.

type ipython3 and press Enter.

Highlight the prompt

You will also see the Ipython prompt on the terminal.

Prompt indicates that Ipython is installed successfully.

What is a string?

A string is a data in the form of a text.

Let us go back to the terminal.

Let us first clear the terimal by typing clear and press Enter.

my_DNA = "ATGCGCAT"

Highlight my_DNA

Press Enter

my_DNA is equal to within double quotes ATGCGCAT.

Press Enter.

print(my_DNA) and press Enter

we will use print function.

For that type,

print inside brackets my underscore DNA and press Enter.

ATGCGCAT

Add \n and DNA after ATGCGCAT.

my_DNA = "ATGCGCAT\nDNA"

Press Enter

my_DNA = "ATGCGCAT”

Lets edit this line.

Type \n DNA after the sequence within double quotes.

Press Enter.

print(my_DNA) and press Enter

print inside brackets my underscore DNA and press Enter.

ATGCGCAT

DNA

Assignment

• Using example of a short proteinsequence given
• Print the sequence on a single line,
• And print the sequence on two separate lines.

It is used to calculate the length of a string.

Press up arrow key

my_DNA = "ATGCGCAT"

Press Enter

Press up arrow on the key board till we get this command on the terminal.

my_DNA = "ATGCGCAT”

Press Enter

len(my_DNA)

len within brackets my_DNA

Press Enter.

This is the length of the DNA sequence stored in the variable my_DNA.

Assignment

• Calculate the length of the given DNA sequence 'ATGGCATGCGC'
• And Store the output in a variable.

my_DNA=”ATGCGCAT”

Press Enter

Type my_DNA.lower()

Press Enter.

Let us go back to the terminal.

Type,

my_DNA=”ATGCGCAT” and press Enter

Then type, my_DNA dot lower open and close brackets .

In a method, we write,

• The name of the variable first,
• followed by a period(.),
• then the name of the method,
• then we open and close parentheses.

Press Enter.

Assignment

• Using example of a short protein sequence given
• Convert the sequence to uppercase
• Hint: Use upper() method.

my_protein = "alspadkanl"

Store it in a variable called my_protein.

So type my_protein = "alspadkanl" and press Enter.

my_protein.count ('a')

Press Enter

For example, to know the number of times amino acid Alanine occurs in the string, type

my_protein.count ('a') my underscore protein dot count open and close brackets within single quotes a

Press Enter

There are 3 Alanines in the string.

my_protein.count('l')

Press Enter

my_protein.count('l') my underscore protein dot count open and close brackets within single quotes l

Press Enter

There are 2 Leucines in the string.

Summary

In this tutorial we learnt:

• Installation of IPython Interpreter
• Storing data in variables using examples of DNA and Protein sequences.
• Printing a sequence in single and on two separate lines

Summary

• Find the length of the string
• Change case of the string
• Count the number of times a character appears in a string

Assignment

• Calculate GC content in the given DNA sequence.
• 'ATGGCATGCGC'

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Acknowledgement

More information on this Mission is available at this link.

And this is Trupti Kini from IIT Bombay signing off.

Thanks for joining.