Difference between revisions of "Python for Biologists/C2/Introduction-to-Python-for-Biologists/English"
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You can also refer to '''Spoken Tutorials''' on '''Python''' for better understanding of this tutorial. | You can also refer to '''Spoken Tutorials''' on '''Python''' for better understanding of this tutorial. | ||
| − | These are available at '''www.spoken-tutorial.org''' | + | These are available at the given link '''www.spoken-tutorial.org''' |
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| style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| In '''Python''' language, data such as '''protein''' and '''DNA''' sequences are called as '''strings'''. | | style="background-color:#ffffff;border-top:none;border-bottom:0.75pt solid #000001;border-left:0.75pt solid #000001;border-right:0.75pt solid #000001;padding-top:0cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| In '''Python''' language, data such as '''protein''' and '''DNA''' sequences are called as '''strings'''. | ||
| − | A '''string''' is a data in the form of a text. | + | A '''string''' is a data in the form of a text. Letus go back to the terminal. Let us first clear the terimal by typing clear and press enter. |
|- | |- | ||
Revision as of 13:03, 13 August 2014
Title of script: Introduction to Python for Biologists
Author: Trupti Rajesh Kini & Snehalatha
Keywords: video tutorial, Python, DNA seqences, Protein sequences, Biologists
| Visual Cue | Narration |
| Slide 1 | Welcome to the spoken-tutorial on Introduction to Python for Biologists. |
| Slide 2
Learning Objectives |
In this tutorial we will learn,
|
| Slide 3
System Requirements
|
To record this tutorial, I am using
|
| Slide 4
Prerequisites
|
To practice this tutorial you should be familiar with,
You can also refer to Spoken Tutorials on Python for better understanding of this tutorial. These are available at the given link www.spoken-tutorial.org |
| Slide 5
Why Python for biologists? |
Some of the features of Python useful for biologists are as follows:
|
| Slide 6
Why Pyhton for biologists? |
Biopython, Modeller, chemopy, BLASTorage, Pymol For more information, refer the given website : |
| Slide 7
Installation |
|
| Open terminal by pressing Ctrl+Alt+T at the same time. | Open the terminal by pressing Ctrl+Alt+T simultaneously.
Python comes installed, by default on Ubuntu.
|
| Type sudo apt-get install ipython3
and press Enter. |
In case you don't, then manually install the latest version of IPython, by typing
sudo apt-get install ipython3 and press Enter. Give root password if asked. |
| Cursor on the terminal. | Wait for a few minutes for the installation to complete.
Note : Python3 does not overwrite the default Python on the system |
| Open the terminal
Type ipython3 and press Enter. |
To check whether ipython3 is installed successfully on your system,
Type ipython3 and press Enter. |
| Cursor on the terminal
Highlight the prompt |
You will see few lines of information on Python like, the version number etc.
You will also see the Ipython prompt on the terminal. Prompt indicates that Ipython is installed successfully. |
| Cursor on terminal | Let's type a few simple Python commands with an example of a DNA sequence. |
| Cursor on terminal | To begin with, we will store data, i.e DNA sequence in a variable called my_DNA. |
| Slide 8
What is a string? |
In Python language, data such as protein and DNA sequences are called as strings.
A string is a data in the form of a text. Letus go back to the terminal. Let us first clear the terimal by typing clear and press enter. |
| Type in the terminal,
my_DNA = "ATGCGCAT" Highlight my_DNA Press Enter |
Let us go back to the terminal.
Type, my_DNA is equal to within double quotes ATGCGCAT.Press Enter. |
| Highlight my_DNA | We call this as assigning a variable. |
| Highlight my_DNA | For writing a code, we can use the variable name instead of the string itself. |
| Type,
print(my_DNA) and press Enter |
To print the DNA sequence,
we will use print function. For that type, print(my_DNA) and press Enter. |
| Highlight the output,
ATGCGCAT |
We get the sequence as output. |
| Cursor on the terminal. | Now let us print the sequence on two separate lines. |
| Press up arrow
Add \n and DNA after ATGCGCAT . my_DNA = "ATGCGCAT\nDNA" Press Enter |
Press up arrow on the key board till we get this command on the terminal.
my_DNA = "ATGCGCAT” Lets edit this line. Type \n and DNA after the sequence within double quotes. Press Enter. |
| Type,
print(my_DNA) and press Enter |
Type,
print(my_DNA) and press Enter.
|
| Highlight the output
ATGCGCAT DNA |
The output prints the sequence on two separate lines ,
|
| Slide 9
Assignment |
As an assignment,
|
| Cursor on the terminal | Let us now learn a few more functions and methods. |
| Slide 10 | Another useful built-in tool in Python is the len function.
It is used to calculate the length of a string. |
| Let us go back to the terminal.
Press up arrow key my_DNA = "ATGCGCAT" Press Enter |
Let us go back to the terminal.
Press up arrow on the key board till we get this command on the terminal. my_DNA = "ATGCGCAT” Press Enter |
| Type:
len(my_DNA) |
To find the length of the DNA sequence in a variable, type,
len within brackets my_DNA Press Enter. |
| Cursor on the terminal | The output on the screen shows the number 8.
This is the length of the DNA sequence stored in the variable my_DNA. |
| Slide 11
Assignment |
Another assignment for you
|
| Slide 12 | Many times in biochemistry, sequences are represented either in lowercase or uppercase alphabets.
|
| Type,
my_DNA=”ATGCGCAT” Press Enter Type my_DNA.lower() Press Enter. |
To convert the uppercase alphabets in a string to lowercase:
We make use of lower() method. Let us go back to the terminal. Type, my_DNA=”ATGCGCAT”. Press Enter Then type, my_DNA.lower(). In a method, we write,
Press Enter. |
| Highlight 'atgcgcat' | The output shows the string in lowercase. |
| Slide 13
Assignment |
As an assignment,
Using example of a short protein sequence given Convert the sequence to uppercase. Hint: Use upper() method. |
| Let us go back to terminal again | |
| Type
my_protein = "alspadkanl" |
Lets take an example of an amino acid sequence.
Store it in a variable called my_protein my_protein = "alspadkanl"
|
| Slide 14 | To find out the number of times an amino acid or a sequence of amino acids occurs in a string.
We make use of count function
|
| Type
my_protein.count ('a') Press Enter |
Let us go back to the terminal.
For example to know the number of times amino acid Alanine occurs in the string Type my_protein.count ('a') Press Enter |
| Highlight 3 | Output shows number 3.
There are 3 Alanines in the string.
|
| Type
my_protein.count('l') Press Enter |
Similarly to find number of Leucines in the string
Type my_protein.count('l') Press Enter
|
| Highlight 2 | We get an output as 2, there are 2 Leucines in the string. |
| Cursor on the terminal | Similarly we can use DNA or an RNA sequence as string to count the ocurrences of basepairs . |
| Slide 15
Summary
|
Let us summarize,
In this tutorial we learnt:
examples of DNA and Protein sequences.
|
| Slide 16
Summary |
|
| Slide 17
Assignment |
Here is an assignment,
Calculate GC content in the given DNA sequence. 'ATGGCATGCGC'
|
| Slide 18
About Spoken Tutorial Project
|
The video available at the following link summarizes the Spoken Tutorial project. Pls watch it. |
| Slide 19
About Spoken Tutorial workshops
|
The Spoken Tutorial Project Team conducts workshops and gives certificates to those who pass an online test.
For more details, please write to us. |
| Slide 20
Acknowledgement
|
Spoken Tutorial Project is supported by the NMEICT, MHRD, Government of India.
More information on this Mission is available at this link. |
| This script is contributed by Snehalatha and Trupti Kini.
And this is Trupti Kini from IIT Bombay signing off. Thanks for joining. |
