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 | + | These are available at the given link. |
|- | |- | ||
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* It has built-in-libraries for common tasks. | * It has built-in-libraries for common tasks. | ||
* We can manipulate DNA and protein sequences easily . | * We can manipulate DNA and protein sequences easily . | ||
− | |||
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'''Why Pyhton for biologists?''' | '''Why Pyhton for biologists?''' | ||
| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| | ||
− | * It has a large user base as it is commonly used in bioinformatics. | + | * It has a large user base as it is commonly used in '''bioinformatics'''. |
− | * Listed here are examples of few bioinformatic tools in Python: | + | * Listed here are examples of few '''bioinformatic''' tools in '''Python''': |
'''Biopython, Modeller, chemopy, BLASTorage, Pymol''' | '''Biopython, Modeller, chemopy, BLASTorage, Pymol''' | ||
− | For more information, refer the given website | + | For more information, refer the given website: |
[http://pythonforbiologists.com/ http://pythonforbiologists.com] | [http://pythonforbiologists.com/ http://pythonforbiologists.com] | ||
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'''Installation''' | '''Installation''' | ||
| 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;"| | | 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;"| | ||
− | * '''Python''' comes installed, by default on Ubuntu. | + | * '''Python''' comes installed, by default on '''Ubuntu'''. |
− | * IPython is an interactive terminal for Python | + | * '''IPython''' is an '''interactive terminal''' for '''Python''' |
− | * To install '''Python '''on '''Windows, Mac OS '''and '''Android '''devices, visit the given link | + | * To install '''Python '''on '''Windows, Mac OS '''and '''Android '''devices, visit the given link |
− | + | ||
|- | |- | ||
| 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;"| Open terminal by pressing '''Ctrl+Alt+T''' at the same time. | | 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;"| Open terminal by pressing '''Ctrl+Alt+T''' at the same time. | ||
− | | 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;"| Open the terminal by pressing '''Ctrl+Alt+T''' simultaneously. | + | | 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;"| Open the '''terminal''' by pressing '''Ctrl+Alt+T''' simultaneously. |
− | + | ||
− | + | ||
− | + | ||
+ | '''Python''' comes installed, by default on '''Ubuntu'''. | ||
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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 case you don't, then manually install the latest version of '''IPython''', by typing | | 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 case you don't, then manually install the latest version of '''IPython''', by typing | ||
− | '''sudo apt-get install ipython3''' | + | '''sudo apt-get install ipython3''' and press '''Enter.''' |
− | + | ||
− | and press '''Enter.''' | + | |
− | Give root password if asked. | + | Give '''root password''' if asked. |
|- | |- | ||
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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;"| Wait for a few minutes for the installation to complete. | | 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;"| Wait for a few minutes for the installation to complete. | ||
− | Note : '''Python3''' does not overwrite the default Python on the system | + | Note : '''Python3''' does not overwrite the default '''Python''' on the system. |
|- | |- | ||
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| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| To check whether '''ipython3''' is installed successfully on your system, | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| To check whether '''ipython3''' is installed successfully on your system, | ||
− | + | type '''ipython3 '''and press '''Enter.''' | |
|- | |- | ||
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Highlight the prompt | Highlight the prompt | ||
− | | 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;"| You will see few lines of information on '''Python '''like, the version number | + | | 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;"| You will see few lines of information on '''Python '''like, the version number. |
− | You will also see the '''Ipython ''' | + | You will also see the '''Ipython prompt''' on the '''terminal'''. |
− | Prompt indicates that '''Ipython '''is installed successfully. | + | '''Prompt''' indicates that '''Ipython '''is installed successfully. |
|- | |- | ||
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|- | |- | ||
| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on terminal | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Cursor on terminal | ||
− | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| To begin with, we will store data, i.e '''DNA sequence '''in a variable called '''my_DNA.''' | + | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| To begin with, we will store data, i.e '''DNA sequence, '''in a variable called '''my_DNA.''' |
|- | |- | ||
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A '''string''' is a data in the form of a text. | 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'''. | ||
|- | |- | ||
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Press '''Enter''' | Press '''Enter''' | ||
− | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| | + | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"|Type, |
− | + | '''my_DNA is equal to within double quotes ATGCGCAT.''' | |
− | + | Press '''Enter'''. | |
|- | |- | ||
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|- | |- | ||
| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Highlight '''my_DNA''' | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Highlight '''my_DNA''' | ||
− | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| For writing a code, we can use the variable name instead of the string itself. | + | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| For writing a code, we can use the variable name instead of the '''string''' itself. |
|- | |- | ||
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| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| To print the DNA sequence, | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| To print the DNA sequence, | ||
− | we will use '''print ''' | + | we will use '''print function.''' |
For that type, | For that type, | ||
− | '''print | + | '''print inside brackets my underscore DNA''' and press '''Enter.''' |
|- | |- | ||
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| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Press '''up '''arrow | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Press '''up '''arrow | ||
− | Add '''\n '''and '''DNA '''after '''ATGCGCAT | + | Add '''\n '''and '''DNA '''after '''ATGCGCAT'''. |
'''my_DNA = "ATGCGCAT\nDNA"''' | '''my_DNA = "ATGCGCAT\nDNA"''' | ||
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Lets edit this line. | Lets edit this line. | ||
− | Type '''\n | + | Type '''\n DNA '''after the sequence within double quotes. |
Press '''Enter.''' | Press '''Enter.''' | ||
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| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Type, | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Type, | ||
− | '''print | + | '''print inside brackets my underscore DNA''' and press '''Enter.''' |
− | + | ||
− | + | ||
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'''DNA''' | '''DNA''' | ||
− | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| The output prints the sequence on two separate lines | + | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| The output prints the sequence on two separate lines. |
− | + | ||
− | + | ||
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* Using example of a short proteinsequence given | * Using example of a short proteinsequence given | ||
− | + | * Print the sequence on a single line, | |
− | * Print the sequence on a single line, | + | * And print the sequence on two separate lines. |
− | + | ||
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|- | |- | ||
| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 10''' | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| '''Slide 10''' | ||
− | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Another useful built-in tool in '''Python''' is the '''len | + | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Another useful built-in tool in '''Python''' is the '''len function'''. |
It is used to calculate the length of a string. | It is used to calculate the length of a string. | ||
|- | |- | ||
− | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Let us go back to the terminal. | + | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Let us go back to the '''terminal'''. |
Press up arrow key | Press up arrow key | ||
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Press '''Enter''' | Press '''Enter''' | ||
− | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Let us go back to the terminal. | + | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Let us go back to the '''terminal'''. |
Press '''up '''arrow on the key board till we get this command on the '''terminal.''' | Press '''up '''arrow on the key board till we get this command on the '''terminal.''' | ||
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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;"| Another assignment for you | | 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;"| Another assignment for you | ||
− | * Calculate the length of the given '''DNA '''sequence | + | * Calculate the length of the given '''DNA '''sequence ''''ATGGCATGCGC'''' |
− | + | * And Store the output in a variable. | |
− | * | + | |
− | + | ||
|- | |- | ||
| 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;"| '''Slide 12''' | | 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;"| '''Slide 12''' | ||
− | | 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;"| Many times in biochemistry, sequences are represented either in | + | | 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;"| Many times in '''biochemistry''', sequences are represented either in lowercase or uppercase alphabets. |
− | + | ||
− | + | ||
− | + | ||
|- | |- | ||
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Press '''Enter.''' | Press '''Enter.''' | ||
− | | 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;"| To convert the uppercase alphabets in a string to | + | | 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;"| To convert the uppercase alphabets in a string to lowercase, we make use of '''lower() method. ''' |
− | + | Let us go back to the '''terminal.''' | |
− | + | ||
− | Let us go back to the terminal. | + | |
Type, | Type, | ||
− | '''my_DNA=”ATGCGCAT” | + | '''my_DNA=”ATGCGCAT”''' and press '''Enter''' |
+ | |||
− | Then type, '''my_DNA'''. | + | Then type, '''my_DNA dot lower open and close brackets''' . |
In a method, we write, | In a method, we write, | ||
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* The name of the variable first, | * The name of the variable first, | ||
* followed by a period(.), | * followed by a period(.), | ||
− | * then the name of the method | + | * then the name of the method, |
* then we open and close parentheses. | * then we open and close parentheses. | ||
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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;"| Highlight ''''atgcgcat'''' | | 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;"| Highlight ''''atgcgcat'''' | ||
− | | 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;"| The output shows the string in lowercase. | + | | 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;"| The output shows the '''string''' in lowercase. |
|- | |- | ||
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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;"| As an assignment, | | 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;"| As an assignment, | ||
− | Using example of a short protein | + | *Using example of a short protein sequence given |
− | + | *Convert the sequence to uppercase | |
− | sequence given | + | * Hint: Use '''upper() method.''' |
− | + | ||
− | Convert the sequence to uppercase | + | |
− | + | ||
− | ''' | + | |
|- | |- | ||
| 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;"| | | 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;"| | ||
− | | 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;"| Let us go back to terminal again | + | | 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;"| Let us go back to '''terminal''' again. |
|- | |- | ||
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my_protein = <tt>"alspadkanl"</tt> | my_protein = <tt>"alspadkanl"</tt> | ||
− | | 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;"| Lets take an example of an | + | | 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;"| Lets take an example of an '''amino acid''' sequence. |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
+ | Store it in a variable called '''my_protein'''. | ||
+ | So type '''my_protein = <tt>"alspadkanl"</tt>''' and press '''Enter'''. | ||
|- | |- | ||
| 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;"| Slide 14 | | 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;"| Slide 14 | ||
− | | 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;"| To find out the number of times an amino acid or a sequence of amino acids occurs in a string | + | | 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;"| 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. ''' |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
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Press '''Enter''' | Press '''Enter''' | ||
− | | 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;"| Let us go back to the terminal. | + | | 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;"| Let us go back to the '''terminal'''. |
− | For example to know the number of times | + | 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]] | |
− | + | ||
− | my_protein.count ('a') | + | |
Press '''Enter''' | Press '''Enter''' | ||
Line 405: | Line 379: | ||
|- | |- | ||
| 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;"| Highlight 3 | | 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;"| Highlight 3 | ||
− | | 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;"| | + | | 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;"| Output shows number 3. |
− | + | ||
− | + | ||
− | + | ||
+ | There are 3 '''Alanines''' in the '''string.''' | ||
Line 418: | Line 390: | ||
Press '''Enter''' | Press '''Enter''' | ||
− | | 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;"| Similarly to find number of''' Leucines''' in the string | + | | 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;"| Similarly to find number of''' Leucines''' in the '''string''', type |
− | + | my_protein.count('l') [[my underscore protein dot count open and close brackets within single quotes l]] | |
− | + | ||
− | my_protein.count('l') | + | |
Press '''Enter''' | Press '''Enter''' | ||
− | |||
− | |||
− | |||
|- | |- | ||
| 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;"| Highlight 2 | | 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;"| Highlight 2 | ||
− | | 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;"| We get an output as '''2''' | + | | 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;"| We get an output as '''2'''. |
+ | |||
+ | There are '''2 Leucines''' in the '''string'''. | ||
|- | |- | ||
| 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;"| Cursor on the terminal | | 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;"| Cursor on the terminal | ||
− | | 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;"| Similarly we can use DNA or an RNA sequence as string to count the | + | | 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;"| Similarly, we can use '''DNA''' or an '''RNA''' sequence as '''string''' to count the ocurrances of '''basepairs'''. |
|- | |- | ||
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− | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Let us summarize | + | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Let us summarize. |
In this tutorial we learnt: | In this tutorial we learnt: | ||
* Installation of '''IPython Interpreter''' | * Installation of '''IPython Interpreter''' | ||
− | + | * Storing data in variables using examples of '''DNA''' and '''Protein''' sequences. | |
− | * Storing data in variables using | + | |
− | + | ||
− | examples of '''DNA''' and '''Protein''' | + | |
− | + | ||
− | sequences. | + | |
− | + | ||
− | + | ||
* Printing a sequence in single and on two separate lines | * Printing a sequence in single and on two separate lines | ||
− | |||
− | |||
|- | |- | ||
Line 466: | Line 426: | ||
'''Summary''' | '''Summary''' | ||
| 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;"| | | 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;"| | ||
− | * Find the length of the string | + | * Find the length of the '''string''' |
− | + | * Change case of the '''string''' | |
− | * Change case of the string | + | * Count the number of times a character appears in a '''string''' |
− | + | ||
− | * Count the number of times a character appears in a string | + | |
− | + | ||
− | + | ||
|- | |- | ||
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'''Assignment''' | '''Assignment''' | ||
− | | 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;"| | + | | 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;"| As an assignment, |
− | + | ||
− | + | ||
− | + | ||
− | + | ||
− | + | ||
+ | *Calculate '''GC content''' in the given DNA sequence. | ||
+ | *'ATGGCATGCGC' | ||
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− | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Spoken Tutorial Project is supported by | + | | style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.049cm;padding-bottom:0.049cm;padding-left:0.191cm;padding-right:0.191cm;"| Spoken Tutorial Project is supported by NMEICT, MHRD, Government of India. |
More information on this Mission is available at this link. | More information on this Mission is available at this link. | ||
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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;"| This script is contributed by Snehalatha and Trupti Kini. | | 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;"| This script is contributed by Snehalatha and Trupti Kini. | ||
− | And this is Trupti Kini from | + | And this is Trupti Kini from IIT Bombay signing off. |
Thanks for joining. | Thanks for joining. | ||
|} | |} |
Latest revision as of 14:51, 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. |
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.
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. Let us 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 |
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 inside brackets my underscore 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 DNA after the sequence within double quotes. Press Enter. |
Type,
print(my_DNA) and press Enter |
Type,
print inside brackets my underscore 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” and press Enter
In a method, we write,
Press Enter. |
Highlight 'atgcgcat' | The output shows the string in lowercase. |
Slide 13
Assignment |
As an assignment,
|
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. So type my_protein = "alspadkanl" and press Enter. |
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') my underscore protein dot count open and close brackets within single quotes 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') my underscore protein dot count open and close brackets within single quotes 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 ocurrances of basepairs. |
Slide 15
Summary
|
Let us summarize.
In this tutorial we learnt:
|
Slide 16
Summary |
|
Slide 17
Assignment |
As an assignment,
|
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 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. |