PoojaMoolya at 11:56, 10 March 2017

2017-03-10T11:56:55Z

PoojaMoolya at 07:48, 10 March 2017

2017-03-10T07:48:13Z

Sandhya.np14 at 12:51, 3 August 2016

2016-08-03T12:51:17Z

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Sandhya.np14 at 18:00, 2 August 2016

2016-08-02T18:00:34Z

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PoojaMoolya: Created page with "{| Border=1 ! Time ! Narration |- | 00:01 | Hello everyone. |- | 00:02 | Welcome to this tutorial on '''Parsing Data.''' |- | 00:06 | In t..."

2016-06-06T06:44:29Z

Created page with "{| Border=1 ! <center>Time</center> ! <center>Narration</center> |- | 00:01 | Hello everyone. |- | 00:02 | Welcome to this tutorial on '''Parsing Data.''' |- | 00:06 | In t..."

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{| Border=1
! <center>Time</center>
! <center>Narration</center>

|-
| 00:01
| Hello everyone.

|-
| 00:02
| Welcome to this tutorial on '''Parsing Data.'''

|-
| 00:06
| In this tutorial, we will learn to, Download '''FASTA''' and '''GenBank''' files from '''NCBI''' database website.

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| 00:14
| And '''Parse''' data files using functions in '''Sequence Input/Output''' module.

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| 00:19
| To follow this tutorial you should be familiar with, Undergraduate Biochemistry or Bioinformatics

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| 00:26
| And basic '''Python''' programming

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| 00:30
| Refer to the '''Python''' tutorials at the given link.

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| 00:34
| To record this tutorial I am using '''Ubuntu''' OS version. 14.10

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| 00:40
| '''Python''' version 2.7.8

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| 00:44
| '''Ipython interpretor''' version 2.3.0

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| 00:48
| '''Biopython''' 1.64 and '''Mozilla Firefox '''browser 35.0

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| 00:56
| Scientific data in biology is generally stored in text files such as '''FASTA''', '''GenBank''', '''EMBL''', '''Swiss-Prot''' etc

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| 01:07
|Data files can be download from the database websites.

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| 01:12
|Open the website link given below in any web browser.

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| 01:17
| A web-page opens.

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| 01:19
|Let us download '''FASTA''' and '''GenBank''' files for human '''insulin''' gene.

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| 01:25
|In the search box type, '''human insulin''' click on search button.

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| 01:31
| The web-page shows many files for human insulin gene.

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| 01:35
|For demonstration, I will select 4 files with the name “'''Homo sapiens Insulin mRNA”. '''

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| 01:43
|I will choose files that have less than 500 base pairs.

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| 01:48
|Click on the check box to select the file to download.

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| 01:56
| Bring the cursor to the “'''Send to'''” option, located at the top right corner of the page.

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| 02:02
|Click on the small selection button with a down arrow present next to the “'''Send to'''” button.

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| 02:09
| Under the heading “'''Choose destination'''” Click on “'''File'''” option.
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| 02:13
|You can save this file in any file format listed under “'''format'''” drop down list box.

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| 02:21
|Choose “'''FASTA'''” from the given options.

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| 02:25
|Then click on “'''Create file'''” option.

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| 02:29
| A dialog box appears on the screen.

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|02:32
|Select “'''Open with'''” click on '''OK .'''

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| 02:36
| A file opens in a text editor.

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| 02:39
|The file shows 4 records, since we had selected four files to download.

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| 02:46
|The first line in each record is an '''identifier''' line,

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| 02:50
|It starts with a “greater than (>) symbol”.

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| 02:53
|This is followed by a '''sequence'''.

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| 02:56
|Save the file in your home folder as “'''sequence.fasta'''”.

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| 03:01
|Close the text editor.

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| 03:03
| Follow the same steps as above to download the files in '''GenBank''' format

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| 03:08
|For the same files selected earlier.

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| 03:12
|Select the file format as '''GenBank.'''

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| 03:16
|'''Create file''', open with a text editor.

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| 03:21
| Notice that the sequence file in '''GenBank''' format has more features than a '''FASTA''' file.

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| 03:27
|Save the file as '''sequence.gb '''in your home folder'''.'''Close the text editor'''.'''

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| 03:34
| For demonstration purpose we need a FASTA file with a single record.

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| 03:39
|For this, clear the earlier selection by again clicking on the check boxes.

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| 03:48
|Now select the file “'''Human insulin gene complete cds'''”.

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| 03:54
|Click on the check box.

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| 03:57
| And Follow the same steps shown earlier to save the file in the home folder.

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| 04:01
|Save the file as '''insulin.fasta.'''

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| 04:08
| Biological data stored in these files can be extracted and modified using '''Biopython''' libraries.

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| 04:16
|Close the text editor.

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| 04:19
| Extracting data from data files is called as '''Parsing'''.

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| 04:23
|Most file formats can be parsed using functions available in '''SeqIO''' module.

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| 04:30
|Most commonly used functions of '''SeqIO''' module are, '''parse''', '''read''', '''write''', and '''convert'''.

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| 04:38
| Open the terminal by pressing '''ctrl''', '''alt''' and '''t''' keys simultaneously.

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| 04:44
| Start '''Ipython''' by typing '''ipython''' at the prompt. Press enter.

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| 04:51
| Next import '''SeqIO''' module from '''Bio''' package.

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| 04:56
| At the prompt type,'''from Bio import SeqIO'''. Press enter

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| 05:04
| We will start with the most important function “'''parse'''”.

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|05:07
|For demonstration, I will use a '''FASTA''' file that has many records, which we had downloaded earlier from the database.

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| 05:17
| For simple '''FASTA''' parsing, type the following at the prompt.

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| 05:22
|Here we are using the '''parse''' function to read contents of '''sequence.fasta''' file.

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| 05:30
|For the output print, '''record id''', sequence present in the record and also the length of the sequence.
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| 05:41
|Also notice that the '''parse''' function is used to read sequence data as '''Sequence record objects'''.

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| 05:48
|It is generally used with a '''for''' loop.

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| 05:52
|It can accept two '''arguments''', the first one is the file name to read the data.

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| 05:59
|The second specifies the file format.

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| 06:02
|Press enter key twice to get the output.

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| 06:07
| The output shows the''' identifier line, '''followed by the sequence contained in the file, also the length of the sequence for all the records in the file.

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| 06:21
|Notice that the '''FASTA''' format does not specify the alphabet.

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| 06:26
|So, the output does not specifies it as as a '''DNA sequence'''.

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| 06:31
| The same steps can be repeated for parsing '''GenBank''' file.

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| 06:36
|For Demonstration we will use the '''GenBank''' file which we have download earlier from the database.

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| 06:43
|Press up arrow key to get the lines of code which we had used earlier.

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| 06:49
|Change the file name to '''sequence.gb '''
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| 06:53
|Change the file format to '''genbank.'''

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| 06:56
|The rest of the code remains same.

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| 06:58
| Press enter key twice to get the output.

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| 07:03
|Here too the output shows the '''record id''', sequence and the length of the sequence for all the records in the file.

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| 07:12
|Notice that the '''GenBank''' format specifies the sequence as DNA sequence.

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| 07:19
| Similarly '''Swiss-prot''' and '''EMBL''' files can be parsed using same code as above.

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| 07:27
| If your file contains a single record then type the following lines for '''parsing'''.

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| 07:34
| Here we will use the previously saved FASTA file with a single record, that is '''insulin.fasta '''as an example'''.'''

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| 07:43
|Notice that we have used '''read''' function instead of parse function. Press Enter

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| 07:50
| The output shows the contents for the file '''insulin.fasta'''.

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| 07:55
|It shows the sequence as sequence record object.

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| 07:59
|And other attributes such as '''GI, accession number '''and '''description'''.

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| 08:06
| We can also view the individual attributes of this record as follows.

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| 08:11
|At the prompt type, '''record dot seq '''. Press enter

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| 08:18
| The output shows the sequence present in the file.

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| 08:22
| To view the identifiers for this record, type, '''record dot id.''' Press enter

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| 08:29
|The output shows the GI number and accession number etc.

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| 08:34
|You can use the function described above to parse the data files of your choice.

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| 08:40
| Now Let's summarize,

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| 08:42
|In this tutorial we have learnt, to Download '''FASTA''' and '''GenBank''' files from '''NCBI''' database website, and use '''parse''' and '''read''' functions from the '''SeqIO''' module:

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| 08:55
|To extract data such as record ids, description and sequences, from '''FASTA''' and '''GenBank''' files.

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| 09:03
| Now for the assignment,

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| 09:06
|Download '''FASTA''' files for nucleotide sequence of your choice from '''NCBI''' database.

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| 09:13
|Convert the file of sequences to their reverse complements.

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| 09:17
| Your completed assignment should have the following lines of code.

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| 09:22
|Use '''parse''' function to load nucleotide sequences from the '''FASTA''' file.

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| 09:28
|Next print reverse complements using the Sequence object’s built in reverse complement method.

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| 09:37
| Video at the following link, summarizes the spoken-tutorial project.

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| 09:42
|Please download and watch it.

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| 09:44
| The Spoken Tutorial Project Team Conducts workshops and gives certificates to those who pass an on-line test.

|-
| 09:51
|For more details, please write to us.

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| 09:55
| The Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

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| 10:01
|More information on this Mission is available at the link shown.

|-
| 10:06
|This is Snehalatha from IIT Bombay signing off. Thank you for joining.

|}

@@ Line 370: / Line 370: @@
 |-
 | 08:42
-|In this tutorial, we have learnt:
+|In this tutorial, we have learnt:to download '''FASTA''' and '''GenBank''' files from '''NCBI''' database website and use '''parse''' and '''read''' functions from the '''SeqIO''' module
- to download '''FASTA''' and '''GenBank''' files from '''NCBI''' database website
- and use '''parse''' and '''read''' functions from the '''SeqIO''' module
 |-

@@ Line 5: / Line 5: @@
 |-
 | 00:01
-| Hello everyone.
+| Hello everyone.Welcome to this tutorial on '''Parsing Data.'''
-−
-|-
-| 00:02
-| Welcome to this tutorial on '''Parsing Data.'''
 |-
@@ Line 37: / Line 33: @@
 |-
 | 00:40
-|* '''Python''' version 2.7.8
+| '''Python''' version 2.7.8
 |-
 | 00:44
-|* '''Ipython interpretor''' version 2.3.0
+| '''Ipython interpretor''' version 2.3.0
 |-
 | 00:48
-|* '''Biopython''' version 1.64 and * '''Mozilla Firefox '''browser 35.0.
+|'''Biopython''' version 1.64 and * '''Mozilla Firefox '''browser 35.0.
 |-
@@ Line 375: / Line 371: @@
 | 08:42
 |In this tutorial, we have learnt:
-* to download '''FASTA''' and '''GenBank''' files from '''NCBI''' database website
+ to download '''FASTA''' and '''GenBank''' files from '''NCBI''' database website
-* and use '''parse''' and '''read''' functions from the '''SeqIO''' module
+ and use '''parse''' and '''read''' functions from the '''SeqIO''' module
 |-

Biopython/C2/Parsing-Data/English-timed - Revision history

PoojaMoolya at 11:56, 10 March 2017

PoojaMoolya at 07:48, 10 March 2017

Sandhya.np14 at 12:51, 3 August 2016

Sandhya.np14 at 18:00, 2 August 2016

PoojaMoolya: Created page with "{| Border=1 ! Time ! Narration |- | 00:01 | Hello everyone. |- | 00:02 | Welcome to this tutorial on '''Parsing Data.''' |- | 00:06 | In t..."