Biopython/C2/Parsing-Data/English-timed

Time	Narration
00:01	Hello everyone.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.
00:14	And, Parse data files using functions in Sequence Input/Output module.
00:19	To follow this tutorial, you should be familiar with undergraduate biochemistry or bioinformatics
00:26	and basic Python programming.
00:30	Refer to the Python tutorials at the given link.
00:34	To record this tutorial, I am using: * Ubuntu OS version 14.10
00:40	Python version 2.7.8
00:44	Ipython interpretor version 2.3.0
00:48	Biopython version 1.64 and * Mozilla Firefox browser 35.0.
00:56	Scientific data in biology is generally stored in text files such as FASTA, GenBank, EMBL, Swiss-Prot etc.
01:07	Data files can be downloaded from the database websites.
01:12	Open the website link given below, in any web browser.
01:17	A web-page opens.
01:19	Let us download FASTA and GenBank files for human insulin gene.
01:25	In the search box, type: "human insulin", click on Search button.
01:31	The web-page shows many files for human insulin gene.
01:35	For demonstration, I will select 4 files with the name “Homo sapiens Insulin mRNA”.
01:43	I will choose files that have less than 500 base pairs.
01:48	Click on the check-box to select the file, to download.
01:56	Bring the cursor to the “Send to” option, located at the top right corner of the page.
02:02	Click on the small selection button with a down arrow, present next to the “Send to” button.
02:09	Under the heading “Choose destination”, click on File option.
02:13	You can save this file in any file format, listed under format drop-down list box.
02:21	Choose FASTA from the given options.
02:25	Then click on Create file option.
02:29	A dialog-box appears on the screen.
02:32	Select Open with, click on OK.
02:36	A file opens in a text editor.
02:39	The file shows 4 records, since we had selected four files to download.
02:46	The first line in each record is an identifier line.
02:50	It starts with a “greater than (>)” symbol.
02:53	This is followed by a sequence.
02:56	Save the file in your home folder as “sequence.fasta'”.
03:01	Close the text editor.
03:03	Follow the same steps as above, to download the files in GenBank format
03:08	for the same files selected earlier.
03:12	Select the file format as GenBank.
03:16	Create a file. Open with a text editor.
03:21	Notice that the sequence file in GenBank format has more features than a FASTA file.
03:27	Save the file as "sequence.gb" in your home folder. Close the text editor.
03:34	For demonstration purpose, we need a FASTA file with a single record.
03:39	For this, clear the earlier selection by again clicking on the check boxes.
03:48	Now, select the file “Human insulin gene complete cds”.
03:54	Click on the check-box.
03:57	And follow the same steps shown earlier to save the file in the home folder.
04:01	Save the file as "insulin.fasta".
04:08	Biological data stored in these files can be extracted and modified using Biopython libraries.
04:16	Close the text-editor.
04:19	Extracting data from data files is called as Parsing.
04:23	Most file formats can be parsed using functions available in SeqIO module.
04:30	Most commonly used functions of SeqIO module are: parse, read, write and convert.
04:38	Open the terminal by pressing Ctrl, Alt and t keys simultaneously.
04:44	Start Ipython by typing "ipython" at the prompt. Press Enter.
04:51	Next, import "SeqIO" module from Bio package.
04:56	At the prompt, type: from Bio import SeqIO. Press Enter.
05:04	We will start with the most important function “parse”.
05:07	For demonstration, I will use a FASTA file that has many records which we had downloaded earlier from the database.
05:17	For simple FASTA parsing, type the following at the prompt.
05:22	Here, we are using the parse function to read the contents of the sequence.fasta file.
05:30	For the output, print record id, sequence present in the record and also the length of the sequence.
05:41	Also notice that the parse function is used to read sequence data as Sequence record objects.
05:48	It is generally used with a for loop.
05:52	It can accept two arguments, the first one is the file name to read the data.
05:59	The second specifies the file format.
06:02	Press Enter key twice to get the output.
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.
06:21	Notice that the FASTA format does not specify the alphabet.
06:26	So, the output does not specifies it as a DNA sequence.
06:31	The same steps can be repeated for parsing GenBank file.
06:36	For Demonstration we will use the GenBank file which we have downloaded earlier from the database.
06:43	Press up-arrow key to get the lines of code which we had used earlier.
06:49	Change the file name to sequence.gb .
06:53	Change the file format to genbank.
06:56	The rest of the code remains same.
06:58	Press Enter key twice to get the output.
07:03	Here too the output shows the record id, sequence and the length of the sequence for all the records in the file.
07:12	Notice that the GenBank format specifies the sequence as DNA sequence.
07:19	Similarly, Swiss-prot and EMBL files can be parsed using the same code as above.
07:27	If your file contains a single record then type the following lines for parsing.
07:34	Here, we will use the previously saved FASTA file with a single record, that is, insulin.fasta as an example.
07:43	Notice that we have used read function instead of parse function. Press Enter.
07:50	The output shows the contents for the file insulin.fasta.
07:55	It shows the sequence as sequence record object.
07:59	And other attributes such as GI, accession number and description.
08:06	We can also view the individual attributes of this record as follows.
08:11	At the prompt, type: record dot seq. Press Enter.
08:18	The output shows the sequence present in the file.
08:22	To view the identifiers for this record, type: record dot id. Press Enter.
08:29	The output shows the GI number and accession number etc.
08:34	You can use the function described above to parse the data files of your choice.
08:40	Now, let's summarize.
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
08:55	to extract data such as record ids, description and sequences from FASTA and GenBank files.
09:03	Now, for the assignment-
09:06	Download FASTA files for nucleotide sequence of your choice from NCBI database.
09:13	Convert the file of sequences to their reverse complements.
09:17	Your completed assignment should have the following lines of code.
09:22	Use parse function to load nucleotide sequences from the FASTA file.
09:28	Next, print reverse complements using the Sequence object’s built in reverse complement method.
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10:06	This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14