Difference between revisions of "Biopython/C2/Parsing-Data/English-timed"

| Hello everyone.

 

| Welcome to this tutorial on '''Parsing Data.'''

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

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

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

| And basic '''Python''' programming  

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

| '''Biopython''' 1.64 and '''Mozilla Firefox '''browser 35.0

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

|Data files can be download from the database websites.

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

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

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

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

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

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

|Click on the check box to select the file to download.

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

| Under the heading “'''Choose destination'''” Click on “'''File'''” option.

|You can save this file in any file format listed under “'''format'''” drop down list box.

|Choose “'''FASTA'''” from the given options.

|Then click on “'''Create file'''” option.  

| A dialog box appears on the screen.  

|Select “'''Open with'''” click on '''OK .'''

| A file opens in a text editor.

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

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

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

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

|For the same files selected earlier.

|Select the file format as '''GenBank.'''

|'''Create file''', open with a text editor.  

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

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

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

|Click on the check box.

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

|Save the file as '''insulin.fasta.'''

|Close the text editor.

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

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

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

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

| Next import '''SeqIO''' module from '''Bio''' package.

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

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

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

|For the output print, '''record id''', sequence present in the record and also the length of the sequence.

|Press enter key twice to get the output.

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

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

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

|Change the file name to '''sequence.gb '''

| Press enter key twice to get the output.

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

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

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

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

|It shows the sequence as sequence record object.

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

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

|The output shows the GI number and accession number etc.

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

| Now Let's summarize,

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

| Now for the assignment,

|Convert the file of sequences to their reverse complements.

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

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

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

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

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

|This is Snehalatha from IIT Bombay signing off. Thank you for joining.