Biopython/C2/Writing-Sequence-Files/English-timed - Revision history

Pratik kamble at 12:57, 23 March 2017

2017-03-23T12:57:41Z

Priyacst at 06:37, 14 March 2017

2017-03-14T06:37:14Z

PoojaMoolya at 07:49, 10 March 2017

2017-03-10T07:49:53Z

Sandhya.np14 at 10:56, 4 August 2016

2016-08-04T10:56:23Z

Sandhya.np14 at 18:25, 2 August 2016

2016-08-02T18:25:59Z

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PoojaMoolya: Created page with " {|Border=1 ! Time ! Narration |- | 00:01 | Hello everyone. |- | 00:02 | Welcome to this tutorial on '''Writing Sequence Files'''. |- | 00..."

2016-06-06T06:45:12Z

Created page with " {|Border=1 ! <center>Time</center> ! <center>Narration</center> |- | 00:01 | Hello everyone. |- | 00:02 | Welcome to this tutorial on '''Writing Sequence Files'''. |- | 00..."

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

|-
| 00:01
| Hello everyone.

|-
| 00:02
| Welcome to this tutorial on '''Writing Sequence Files'''.

|-
| 00:07
| In this tutorial, we will learn: How to create Sequence Record Objects.

|-
| 00:13
| Write sequences files.

|-
| 00:15
| Convert between file formats.

|-
| 00:19
| And sort records in a file by length.

|-
| 00:23
| To follow this tutorial you should be familiar with,

|-
| 00:27
| Undergraduate '''Biochemistry''' or '''Bioinformatics'''

|-
| 00:31
| And basic '''Python''' programming

|-
| 00:34
| Refer to the '''Python''' tutorials at the given link.

|-
| 00:38
| To record this tutorial I am using '''Ubuntu OS''' version. 14.10

|-
| 00:45
|'''Python''' version 2.7.8
|-
| 00:48
| '''Ipython interpretor''' version 2.3.0 and '''Biopython''' version 1.64

|-
| 00:55
|We have earlier learnt about '''parse''' and '''read''' functions to read contents of a file.

|-
|01:03
|In this tutorial we will learn how to use '''write''' function to write sequences to a file.

|-
| 01:09
|And use '''Convert''' function for interconversion between various file formats.

|-
| 01:16
|Let me now demonstrate how to use '''write''' function.

|-
| 01:20
|Here is a text file with a protein sequence.

|-
|01:24
|The sequence shown here is '''insulin protein.'''

|-
|01:28
|The file also has information such as '''GI''' accession number and also description.

|-
|01:36
|We will now create a file for this sequence in '''FASTA''' format.

|-
|01:41
|The first step is to create sequence record object.

|-
| 01:45
|More information about Sequence Record Objects:

|-
|01:49
|It is the basic data type for the sequence input/output interface.

|-
|01:55
|In sequence record object, a sequence is associated with higher level features: such as identifiers and descriptions.

|-
|02:04
|Open the terminal by pressing ctrl, alt and t keys simultaneously .

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| 02:10
|At the prompt type '''ipython''', Press Enter.

|-
|02:15
|At the prompt type the following lines:

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|02:18
|'''from Bio dot Seq module import Seq class'''.

|-
|02:24
|'''from Bio dot SeqRecord module import Sequence Record class'''

|-
|02:31
| Next '''from Bio dot Alphabet module import generic protein class'''

|-
|02:38
|Next I will save the sequence record object in a variable '''record1.'''

|-
|02:45
|Copy the sequence, id and description from the text file and paste in the respective lines on the terminal.

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|02:56
|Press '''Enter.'''

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| 02:58
|To view the output, type, '''record1'''.

|-
|03:02
|Press '''Enter.'''

|-
|03:04
|The output shows the '''insulin protein''' sequence as '''sequence record '''object.

|-
|03:10
|It shows the sequence along with id and description.

|-
| 03:13
|We will use write function to convert the above sequence record object to a '''FASTA''' file.

|-
|03:21
|'''Import SeqIO module''' from '''Bio package.'''

|-
|03:26
|Next type the command line with a '''write''' function to convert the sequence object to '''FASTA''' file.

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|03:40
|The '''write '''function takes 3 arguments

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|03:44
|The first one is the variable storing the sequence record object.

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|03:49
|The Second is the file name to write the '''FASTA''' file.

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|03:54
|The Third is the file format to write. Press '''enter.'''

|-
| 03:58
|The Output shows “one”, that is we have converted one sequence record object to a '''FASTA''' file.

|-
|04:07
|The file in '''FASTA''' format is saved in the home folder as '''"example.fasta".'''

|-
|04:13
|Let me warn you:

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|04:14
|The output will over-write any pre-existing file of the same name.

|-
| 04:18
|To view the file, navigate to the file in the '''home''' folder.

|-
|04:24
|Open this file in a '''text editor.'''

|-
|04:27
|The protein sequence is now in '''FASTA''' format.

|-
|04:31
|Close the '''text editor.'''

|-
| 04:33
|Many '''bioinformatics''' tools take different input file formats.

|-
|04:38
|So sometimes there is a need to interconvert between sequence file formats.

|-
|04:44
|We can do file conversions using''' convert '''function in '''SeqIO module.'''

|-
| 04:50
|For demonstration I will convert a '''GenBank''' file to a '''FASTA''' file.

|-
|04:55
|Have a '''GenBank''' file in my home folder.

|-
|04:59
|Let me open this in a text editor.

|-
|05:02
|The file contains '''HIV genome''' in '''GenBank''' format.

|-
|05:07
|This '''GenBank''' file has descriptions of all the '''genes''' in the '''genome''' in the first part of the file.

|-
|05:14
|It is followed by a complete '''genome''' sequence.
|-
|05:18
|Close the text editor.

|-
| 05:19
|Type the following lines on the terminal.

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|05:23
|Here the '''convert''' function converts the complete '''genome''' sequence present in the '''GenBank''' file to '''FASTA''' file. Press '''enter'''

|-
|05:33
|The new file in '''FASTA''' format is now saved as '''HIV.fasta''' in the home folder.

|-
| 05:39
|Navigate to the file and open in the text editor.

|-
|05:46
|Close the text editor.

|-
|05:49
|Even though we can convert the file formats easily using '''convert''' function, it has limitations.

|-
|05:56
|Writing some formats requires information which other file formats don’t contain.

|-
|06:02
|For example: We can convert a '''GenBank''' file to a '''FASTA''' file, we can't do the reverse.

|-
|06:09
|Similarly we can turn a '''FASTQ''' file into a '''FASTA''' file, but can’t do the reverse.

|-
|06:15
|For more information regarding convert function, type the '''help''' command.

|-
|06:21
|Press '''enter'''.

|-
|06:24
|Press “'''q'''” on the key board to get back to the prompt.

|-
|06:28
|We can also extract individual '''genes''' from the '''HIV genome''' in '''GenBank''' format.

|-
|06:35
|These individual '''genes''' can be saved in '''FASTA''' or any other formats.

|-
|06:41
| For this type the following code at the prompt.

|-
|06:47
|This code will write all individual '''CDS''' gene sequences , their ids and name of the gene in a file.

|-
|06:56
|The file is saved as “'''HIV_geneseq.fasta'''” in your '''home''' folder. Press '''enter'''

|-
| 07:07
|Using '''Biopython''' tools we can sort the records in a file by length.

|-
|07:12
|Here I have opened a FASTA file “'''hemoglobin.fasta'''” which has six records.

|-
|07:19
|Each record is of a different length.

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| 07:23
| Type the following lines to arrange the longest record first.

|-
|07:27
|The new file with the sorted sequences will be saved as''' "sorted_hemoglobin.fasta" '''in your '''home''' folder

|-
|07:38
|For Short records first, reverse the arguments in the '''records.sort''' command line.

|-
| 07:45
| Lets Summarize,
|-
|07:46
|In this tutorial we have learnt : to create Sequence Record Objects.

|-
|07:51
|Write sequence files using''' write''' function of Sequence Input/Output module.

|-
|07:58
|Convert between sequence file formats using '''convert''' function.

|-
|08:03
|And sort records in a file by length.

|-
| 08:07
|For the Assignment:

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|08:09
|Extract the gene "'''HIV1gp3'''" at positions 4587 to 5165 from the '''genomic''' sequence of HIV.

|-
|08:21
|The file “'''HIV.gb'''” is included in code files of this tutorial.

|-
|08:28
|Your completed assignment will have the following code.

|-
| 08:43
|The video at the following link summarizes the Spoken Tutorial project.

|-
|08:48
|Please download and watch it.

|-
|08:49
|The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test.

|-
|08:57
|For more details, please write to us.

|-
|09:00
|The Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

|-
|09:06
|More information on this Mission is available at the link shown.

|-
| 09:10
| This is Snehalatha from IIT Bombay signing off. Thank you for joining.

|}

@@ Line 1: / Line 1: @@
 {|Border=1
-! <center>Time</center>
+|'''Time'''
-! <center>Narration</center>
+|'''Narration'''
 |-

@@ Line 246: / Line 246: @@
 |-
 |05:18
-|Close the text editor.
+|Close the text editor. Type the following lines on the terminal.
-−
-|-
-| 05:19
-|Type the following lines on the terminal.
 |-

@@ Line 6: / Line 6: @@
 |-
 | 00:01
-| Hello everyone.
+| Hello everyone.Welcome to this tutorial on '''Writing Sequence Files'''.
-−
-|-
-| 00:02
-| Welcome to this tutorial on '''Writing Sequence Files'''.
 |-
@@ Line 18: / Line 14: @@
 |-
 | 00:13
-|* Write sequences files
+| Write sequences files
 |-
 | 00:15
-|* Convert between '''file format'''s
+| Convert between '''file format'''s
 |-
 | 00:19
-|*  And, sort '''record'''s in a file by length.
+| And, sort '''record'''s in a file by length.
 |-
@@ Line 50: / Line 46: @@
 |-
 | 00:45
-|* '''Python''' version 2.7.8
+| '''Python''' version 2.7.8
 |-
 | 00:48
-|* '''Ipython interpretor''' version 2.3.0 and * '''Biopython''' version 1.64.
+| '''Ipython interpretor''' version 2.3.0 and * '''Biopython''' version 1.64.
 |-
@@ Line 193: / Line 190: @@
 |-
 |04:13
-|Let me warn you,
+|Let me warn you,the output will over-write any pre-existing file of the same name.
-−
-|-
-|04:14
-|the output will over-write any pre-existing file of the same name.
 |-
@@ Line 250: / Line 243: @@
 |05:14
 |It is followed by a complete '''genome''' sequence.
 |-
 |05:18
@@ Line 348: / Line 342: @@
 |-
 | 07:45
-| Let's summarize.
+| Let's summarize.In this tutorial, we have learnt :* to create Sequence Record Objects
-|-
-|07:46
-|In this tutorial, we have learnt :* to create Sequence Record Objects
 |-
 |07:51
-|* Write sequence files using''' write''' function of '''Sequence Input/Output''' module.
+| Write sequence files using''' write''' function of '''Sequence Input/Output''' module.
 |-
 |07:58
-|* Convert between '''sequence file format'''s using '''convert''' function.
+| Convert between '''sequence file format'''s using '''convert''' function.
 |-
 |08:03
-|* And, sort records in a file by length.
+| And, sort records in a file by length.
 |-
@@ Line 387: / Line 378: @@
 |-
 |08:48
-|Please download and watch it.
+|Please download and watch it. The Spoken Tutorial Project team conducts workshops and gives certificates for those who pass an online test.
-−
-|-
-|08:49
-|The Spoken Tutorial Project team conducts workshops and gives certificates for those who pass an online test.
 |-

@@ Line 14: / Line 14: @@
 |-
 | 00:07
-| In this tutorial, we will learn: * How to create Sequence Record Objects
+| In this tutorial, we will learn: * How to create '''Sequence Record Objects'''
 |-
@@ Line 22: / Line 22: @@
 |-
 | 00:15
-|* Convert between file formats
+|* Convert between '''file format'''s
 |-
 | 00:19
-|*  And, sort records in a file by length.
+|*  And, sort '''record'''s in a file by length.
 |-
@@ Line 81: / Line 81: @@
 |-
 |01:28
-|The file also has information such as '''GI accession number''' and also description.
+|The file also has information such as '''GI accession number''' and also '''description'''.
 |-
@@ Line 125: / Line 125: @@
 |-
 |02:31
-| Next '''from Bio dot Alphabet module import generic protein class'''
+| Next, '''from Bio dot Alphabet module import generic protein class'''.
 |-
@@ Line 133: / Line 133: @@
 |-
 |02:45
-|'''Copy''' the sequence, id and description from the text file and '''paste''' in the respective lines on the terminal.
+|'''Copy''' the '''sequence, id''' and '''description''' from the text file and '''paste''' it in the respective lines on the terminal.
 |-
@@ Line 153: / Line 153: @@
 |-
 |03:10
-|It shows the sequence along with id and description.
+|It shows the sequence along with '''id''' and '''description'''.
 |-
@@ Line 173: / Line 173: @@
 |-
 |03:44
-|The first one is the variable storing the sequence record object.
+|The first one is the variable storing the '''sequence record object'''.
 |-
@@ Line 185: / Line 185: @@
 |-
 | 03:58
-|The Output shows “one”, that is, we have converted one '''sequence record object''' to a '''FASTA''' file.
+|The Output shows one, that is, we have converted one '''sequence record object''' to a '''FASTA''' file.
 |-
@@ Line 197: / Line 197: @@
 |-
 |04:14
-|the output will over-write any pre existing file of the same name.
+|the output will over-write any pre-existing file of the same name.
 |-
@@ Line 264: / Line 264: @@
 |-
 |05:33
-|The new file in '''FASTA''' format is now saved as '''HIV.fasta''' in the '''home''' folder.
+|The new file in the '''FASTA''' format is now saved as '''HIV.fasta''' in the '''home''' folder.
 |-
@@ Line 316: / Line 316: @@
 |-
 |06:47
-|This code will write all individual '''CDS''' gene sequences , their ids and name of the '''gene''' in a file.
+|This code will write all individual '''CDS''' gene sequences, their ids and name of the '''gene''' in a file.
 |-
 |06:56
-|The file is saved as “'''HIV_geneseq.fasta'''” in your '''home''' folder. Press '''Enter'''.
+|The file is saved as “HIV_geneseq.fasta” in your '''home''' folder. Press '''Enter'''.
 |-
@@ Line 351: / Line 351: @@
 |-
 |07:46
-|In this tutorial, we have learnt :* to create Sequence Record Objects.
+|In this tutorial, we have learnt :* to create Sequence Record Objects
 |-
 |07:51
-|* Write sequence files using''' write''' function of Sequence Input/Output module.
+|* Write sequence files using''' write''' function of '''Sequence Input/Output''' module.
 |-
@@ Line 375: / Line 375: @@
 |-
 |08:21
-|The file “HIV.gb” is included in code files of this tutorial.
+|The file “HIV.gb” is included in the code files of this tutorial.
 |-