Hezekiah2016 at 09:50, 31 May 2018

2018-05-31T09:50:48Z

Hezekiah2016 at 09:49, 31 May 2018

2018-05-31T09:49:45Z

Hezekiah2016: Created page with "{|Border=1 |'''Time''' |'''Narration''' |- | 00:01 | Hello everyone.Welcome to this tutorial on '''Writing Sequence Files'''. (Khublei ia phi baroh. Ngi pdiang sngewbha ia ph..."

2018-02-02T12:12:53Z

Created page with "{|Border=1 |'''Time''' |'''Narration''' |- | 00:01 | Hello everyone.Welcome to this tutorial on '''Writing Sequence Files'''. (Khublei ia phi baroh. Ngi pdiang sngewbha ia ph..."

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{|Border=1
|'''Time'''
|'''Narration'''

|-
| 00:01
| Hello everyone.Welcome to this tutorial on '''Writing Sequence Files'''.
(Khublei ia phi baroh. Ngi pdiang sngewbha ia phi sha kane ka jingbatai shaphang ka '''Writing Sequence Files'''.

|-
| 00:07
| In this tutorial, we will learn: * How to create '''Sequence Record Objects'''
(Ha kane ka tutorial, ngin sa nang ban : * Kumno ban shna '''Sequence Record Objects'''

|-
| 00:13
| Write sequences files
(Ban write ia ki sequences files

|-
| 00:15
| Convert between '''file format'''s
(Pynkylla hapdeng '''file format'''s

|-
| 00:19
| And, sort '''record'''s in a file by length.
(Bad, jied '''record'''s ha ka file da ka jingjrong.

|-
| 00:23
| To follow this tutorial, you should be familiar with
(Ban kham sngewthuh ia kane ka tutorial, phi dei ban long kiba shemphang bad

|-
| 00:27
| undergraduate Biochemistry or Bioinformatics
(undergraduate Biochemistry lane Bioinformatics.

|-
| 00:31
| and basic '''Python''' programming.
(Bad basic '''Python''' programming.

|-
| 00:34
| Refer to the '''Python''' tutorials at the given link.
(Pyndonkam da ka '''Python''' tutorials na ka link harum .

|-
| 00:38
| To record this tutorial, I am using: * '''Ubuntu OS''' version 14.10
(Ban record ia kane ka tutorial, nga pyndonkam da ka: * '''Ubuntu OS''' version 14.10

|-
| 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 bad * '''Biopython''' version 1.64.

|-
| 00:55
|We have earlier learnt about '''parse''' and '''read''' '''function'''s to read contents of a file.
(Ha kaba nyngkong ngi lah dep pule kumno ban '''parse''' bad'''read''' '''function'''s ban read ia ki contents jong ka file.

|-
|01:03
|In this tutorial, we will learn how to use '''write''' function to write sequences to a file.
(Ha kane ka tutorial, ngin sa nang kumno ban pyndonkam ia ka '''write''' function sha ka write sequences jong ka file.

|-
| 01:09
|And, use '''Convert''' function for inter-conversion between various '''file format'''s.
(Bad ban pyndonkam '''Convert''' function na ka bynta ka inter-conversion hapdeng ba bun ki '''file format'''s.

|-
| 01:16
|Let me now demonstrate how to use '''write''' function.
(Mynta ngan pyni ia phi kumno ban pyndonkam ia '''write''' function.

|-
| 01:20
|Here is a text file with a protein sequence.
(Hangne don ka text file ba don u protein sequence.

|-
|01:24
|The sequence shown here is '''insulin protein.'''
(Ka sequence ba pyni hangne dei u '''insulin protein.'''

|-
|01:28
|The file also has information such as '''GI accession number''' and also '''description'''.
(Kane ka file ka don ruh ki jingpyntip kum '''GI accession number''' bad '''description'''.

|-
|01:36
|We will now create a file for this sequence in '''FASTA''' format.
(Mynta ngin ia shna ka sequence jong kane ka file ha ka '''FASTA''' format.

|-
|01:41
|The first step is to create '''sequence record object'''.
(Nyngkong eh ngi shna '''sequence record object'''.

|-
| 01:45
|More information about Sequence Record Objects:
(Ki jingtip ba kham bniah shaphang Sequence Record Objects:

|-
|01:49
|It is the basic data type for the '''sequence input/output interface'''.
(Ka dei ka basic data type na ka bynta ka '''sequence input/output interface'''.

|-
|01:55
|In sequence record object, a sequence is associated with higher level features such as '''identifier'''s and descriptions.
(Ha ka sequence record object, ia ka sequence la pyniasoh bad ka features ba kham halor kum ki '''identifier'''s bad descriptions.

|-
|02:04
|Open the terminal by pressing '''Ctrl, Alt''' and '''t''' keys simultaneously .
(Plie ia ka terminal da kaba nion sah ia ki '''Ctrl, Alt''' and '''t''' keys.

|-
| 02:10
|At the prompt, type: '''ipython''', press '''Enter'''.
(Ha ka prompt, type: '''ipython''', nion '''Enter'''.

|-
|02:15
|At the prompt, type the following lines:
(Ha ka prompt, type kumne harum:

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

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

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

|-
|02:38
|Next, I will save the sequence record object in a variable '''record1.'''
(Nangta , ngan sa save ia ka sequence record object ha ka variable '''record1.'''

|-
|02:45
|'''Copy''' the '''sequence, id''' and '''description''' from the text file and '''paste''' it in the respective lines on the terminal.
('''Copy''' ia ka '''sequence, id''' bad '''description''' na ka text file bad '''paste''' ia ka ha ki lines ba lah buh ha ka terminal.

|-
|02:56
|Press '''Enter.'''
(Nion '''Enter.'''

|-
| 02:58
|To view the output, type: '''record1'''.
(Ban peit ia ka output, type: '''record1'''.

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

|-
|03:04
|The output shows the '''insulin protein''' sequence as '''sequence record '''object.
(Ka output ka pyni ia ka '''insulin protein''' sequence kum '''sequence record '''object.

|-
|03:10
|It shows the sequence along with '''id''' and '''description'''.
(Ka pyni ia ka sequence ryngkat bad '''id''' bad '''description'''.

|-
| 03:13
|We will use '''write''' function to convert the above sequence record object to a '''FASTA''' file.
(Ngin pyndonkam '''write''' function ban pynkylla ia ka sequence record object haneng sha ka '''FASTA''' file.

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

|-
|03:26
|Next, type the '''command line''' with a '''write''' function to convert the sequence object to '''FASTA''' file.
(Hadien , type ia ka '''command line''' bad ka '''write''' function ban pynkylla ia ka sequence object sha ka '''FASTA''' file.

|-
|03:40
|The '''write '''function takes 3 '''argument'''s.
(Ka '''write '''function ka shim 3 '''argument'''s .

|-
|03:44
|The first one is the variable storing the '''sequence record object'''.
(Ka ba nyngkong ka dei ka variable ba store ia ka '''sequence record object'''.

|-
|03:49
|The second is the file name to write the '''FASTA''' file.
(Ka ba ar ka dei ka file name ban write ia ka '''FASTA''' file.

|-
|03:54
|The third is the file format to write. Press '''Enter'''.
(Ka ba lai ka dei ka file format ban write. Nion '''Enter'''.

|-
| 03:58
|The Output shows one, that is, we have converted one '''sequence record object''' to a '''FASTA''' file.
(Ka Output ka pyni kawei, kata ka dei, ngi pynkylla ia kawei ka '''sequence record object''' sha ka '''FASTA''' file.

|-
|04:07
|The file in '''FASTA''' format is saved in the '''home''' folder as "example.fasta".
(Ka file ha ka '''FASTA''' format la save ha ka '''home''' folder kum "example.fasta".

|-
|04:13
|Let me warn you,the output will over-write any pre-existing file of the same name.
(Ngan shu maham ia phi ba ka output kan over-write ia kano kano ka file ba lah don lypa kaba don kajuh ka kyrteng.

|-
| 04:18
|To view the file, navigate to the file in the '''home''' folder.
(Ban peit ia ka file, leit sha ka file ha ka '''home''' folder.

|-
|04:24
|Open this file in a '''text editor.'''
(Plie ia kane ka file ha ka '''text editor.'''

|-
|04:27
|The protein sequence is now in '''FASTA''' format.
(Ka protein sequence ka lah don mynta ha ka '''FASTA''' format.

|-
|04:31
|Close the '''text editor.'''
(Khang ia u '''text editor.'''

|-
| 04:33
|Many '''bioinformatics''' tools take different input file formats.
(Bun ki '''bioinformatics''' tools ki shim bun jait ki input file formats.

|-
|04:38
|So, sometimes there is a need to inter-convert between sequence file formats.
(Te, teng teng ngi hap ban inter-convert hapdeng ki sequence file formats.

|-
|04:44
|We can do file conversions using''' convert '''function in '''SeqIO module.'''
(Ngi lah ban pynkylla ia ki files da kaba pyndonkam ''' convert '''function ha '''SeqIO module.'''

|-
| 04:50
|For demonstration, I will convert a '''GenBank''' file to a '''FASTA''' file.
(Ban pyni nuksa, ngan pynkylla ia u '''GenBank''' file sha ka '''FASTA''' file.

|-
|04:55
|Have a '''GenBank''' file in my '''home''' folder.
(Nga don u '''GenBank''' file ha ka '''home''' folder jong nga.

|-
|04:59
|Let me open this in a text editor.
(To ngan plie ia une ha u text editor.

|-
|05:02
|The file contains '''HIV genome''' in '''GenBank''' format.
(U file u don '''HIV genome''' ha '''GenBank''' format.

|-
|05:07
|This '''GenBank''' file has descriptions of all the '''genes''' in the '''genome''', in the first part of the file.
(Une u '''GenBank''' file u don ki jingbatai jong baroh ki '''genes''' ha ka '''genome''', ha ka bynta ba nyngkong jong ka file.

|-
|05:14
|It is followed by a complete '''genome''' sequence.
(Nangta sa bud da u '''genome''' sequence ba pura.

|-
|05:18
|Close the text editor. Type the following lines on the terminal.
(Khang ia u text editor. Type ia ki line ha terminal kumne harum.

|-
|05:23
|Here the '''convert''' function converts the complete '''genome''' sequence present in the '''GenBank''' file to '''FASTA''' file. Press '''Enter'''.
(Hangne u '''convert''' function u pynkylla ia baroh ka '''genome''' sequence kiba don ha '''GenBank''' file sha '''FASTA''' file. Nion '''Enter'''.

|-
|05:33
|The new file in the '''FASTA''' format is now saved as '''HIV.fasta''' in the '''home''' folder.
(Ka file ba thymmai ha ka '''FASTA''' format mynta la shah save kum '''HIV.fasta''' ha ka '''home''' folder.

|-
| 05:39
|Navigate to the file and open in the text editor.
(Leit sha ka file bad plie da u text editor.

|-
|05:46
|Close the text editor.
(Khang ia u text editor.

|-
|05:49
|Even though we can convert the file formats easily using '''convert''' function, it has limitations.
(Wat la ka long kaba suk ban pynkylla ia ka file formats da kaba pyndonkam '''convert''' function,hynrei ka don da u pud.

|-
|05:56
|Writing some formats requires information which other file formats don’t contain.
(Ban write ia katto katne ki formats, donkam ia ki jingtip ba kiwei ki formats kim don.

|-
|06:02
|For example: We can convert a '''GenBank''' file to a '''FASTA''' file, we can't do the reverse.
(Nuksa: Ngi lah ban pynkylla ia u '''GenBank''' file sha u '''FASTA''' file. Hynrei ngim lah ban leh da khongpong.

|-
|06:09
|Similarly, we can turn a '''FASTQ''' file into a '''FASTA''' file but can’t do the reverse.
(Kumjuh ruh, ngi lah ban pynkylla ia '''FASTQ''' file sha ka '''FASTA''' file hynrei ngim lah ban leh da khongpong pat.

|-
|06:15
|For more information regarding '''convert''' function, type the '''help''' command.
(Ban tip khap bniah shaphang ka '''convert''' function, type ia u '''help''' command.

|-
|06:21
|Press '''Enter'''.
(Nion '''Enter'''.)

|-
|06:24
|Press 'q' on the key board to get back to the prompt.
(Nion 'q' ha ka keyboard ban ioh biang ia ka prompt.

|-
|06:28
|We can also extract individual '''genes''' from the '''HIV genome''' in '''GenBank''' format.
(Ngi lah ruh ban sei ia ki '''genes'''ba shimet na ka '''HIV genome''' ha '''GenBank''' format.

|-
|06:35
|These individual '''genes''' can be saved in '''FASTA''' or any other formats.
(Kine ki '''genes''' ba shimet lah ban save ruh ha '''FASTA''' lane kino kino ki formats.

|-
|06:41
| For this, type the following code at the '''prompt'''.
(Ban leh kumta , type ia u code kumne ha ka '''prompt'''.

|-
|06:47
|This code will write all individual '''CDS''' gene sequences, their ids and name of the '''gene''' in a file.
(Une u code un write lut ia baroh ki '''CDS''' gene sequences, ki ids bad kyrteng jong ki '''gene''' ha ka file.

|-
|06:56
|The file is saved as “HIV_geneseq.fasta” in your '''home''' folder. Press '''Enter'''.
(Ia kane ka file la save kum “HIV_geneseq.fasta” ha ka '''home''' folder jong phi. Nion '''Enter'''.
|-
| 07:07
|Using '''Biopython''' tools, we can sort the records in a file by length.
(Da kaba pyndonkam u '''Biopython''' tools, ngi lah ban jied ia ki records jong ka file da ka jingjrong jong ka.

|-
|07:12
|Here, I have opened a FASTA file “hemoglobin.fasta” which has six records.
(Hangne, nga lah plie ia u FASTA file “hemoglobin.fasta” uba don hynriew tylli ki records.

|-
|07:19
|Each '''record''' is of a different length.
(Man ka '''record''' ki pher ha ka jingjrong.

|-
| 07:23
| Type the following lines to arrange the longest record first.
(Type kumne harum ban buh da ka record ba jrong na ba sdang .

|-
|07:27
|The new file with the sorted sequences will be saved as "sorted_hemoglobin.fasta" in your '''home''' folder.
(Ka file ba thymmai kaba don u sequence ba la jied yn shah save kum "sorted_hemoglobin.fasta" ha ka '''home''' folder jong phi.

|-
|07:38
|For short records first, reverse the arguments in the '''records.sort''' command line.
(Ban ioh ia ki records ba lyngkot nyngkong, pynkylla ia ki arguments ha ka '''records.sort''' command line.

|-
| 07:45
| Let's summarize.In this tutorial, we have learnt :* to create Sequence Record Objects
(To ngin ia lum kyllum . Ha kane ka tutorial, ngi lah nang ban:* to create Sequence Record Objects

|-
|07:51
| Write sequence files using''' write''' function of '''Sequence Input/Output''' module.
(Write ia ki sequence files da kaba pyndonkam ''' write''' function jong'''Sequence Input/Output''' module.

|-
|07:58
| Convert between '''sequence file format'''s using '''convert''' function.
(Pynkylla hapdeng '''sequence file format'''s da kaba pyndonkam'''convert''' function.

|-
|08:03
| And, sort records in a file by length.
(Bad, wad ia ki records ha ka file da ka jingjrong.

|-
| 08:07
|For the assignment:
(Na ka bynta ka assignment:

|-
|08:09
|'''Extract''' the gene "HIV1gp3" at positions 4587 to 5165 from the '''genomic''' sequence of HIV.
('''Extract''' ia u gene "HIV1gp3" ha positions 4587 sha 5165 na ka '''genomic''' sequence jong HIV.

|-
|08:21
|The file “HIV.gb” is included in the code files of this tutorial.
(Ka file “HIV.gb” la kynthup lang ha ka code files jong kane ka tutorial.

|-
|08:28
|Your completed assignment will have the following code.
(Ka assignment ba lah dep jong phi kan don ia u code ba harum.

|-
| 08:43
|The video at the following link summarizes the Spoken Tutorial project.
(Ka video ha ka link ba bud ka batai bniah shaphang ka Spoken Tutorial project.

|-
|08:48
|Please download and watch it. The Spoken Tutorial Project team conducts workshops and gives certificates for those who pass an online test.
(Sngewbha download bad peit ia ka. Ka Spoken Tutorial Project team ka ju pynlong workshops bad ai certificates ruh ia kito kiba pass ia ka online test.

|-
|08:57
|For more details, please write to us.
((Na ka bynta ka jingtip ba kham bniah, sngewbha thoh sha ngi.

|-
|09:00
|The Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.
(Ia ka Spoken Tutorial Project la bei tyngka da ka NMEICT, MHRD, Government of India.

|-
|09:06
|More information on this mission is available at the link shown.
(Ki jingtip ba kham pura ia kane ka mission lah ban ioh na ka link harum .

|-
| 09:10
| This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining.
(Nga dei ka Snehalatha na '''IIT Bombay''', signing off. Khublei shibun )
|}

@@ Line 10: / Line 10: @@
 | 00:07
 | Ha kane ka tutorial, ngin pule: * Kumno ban shna '''Sequence Record Objects'''
 |-
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 | 09:10
-| Ia kane ka script la pynkylla sha ka Ktien Khasi da i Yuwanki Kharlukhi na Shillong, bad ma nga U Hezekiah Lyngdoh ngan pynkutnoh. khublei ba phi la ïasnoh lang.|}
+| Ia kane ka script la pynkylla sha ka Ktien Khasi da i Yuwanki Kharlukhi na Shillong, bad ma nga U Hezekiah Lyngdoh ngan pynkutnoh. khublei ba phi la ïasnoh lang.

Biopython/C2/Writing-Sequence-Files/Khasi - Revision history

Hezekiah2016 at 09:50, 31 May 2018

Hezekiah2016 at 09:49, 31 May 2018

Hezekiah2016: Created page with "{|Border=1 |'''Time''' |'''Narration''' |- | 00:01 | Hello everyone.Welcome to this tutorial on '''Writing Sequence Files'''. (Khublei ia phi baroh. Ngi pdiang sngewbha ia ph..."