Hezekiah2016 at 09:48, 31 May 2018

2018-05-31T09:48:50Z

Hezekiah2016: Created page with "{| Border=1 ! Time ! Narration |- | 00:01 | Hello everyone.Welcome to this tutorial on '''Parsing Data.''' (Khublei baroh. Ngi pdiang sngewb..."

2018-02-02T12:12:02Z

Created page with "{| Border=1 ! <center>Time</center> ! <center>Narration</center> |- | 00:01 | Hello everyone.Welcome to this tutorial on '''Parsing Data.''' (Khublei baroh. Ngi pdiang sngewb..."

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

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

|-
| 00:06
| In this tutorial, we will learn to download '''FASTA''' and '''GenBank''' files from '''NCBI''' database website.
(Ha kane ka tutorial, ngin sa nang kumno ban download ia ki '''FASTA''' bad '''GenBank''' files na ka database website.

|-
| 00:14
| And, '''Parse''' data files using '''function'''s in '''Sequence Input/Output''' module.
(Bad ban '''Parse'''ia ki data files da kaba pyndonkam ia ki '''function'''s ha ka '''Sequence Input/Output''' module.

|-
| 00:19
| To follow this tutorial, you should be familiar with undergraduate biochemistry or bioinformatics
(Ban sngewthuh bha ia kane ka tutorial, phi dei ban long kiba shemphang ha ka undergraduate biochemistry lane bioinformatics.

|-
| 00:26
| and basic '''Python''' programming.
(bad ka basic '''Python''' programming.

|-
| 00:30
| Refer to the '''Python''' tutorials at the given link.
(Peit ia ka '''Python''' tutorials na ka link ba ai hapoh.

|-
| 00:34
| 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

|-
| 00:40
| '''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 bad * '''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.
(Ki scientific data jong ka biology ju store barabor ia ki ha ka text file kum '''FASTA''', '''GenBank''', '''EMBL''', '''Swiss-Prot''' kumta ter ter.

|-
| 01:07
|Data files can be downloaded from the database websites.
(Ia ki data files lah ban download na ka database websites.

|-
| 01:12
|Open the website link given below, in any web browser.
(Plie ia ka website link ba lah ai harum, da uno uno u web browser.

|-
| 01:17
| A web-page opens.
(Ka web-page kan sa plie.

|-
| 01:19
|Let us download '''FASTA''' and '''GenBank''' files for human '''insulin gene'''.
(To ngin ia download '''FASTA''' bad '''GenBank''' files na ka bynta ka human '''insulin gene'''.

|-
| 01:25
|In the search box, type: "human insulin", click on '''Search''' button.
(Ha ka search box, type: "human insulin", click ha '''Search''' button.

|-
| 01:31
| The web-page shows many files for human '''insulin gene'''.
(Ka web-page kan pyni bun ki flies na ka bynta ka human '''insulin gene'''.

|-
| 01:35
|For demonstration, I will select 4 files with the name “Homo sapiens Insulin mRNA”.
(Ban pyni nuksa, ngan jied 4 tylli ki files kiba kyrteng “Homo sapiens Insulin mRNA”.

|-
| 01:43
|I will choose files that have less than 500 '''base''' pairs.
(Ngan jied ia ki files ba duna ia ka 500 '''base''' pairs.

|-
| 01:48
|Click on the check-box to select the file, to download.
(Click ha ka check-box ban select ia ka file ban download.

|-
| 01:56
| Bring the cursor to the “'''Send to'''” option, located at the top right corner of the page.
(Wanrah ia u cursor sha “'''Send to'''” option, kaba don ha jrong duh sha ka liang ka mon jong ka page.

|-
| 02:02
|Click on the small selection button with a down arrow, present next to the “'''Send to'''” button.
(Click ha i selection button barit ba don u khnam ba kdew shapoh, ba don hajan ka “'''Send to'''” button.

|-
| 02:09
| Under the heading “'''Choose destination'''”, click on '''File''' option.
(Hapoh ka heading “'''Choose destination'''”, click ha '''File''' option.

|-
| 02:13
|You can '''save''' this file in any file format, listed under '''format''' drop-down list box.
(Phi lah ban '''save''' ia kane ka file ha kano kano ka format, kiba don hapoh '''format''' drop-down list box.

|-
| 02:21
|Choose '''FASTA''' from the given options.
(Jied '''FASTA''' na ki options ba ai hapoh.
|-
| 02:25
|Then click on '''Create file''' option.
(Nangta sa click ha '''Create file''' option.

|-
| 02:29
| A dialog-box appears on the screen.
(Ka dialog-box kan sa mih ha ka screen.

|-
|02:32
|Select '''Open with''', click on '''OK.'''
(Jied '''Open with''', click ha '''OK.'''

|-
| 02:36
| A file opens in a '''text editor'''.
(Ka file kan sa mih ha ka '''text editor'''.

|-
| 02:39
|The file shows 4 records, since we had selected four files to download.
(Kane ka file ka pyni 4 tylli ki records, namar ngi la jied ban plie 4 tylli ki files ban download.

|-
| 02:46
|The first line in each record is an '''identifier''' line.
(U line banyngkong ha kawei pa kawei ka record u dei u '''identifier''' line.

|-
| 02:50
|It starts with a “greater than (>)” symbol.
(Un sdang da u “greater than (>)” symbol.

|-
| 02:53
|This is followed by a '''sequence'''.
(Nangta sa bud sa da u'''sequence'''.

|-
| 02:56
|'''Save''' the file in your '''home''' folder as “sequence.fasta'”.
('''Save''' ia ka file ha '''home'''folder kum “sequence.fasta'”.

|-
| 03:01
|Close the text editor.
(Khang ia ka text editor.

|-
| 03:03
| Follow the same steps as above, to download the files in '''GenBank''' format
(Leh kumjuh ka rukom kum haneng ban download ia ki files ha '''GenBank''' format

|-
| 03:08
|for the same files selected earlier.
(na ka bynta ki files ba jied nyngkong .

|-
| 03:12
|Select the '''file format''' as '''GenBank.'''
(Select ia ka '''file format''' kum '''GenBank.'''

|-
| 03:16
|Create a file. Open with a text editor.
(Shna ia ka file. Plie da u text editor.

|-
| 03:21
| Notice that the sequence file in '''GenBank''' format has more features than a '''FASTA''' file.
(Ha khmih ba ka sequence file ha '''GenBank''' format ka kham bun features ban ia ka '''FASTA''' file.

|-
| 03:27
|'''Save''' the file as "sequence.gb" in your '''home''' folder. Close the text editor.
('''Save''' ia ka file kum "sequence.gb" ha ka '''home''' folder. Khang noh u text editor.

|-
| 03:34
| For demonstration purpose, we need a FASTA file with a single '''record'''.
(Ban peit nuksa, ngi donkam ia ka FASTA file ba don '''record''' tang iwei.

|-
| 03:39
|For this, clear the earlier selection by again clicking on the check boxes.
(Na ka bynta kane, pynkhuid ia ki selection ba nyngkong da kaba click biang ha ki check boxes.

|-
| 03:48
|Now, select the file “'''Human insulin gene complete cds'''”.
(Mynta, select ia ka file “'''Human insulin gene complete cds'''”.

|-
| 03:54
|Click on the check-box.
(Click ha ka check-box.

|-
| 03:57
| And follow the same steps shown earlier to '''save''' the file in the '''home''' folder.
(Bad sa bud ia ki rukom kumba la pyni nyngkong ban '''save''' ia ka file ha ka '''home''' folder.

|-
| 04:01
|'''Save''' the file as "insulin.fasta".
('''Save''' ia ka file kum "insulin.fasta".

|-
| 04:08
| Biological data stored in these files can be extracted and modified using '''Biopython''' libraries.
(Ki Biological data ba lah store ha kine ki files lah ban sei bad pynkylla da kaba pyndonkam da ka '''Biopython''' libraries.

|-
| 04:16
|Close the text-editor.
(Khang ia u text-editor.

|-
| 04:19
| Extracting data from data files is called as '''Parsing'''.
(Ban sei ia ki data na data files ki ju khot '''Parsing'''.

|-
| 04:23
|Most file formats can be parsed using '''function'''s available in '''SeqIO''' module.
(Bun ia kum kine jait file formats lah ban parsed da kaba pyndonkam '''function'''s kiba don ha '''SeqIO''' module.

|-
| 04:30
|Most commonly used functions of '''SeqIO''' module are: '''parse, read, write''' and '''convert'''.
(Kiba kham paw ki functions jong ka '''SeqIO''' module dei : '''parse, read, write''' bad '''convert'''.

|-
| 04:38
| Open the terminal by pressing '''Ctrl, Alt''' and '''t''' keys simultaneously.
(Plie ia ka terminal da kaba nion sah ia '''Ctrl, Alt''' bad '''t''' keys.

|-
| 04:44
| Start '''Ipython''' by typing "ipython" at the prompt. Press '''Enter'''.
(Plie ia ka '''Ipython''' da kaba type "ipython" ha ka prompt. Nion '''Enter'''.

|-
| 04:51
| Next, '''import''' "SeqIO" module from '''Bio''' package.
(Nangta, '''import''' "SeqIO" module na '''Bio''' package.

|-
| 04:56
| At the prompt, type: '''from Bio import SeqIO'''. Press '''Enter'''.
(Ha ka prompt, type: '''from Bio import SeqIO'''. Nion '''Enter'''.

|-
| 05:04
| We will start with the most important function “'''parse'''”.
(Ngin ia sdang da ka function kaba kham donkam ka “'''parse'''”.

|-
|05:07
|For demonstration, I will use a '''FASTA''' file that has many '''record'''s which we had downloaded earlier from the database.
(Na ka bynta ka nuksa, ngan pyndonkam ka '''FASTA''' file ka ba don bun '''record'''s kaba ngi download shen na ka database.

|-
| 05:17
| For simple '''FASTA''' parsing, type the following at the prompt.
(Na ba bynta ka '''FASTA''' parsing ba kham suk, type kumne harum ha ka prompt.

|-
| 05:22
|Here, we are using the '''parse''' function to read the contents of the '''sequence.fasta''' file.
(Hangne, ngi pyndonkam ia ka '''parse''' function ban read ia ki contents jong ka '''sequence.fasta''' file.

|-
| 05:30
|For the output, print '''record id''', sequence present in the record and also the length of the sequence.
(Na ka bynta ka output, print '''record id''', sequence kaba don ha ka record bad ruh ia ka jingjrong jong ka sequence.

|-
| 05:41
|Also notice that the '''parse''' function is used to read sequence data as '''Sequence record objects'''.
(Peit bha ruh ba ia ka '''parse''' function shait pyndonkam ban read sequence data kum '''Sequence record objects'''.

|-
| 05:48
|It is generally used with a '''for''' loop.
(Shait pyndonkam barabor bad ka '''for''' loop.

|-
| 05:52
|It can accept two '''arguments''', the first one is the file name to read the data.
(Ka lah ban shim ar tylli ki '''arguments''', kaba nyngkong dei ka file name ban read ia ka data.

|-
| 05:59
|The second specifies the file format.
(Ka ba ar pat ka pyntikna ia ka format jong ka file.

|-
| 06:02
|Press '''Enter''' key twice to get the output.
(Nion ia u '''Enter''' key ar sien ban ioh ia ka 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.
(Ka output ka pyni ia u ''' identifier line, nangta bud sa u sequence uba don ha ka file, bad ruh ka jingjrong jong ka sequence na ka bynta baroh ki records ha ka file.

|-
| 06:21
|Notice that the '''FASTA''' format does not specify the alphabet.
(Phin shem ba ka '''FASTA''' format kan nym pyntikna ia u alphabet.

|-
| 06:26
|So, the output does not specifies it as a '''DNA sequence'''.
(Te, ka output kan nym pyni ia ka kum ka '''DNA sequence'''.

|-
| 06:31
| The same steps can be repeated for parsing '''GenBank''' file.
(Ki juh ki rukom lah ban bud ban parsing iaka '''GenBank''' file.

|-
| 06:36
|For Demonstration we will use the '''GenBank''' file which we have downloaded earlier from the database.
(Ban pyni nuksa ngin pyndonkam ia ka '''GenBank''' file kaba ngi lah download mynne na ka database.

|-
| 06:43
|Press up-arrow key to get the lines of code which we had used earlier.
(Nion ia u up-arrow key ban ioh ia ki lines jong ki code kiba ngi lah pyndonkam nyngkong .

|-
| 06:49
|Change the file name to '''sequence.gb '''.
(Pynkylla ia ka kyrteng jong ka file sha ka '''sequence.gb '''.

|-
| 06:53
|Change the file format to '''genbank.'''
(Pynkylla ia ka file format sha ka '''genbank.'''

|-
| 06:56
|The rest of the code remains same.
(Ki code ba sah kin neh kumjuh.

|-
| 06:58
| Press '''Enter''' key twice to get the output.
(Nion ia u '''Enter''' key arsien ban ioh ia ka 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.
(Hangne ruh ka output ka pyni ia ka '''record id''', '''sequence''' bad ka jingjrong jong ka sequence na ka bynta baroh ki records ha ka file.

|-
| 07:12
|Notice that the '''GenBank''' format specifies the sequence as DNA sequence.
(Sa khmih ba ka '''GenBank''' format ka pyntikna ia ka sequence kum ka DNA sequence.

|-
| 07:19
| Similarly, '''Swiss-prot''' and '''EMBL''' files can be parsed using the same code as above.
(Kumjuh ruh, ia ki '''Swiss-prot''' bad '''EMBL''' files lah ban parse da kaba pyndonkam ia u juh u code kum haneng.

|-
| 07:27
| If your file contains a single record then type the following lines for '''parsing'''.
(Lada ka file jong phi ka don uwei u record phi hap type ia ki line harum ban leh '''parsing'''.

|-
| 07:34
| Here, we will use the previously saved '''FASTA''' file with a single record, that is, '''insulin.fasta '''as an example.
(Hangne, ngin pyndonkam ia '''FASTA''' file ba lah save mynne, bad uwei u record, uta u dei '''insulin.fasta ''' kum ka nuksa.

|-
| 07:43
|Notice that we have used '''read''' function instead of '''parse''' function. Press '''Enter'''.
(Phin sa shem ba ngi lah dep pyndonkam ia ka '''read''' function ha jaka jong '''parse''' function. Nion '''Enter'''.

|-
| 07:50
| The output shows the contents for the file '''insulin.fasta'''.
(Ka output ka pyni ki contents na ka bynta ka file '''insulin.fasta'''.

|-
| 07:55
|It shows the sequence as '''sequence record object'''.
(Ka pyni ia ka sequence kum '''sequence record object'''.

|-
| 07:59
|And other attributes such as '''GI, accession number '''and '''description'''.
(Bad kiwei ki attributes kum '''GI, accession number '''bad '''description'''.

|-
| 08:06
| We can also view the individual attributes of this record as follows.
(Ngi lah ruh ban peit ia ki individual attributes jong kane ka record kumne harum.

|-
| 08:11
|At the prompt, type: '''record dot seq'''. Press '''Enter'''.
(Ha ka prompt, type: '''record dot seq'''. Nion '''Enter'''.

|-
| 08:18
| The output shows the sequence present in the file.
(Ka output ka pyni ia ka sequence ba don ha ka file.

|-
| 08:22
| To view the identifiers for this record, type: '''record dot id.''' Press '''Enter'''.
(Ban peit ia ki identifiers jong kane ka record, type: '''record dot id. Nion '''Enter'''.

|-
| 08:29
|The output shows the '''GI''' number and accession number etc.
(Ka output ka pyni ia u '''GI''' number bad accession number bad kumta ter ter.

|-
| 08:34
|You can use the function described above to '''parse''' the data files of your choice.
(Phi lah ban pyndonkam ia u function ba lah ong haneng ban '''parse''' ia ki data files ha ka rukom kaba ngi mon.

|-
| 08:40
| Now, let's summarize.
(To ngin ia khmih ia kiba ngi lah kdew haneng )

|-
| 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
(Ha kane ka jingbatai (tutorial), ngi lah nang ban: download'''FASTA''' bad '''GenBank''' files na
ka '''NCBI''' database website bad pyndonkam ia '''parse''' bad '''read''' functions na ka '''SeqIO''' module.

|-
| 08:55
| to extract data such as '''record id'''s, description and sequences from '''FASTA''' and '''GenBank''' files.
(Ban sei ia ki data kum ki '''record id'''s, description bad sequences na '''FASTA''' bad '''GenBank''' files.

|-
| 09:03
| Now, for the assignment-
(Mynta, na ka bynta ka assignment-

|-
| 09:06
|Download '''FASTA''' files for nucleotide sequence of your choice from '''NCBI''' database.
(Download ia ki '''FASTA''' files na ka bynta ka nucleotide sequence kiba phi sngewiahap na '''NCBI''' database.

|-
| 09:13
|Convert the file of sequences to their '''reverse complement'''s.
(Pynkylla ia ki file jong ki sequences sha '''reverse complement'''s jong ki.

|-
| 09:17
| Your completed assignment should have the following lines of code.
(Ka assignment ba lah dep jong phi ka dei ban don ki lines of code kumne harum.

|-
| 09:22
|Use '''parse''' function to '''load''' nucleotide sequences from the '''FASTA''' file.
(Pyndonkam '''parse''' function ban '''load''' ia nucleotide sequences na ka '''FASTA''' file.

|-
| 09:28
|Next, print reverse complements using the Sequence object’s built in '''reverse complement''' method.
(Nangta, print ia ka reverse complements da kaba pyndonkam ia ka Sequence object’s built in '''reverse complement''' method.

|-
| 09:37
| Video at the following link summarizes the spoken-tutorial project.
(Ka video ha ka link hapoh kan pynsngewthuh shuh shuh ia kane ka spoken-tutorial project.
|-
| 09:42
|Please download and watch it.
(Sngewbha download bad peit ia ka.

|-
| 09:44
| The Spoken Tutorial Project team conducts workshops and gives certificates to those who pass an on-line test.
(Ka Spoken Tutorial Project team ka ju pynlong ia ki workshops bad ai ruh ia ki certificates sha kito ba pass ia ka on-line test.

|-
| 09:51
|For more details, please write to us.
(Na ka bynta ka jingtip ba kham bniah, sngewbha thoh sha ngi.

|-
| 09:55
| 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.

|-
| 10:01
|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.

|-
| 10:06
|This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining.
(Nga dei ka Snehalatha na '''IIT Bombay''', signing off. Khublei shibun )

|}

Biopython/C2/Parsing-Data/Khasi - Revision history

Hezekiah2016 at 09:48, 31 May 2018

Hezekiah2016: Created page with "{| Border=1 ! Time ! Narration |- | 00:01 | Hello everyone.Welcome to this tutorial on '''Parsing Data.''' (Khublei baroh. Ngi pdiang sngewb..."