Difference between revisions of "Biopython/C2/Parsing-Data/Khasi"

| Khublei baroh. Ngi pdiang sngewbha ia phi sha kane ka tutorial halor ka '''Parsing Data.'''

| Ha kane ka tutorial, ngin pule kumno ban download ia ki '''FASTA''' bad '''GenBank''' files na ka '''NCBI''' database website.  

| Bad ban '''Parse'''ia ki data files da kaba pyndonkam ia ki '''function'''s  ha ka  '''Sequence Input/Output''' module.

| Ban bud ia kane ka tutorial, phi dei ban tip bha ia ka undergraduate biochemistry lane bioinformatics.  

| bad ka basic '''Python''' programming.

| Peit ia ka '''Python''' tutorials ha ka link ba la ai.

| Ban record ia kane ka tutorial, nga pyndonkam da ka : * '''Ubuntu OS''' version 14.10

| '''Ipython interpretor''' version 2.3.0

| '''Biopython''' version 1.64 bad * '''Mozilla Firefox '''browser 35.0.

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

| Ia ki data files lah ban download na ka database websites.

| Plie ia ka website link ba lah ai harum, da uno uno u web browser.

| Ka web-page ka plie.

| To ngin download iaka '''FASTA''' bad '''GenBank''' files na ka bynta ka human '''insulin gene'''.

| Ha ka search box, type: "human insulin", click ha '''Search''' button.

| Ka web-page ka pyni shibun tylli ki flies na ka bynta ka human '''insulin gene'''.

| Ban pyni nuksa, ngan jied 4 tylli ki files kiba kyrteng “Homo sapiens Insulin mRNA”.

| Ngan jied ia ki files ba duna ia ka 500 '''base''' pairs.

| Click ha ka check-box ban jied ia ka file ban download.  

| Wanrah ia u cursor sha “'''Send to'''” option, kaba don ha kyndong khlieh ka mon jong ka page.

| Click ha i selection button barit ba don u khnam ba kdew shapoh, ba don hajan ka “'''Send to'''” button.

| Hapoh ka heading “'''Choose destination'''”, click ha '''File''' option.

| Phi lah ban '''save''' ia kane ka file ha kano kano ka format, kiba don hapoh '''format''' drop-down list box.

| Jied '''FASTA''' na ki options ba ai hapoh.

 

| Nangta sa click ha '''Create file''' option.

| Ka dialog-box kan sa mih ha ka screen.  

| Jied '''Open with''', click ha '''OK.'''

| Ka file ka plie ha ka '''text editor'''.

| Kane ka file ka pyni 4 tylli ki records, namar ngi la jied 4 tylli ki files ban download.  

| U line banyngkong ha kawei pa kawei ka record u dei u '''identifier''' line.

| U sdang da u “greater than >)” symbol.

| Nangta la pynbud da u'''sequence'''.

| '''Save''' ia ka file ha '''home'''folder jong phi kum ka“sequence.fasta'”.

| Khang ia ka text editor.  

| Pynbud ki juh ki syn jam kum haneng ban download ia ki files ha '''GenBank''' format

| na ka bynta ki files ba la jied hashwa.  

| Jied ia ka '''file format''' kum '''GenBank.'''

| Shna ia ka file. Plie da u text editor.  

| Peit thuh ba ka sequence file ha '''GenBank''' format ka kham bun features ban ia ka '''FASTA''' file.

| '''Save''' ia ka file kum "sequence.gb" ha ka '''home''' folder. Khang noh u text editor.

| Ban peit nuksa, ngi donkam ia ka FASTA file ba don '''record''' tang iwei.  

| Na ka bynta kane, pynkhuid ia ki jingjied ba hashwa da kaba click biang ha ki check box.

| Mynta, jied ia ka file “'''Human insulin gene complete cds'''”.

| Click ha ka check-box.

| Bad sa bud ia ki rukom kumba la pyni mynne ban '''save''' ia ka file ha ka '''home''' folder.

| '''Save''' ia ka file kum "insulin.fasta".

| Ia ki Biological data ba lah store ha kine ki files lah ban sei bad pynkylla da kaba pyndonkam da ka '''Biopython''' libraries.  

| Khang ia u text-editor.  

| Ban sei ia ki data na data files la khot '''Parsing'''.

| Jan ia baroh ki file formats lah ban parsed da kaba pyndonkam '''function'''s kiba don ha '''SeqIO''' module.

| Ki function jong ka '''SeqIO''' module kiba ju kham pyndonkam bha baroh ki long: '''parse, read, write''' bad '''convert'''.

| Plie ia ka terminal da kaba nion lang ia '''Ctrl, Alt''' bad '''t''' keys.  

| Plie ia ka '''Ipython''' da kaba type "ipython" ha ka prompt. Nion '''Enter'''.

| Nangta, '''import''' "SeqIO" module na '''Bio''' package.

| Ha ka prompt, type: '''from Bio import SeqIO'''. Nion '''Enter'''.

| Ngin ia sdang da ka function kaba kham donkam ka “'''parse'''”.

| Na ka bynta ka nuksa, ngan pyndonkam ka '''FASTA''' file ka ba don bun '''record'''s kaba ngi download hashwa na ka database.  

| Na ba bynta ka '''FASTA''' parsing ba kham suk, type kumne harum ha ka prompt.  

| Hangne, ngi pyndonkam ia ka '''parse''' function ban read ia ki contents jong ka '''sequence.fasta''' file.

| Na ka bynta ka output, print '''record id''', sequence kaba don ha ka record bad ruh ia ka jingjrong jong ka sequence.  

| Peit bha ruh ba ia ka '''parse''' function la pyndonkam ban read sequence data kum '''Sequence record objects'''.

| La ju pyndonkam barabor bad ka '''for''' loop.  

| Ka pdiang ar tylli ki '''arguments''', kaba nyngkong dei ka file name ban read ia ka data.  

| Ka ba ar ka batai shai ia ka format jong ka file.  

| Nion ia u '''Enter''' key ar sien ban ioh ia ka output.  

| 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.  

| Peit thuh ba ka '''FASTA''' format kam batai shai ia u alphabet.  

| Te, ka output kan nym pyni ia ka kum ka '''DNA sequence'''.

| Ki juh ki synjam lah ban leh biang ban parse iaka '''GenBank''' file.

| Ban pyni nuksa ngin pyndonkam ia ka '''GenBank''' file kaba ngi lah download mynne na ka database.  

| Nion ia u up-arrow key ban ioh ia ki lines jong ki code kiba ngi lah pyndonkam hashwa.

| Pynkylla ia ka kyrteng jong ka file sha ka '''sequence.gb '''.

| Pynkylla ia ka file format sha ka '''genbank.'''

| Ki code ba sah kin neh kumjuh.  

| Nion ia u '''Enter''' key arsien ban ioh ia ka output.  

| 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.  

| Peit thuh ba ka '''GenBank''' format ka pyntikna ia ka sequence kum ka DNA sequence.

| Kumjuh ruh, ia ki '''Swiss-prot''' bad ki file '''EMBL''' lah ban parse da kaba pyndonkam ia u juh u code kum haneng.  

| Lada ka file jong phi ka don uwei u record phi hap type ia ki line harum ban leh '''parsing'''.  

| Hangne, ngin pyndonkam iaka  '''FASTA''' file ba lah save mynne, ba tang uwei u record, uta u dei '''insulin.fasta ''' kum ka nuksa.  

| Peit thuh ba ngi lah dep pyndonkam ia ka '''read''' function ha jaka jong '''parse''' function. Nion '''Enter'''.

| Ka output ka pyni ki contents na ka bynta ka file '''insulin.fasta'''.

| Ka pyni ia ka sequence kum '''sequence record object'''.

| Bad kiwei ki jinglong kum '''GI, accession number '''bad '''description'''.

| Ngi lah ruh ban peit ia ki jinglong ba shimet jong kane ka record kumne harum.

| Ha ka prompt, type: '''record dot seq'''. Nion '''Enter'''.

| Ka output ka pyni ia ka sequence ba don ha ka file.  

| Ban peit ia ki identifiers jong kane ka record, type: '''record dot id. Nion '''Enter'''.

| Ka output ka pyni ia u '''GI''' number bad accession number bad kumta ter ter.  

| Phi lah ban pyndonkam ia u function ba lah ong haneng ban '''parse''' ia ki data files kiba phi kwah.  

| Mynta to ngin batai lyngkot).

| Ha kane ka tutorial, ngi lah pule ban: download'''FASTA''' bad '''GenBank''' files na ka '''NCBI''' database website bad pyndonkam iaka  '''parse''' bad '''read''' functions na ka '''SeqIO''' module.

| Ban sei ia ki data kum ki  '''record id'''s, description bad sequences na '''FASTA''' bad '''GenBank''' files.

| Mynta, na ka bynta ka assignment-

| Download ia ki '''FASTA''' files na ka bynta ka nucleotide sequence haka jingjied jong phi na '''NCBI''' database.

| Pynkylla ia ki file jong ki sequences sha ki '''reverse complement'''s jong ki.

| Ka assignment ba lah dep jong phi ka dei ban don ki lines of code kumne harum.

| Pyndonkam ka '''parse''' function ban '''load''' ia nucleotide sequences na ka '''FASTA''' file.

| Nangta, print ia ka reverse complements da kaba pyndonkam ia ka Sequence object’s built in '''reverse complement''' method.

| Ka video ha ka link harum ka batai lyngkot ia kane ka spoken-tutorial project.

 

| Sngewbha download bad peit ia ka.  

| 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.

| Ban tip kham bniah, sngewbha thoh sha ngi.

| Ia ka Spoken Tutorial Project la bei tyngka da ka NMEICT, MHRD, Sorkar India.

| Khambun ki jingtip halor kane ka mission ka don ka ha link harum.

|ïa kane ka script la pynkylla sha ka Ktien Khasi da u Yuwanki Kharlukhi na Shillong,bad ma nga u Hezekiah Lyngdoh ngan pynkut noh. khublei ba phi la ïasnoh lang.