Difference between revisions of "Biopython/C2/Writing-Sequence-Files/Khasi"

| Khublei ia phi baroh. Ngi pdiang sngewbha ia phi sha kane ka tutorial halor ka '''Writing Sequence Files'''.

| Ha kane ka tutorial, ngin pule: * Kumno ban shna '''Sequence Record Objects'''

| Ban write ia ki sequences files  

| Pynkylla hapdeng '''file format'''s

| Bad, jied '''record'''s ha ka file da ka jingjrong.  

| Ban bud ia kane ka tutorial, phi dei ban tip bha ia ka

| undergraduate Biochemistry lane Bioinformatics.

| Bad basic '''Python''' programming.

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

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

| '''Ipython interpretor''' version 2.3.0 bad * '''Biopython''' version 1.64.

| Ngi lah dep pule hashwa shaphang ki '''function''''''parse''' bad'''read'''ban read ia ki contents jong ka file.  

| Ha kane ka tutorial, ngin sa pule kumno ban pyndonkam ia ka '''write''' function ban write ki sequences sha ka file.   

| Bad ban pyndonkam '''Convert''' function na ka bynta ka inter-conversion hapdeng Ki '''file format''' ba bun.

| Mynta ngan pyni ia phi kumno ban pyndonkam ia '''write''' function.

| Kane ka text file ba don u protein sequence.  

| Ka sequence bala pyni hangne kadei u '''insulin protein.'''

| Ka file ka don ruh ki jingpyntip kum '''GI accession number''' bad '''description'''.

| Mynta ngin ia shna ka Ïaka file naka bynta ka sequence haka '''FASTA''' format.

| Ka synjam ba Nyngkong eh ka long ban shna ka '''sequence record object'''.

| Ki jingtip ba kham bniah shaphang Sequence Record Objects:  

| Ka dei ka basic data type na ka bynta ka '''sequence input/output interface'''.

| Ha ka sequence record object, ia ka sequence la pyniasoh bad ka jinglong ba kham halor kum ki '''identifier'''s bad descriptions.

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

| Ha ka prompt, type: '''ipython''', nion '''Enter'''.

| Ha ka prompt, type iaki lain harum:  

| '''from Bio dot Seq module import Seq class'''.

| '''from Bio dot SeqRecord module import Sequence Record class'''

| Kaba bud, '''from Bio dot Alphabet module import generic protein class'''.

| Kaba bud, ngan sa save ia ka sequence record object ha ka variable '''record1.'''

| '''Copy''' ia ka '''sequence, id''' bad '''description''' na ka text file bad '''paste''' ia ka ha la ki jong ki lain ha ka terminal.  

| Nion '''Enter.'''

| Ban peit ia ka output, type: '''record1'''.

| Nion '''Enter.'''

| Ka output ka pyni ia ka '''insulin protein''' sequence kum '''sequence record '''object.

| Ka pyni ia ka sequence ryngkat u '''id''' bad '''description'''.

| Ngin pyndonkam ia ka'''write''' function ban pynkylla ia ka sequence record object haneng sha ka '''FASTA''' file.

| '''Import SeqIO module''' na ka '''Bio package.'''

| Kaba bud, type ia ka '''command line''' da ka '''write''' function ban pynkylla ia ka sequence object sha ka '''FASTA''' file.

| Ka '''write '''function ka shim 3 tylli ki '''argument'''

| Ka ba nyngkong ka dei ka variable ba buh ia ka '''sequence record object'''.

| Ka ba ar ka dei ka kyrteng file ban write ia ka '''FASTA''' file.

| Ka ba lai ka dei ka file format ban write. Nion '''Enter'''.

| Ka Output ka pyni kawei, kata ka dei, ngi la pynkylla kawei ka '''sequence record object''' sha ka '''FASTA''' file.

| Ka file ha ka '''FASTA''' format la save ha ka '''home''' folder kum "example.fasta".

| 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.  

| Ban peit ia ka file, leit sha ka file ha ka '''home''' folder.

| Plie ia kane ka file ha ka '''text editor.'''

| Ka protein sequence ka lah long mynta ha ka '''FASTA''' format.

| Khang ia u '''text editor.'''

| Bun ki '''bioinformatics''' tools ki shim bun jait ki input file formats.

| Te, teng teng ngi hap ban inter-convert hapdeng ki sequence file formats.  

| Ngi lah ban pynkylla ia ki files da kaba pyndonkam ''' convert '''function ha '''SeqIO module.'''

| Ban pyni nuksa, ngan pynkylla ia u '''GenBank''' file sha ka '''FASTA''' file.

| Nga don u '''GenBank''' file ha ka '''home''' folder jong nga.

| To ngan plie ia une ha u text editor.  

| U file u don '''HIV genome''' ha '''GenBank''' format.

| Une u '''GenBank''' file u don ki jingbatai jong baroh ki '''genes''' ha ka  '''genome''', ha ka bynta ba nyngkong jong ka file.  

| Nangta sa bud da u '''genome''' sequence ba pura.  

| Khang ia u text editor. Type ia ki line ha terminal kumne harum.

| Hangne u '''convert''' function u pynkylla ia baroh ka '''genome''' sequence kiba don ha '''GenBank''' file sha '''FASTA''' file. Nion '''Enter'''.

| Ka file ba thymmai ha ka '''FASTA''' format mynta la save kum '''HIV.fasta''' ha ka '''home''' folder.

| Leit sha ka file bad plie ha u text editor.

| Khang ia u text editor.  

| Wat la ka long kaba suk ban pynkylla ia ka file formats da kaba pyndonkam '''convert''' function,hynrei ka don da u pud.

| Ban write ia katto katne ki formats, donkam ia ki jingtip ba kiwei ki formats kim don.

| kum Nuksa: Ngi lah ban pynkylla ia u '''GenBank''' file sha u '''FASTA''' file. Hynrei ngim lah ban leh da khongpong.

| Kumjuh ruh, ngi lah ban pynkylla ia '''FASTQ''' file sha ka '''FASTA''' file hynrei ngim lah ban leh da khongpong pat.  

| Ban tip khap bniah shaphang ka '''convert''' function, type ia u '''help''' command.

| Nion '''Enter'''.)

| Nion 'q' ha ka keyboard ban ioh biang ia ka prompt.  

| Ngi lah ruh ban sei ia ki '''genes'''ba shimet na ka '''HIV genome''' ha '''GenBank''' format.

| Kine ki '''genes''' ba shimet lah ban save ruh ha '''FASTA''' lane kino kino ki formats.

| Na bynta kane, type ia u code harum ha ka '''prompt'''.

| Une u code un write ia baroh ki '''CDS''' gene sequences, ki id bad kyrteng jong ki '''gene''' ha ka file.  

| Ia kane ka file la save kum “HIV_geneseq.fasta” ha ka '''home''' folder jong phi. Nion '''Enter'''.  

 

| Da kaba pyndonkam u '''Biopython''' tools, ngi lah ban jied ia ki records jong ka file da ka jingjrong jong ka.  

| Hangne, nga lah plie ia u FASTA file “hemoglobin.fasta” uba don hynriew tylli ki records.  

| Kawei pa kawei ka '''record''' ki pher ha ka jingjrong.  

| Type iaki lain harum ban pynbeit nyngkong da ka record ba jrong tam.

| Ka file ba thymmai kaba don u sequence ba la jied yn save kum "sorted_hemoglobin.fasta" ha ka '''home''' folder jong phi.  

| Ban ioh ia ki records ba lyngkot nyngkong, leh khongpong ia ki arguments ha ka '''records.sort''' command line.

| To ngin batai lyngkot. Ha kane ka tutorial, ngi lah pule ban:* shna Sequence Record Objects  

| Write ia ki sequence files da kaba pyndonkam ''' write''' function jong'''Sequence Input/Output''' module.

| Pynkylla hapdeng '''sequence file format'''s da kaba pyndonkam'''convert''' function.

| Bad, pynbeit ia ki records ha ka file da ka jingjrong.

| Na ka bynta ka assignment:  

| '''Extract''' ia u gene "HIV1gp3" ha positions 4587 sha 5165 na ka '''genomic''' sequence jong HIV.

| Ka file “HIV.gb” la kynthup lang ha ka code files jong kane ka tutorial.  

| Ka assignment ba lah dep jong phi kan don ia u code ba harum.  

| Ka video ha ka link harum ka batai lyngkot shaphang ka Spoken Tutorial project.

| Sngewbha download bad peit ia ka. Ka Spoken Tutorial Project team ka ju pynlong workshops bad ai certificates naka bynta kito kiba pass ia ka online test.  

| Ban tip kham bniah, sngewbha thoh sha ngi.

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

| Khambun ki jingtip halor kane ka mission kadon haka link bala pyni.

| 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.|}