Biopython/C2/Writing-Sequence-Files/Khasi

Time	Narration
00:01	Khublei ia phi baroh. Ngi pdiang sngewbha ia phi sha kane ka tutorial halor ka Writing Sequence Files.
00:07	Ha kane ka tutorial, ngin pule: * Kumno ban shna Sequence Record Objects
00:13	Ban write ia ki sequences files
00:15	Pynkylla hapdeng file formats
00:19	Bad, jied records ha ka file da ka jingjrong.
00:23	Ban bud ia kane ka tutorial, phi dei ban tip bha ia ka
00:27	undergraduate Biochemistry lane Bioinformatics.
00:31	Bad basic Python programming.
00:34	Peit iaki Python tutorials ha ka link ba la ai harum.
00:38	Ban record ia kane ka tutorial, nga pyndonkam da ka: * Ubuntu OS version 14.10
00:45	Python version 2.7.8
00:48	Ipython interpretor version 2.3.0 bad * Biopython version 1.64.
00:55	Ngi lah dep pule hashwa shaphang ki function'parse' badreadban read ia ki contents jong ka file.
01:03	Ha kane ka tutorial, ngin sa pule kumno ban pyndonkam ia ka write function ban write ki sequences sha ka file.
01:09	Bad ban pyndonkam Convert function na ka bynta ka inter-conversion hapdeng Ki file format ba bun.
01:16	Mynta ngan pyni ia phi kumno ban pyndonkam ia write function.
01:20	Kane ka text file ba don u protein sequence.
01:24	Ka sequence bala pyni hangne kadei u insulin protein.
01:28	Ka file ka don ruh ki jingpyntip kum GI accession number bad description.
01:36	Mynta ngin ia shna ka Ïaka file naka bynta ka sequence haka FASTA format.
01:41	Ka synjam ba Nyngkong eh ka long ban shna ka sequence record object.
01:45	Ki jingtip ba kham bniah shaphang Sequence Record Objects:
01:49	Ka dei ka basic data type na ka bynta ka sequence input/output interface.
01:55	Ha ka sequence record object, ia ka sequence la pyniasoh bad ka jinglong ba kham halor kum ki identifiers bad descriptions.
02:04	Plie ia ka terminal da kaba nion lang ia ki Ctrl, Alt bad t keys.
02:10	Ha ka prompt, type: ipython, nion Enter.
02:15	Ha ka prompt, type iaki lain harum:
02:18	from Bio dot Seq module import Seq class.
02:24	from Bio dot SeqRecord module import Sequence Record class
02:31	Kaba bud, from Bio dot Alphabet module import generic protein class.
02:38	Kaba bud, ngan sa save ia ka sequence record object ha ka variable record1.
02:45	Copy ia ka sequence, id bad description na ka text file bad paste ia ka ha la ki jong ki lain ha ka terminal.
02:56	Nion Enter.
02:58	Ban peit ia ka output, type: record1.
03:02	Nion Enter.
03:04	Ka output ka pyni ia ka insulin protein sequence kum sequence record object.
03:10	Ka pyni ia ka sequence ryngkat u id bad description.
03:13	Ngin pyndonkam ia kawrite function ban pynkylla ia ka sequence record object haneng sha ka FASTA file.
03:21	Import SeqIO module na ka Bio package.
03:26	Kaba bud, type ia ka command line da ka write function ban pynkylla ia ka sequence object sha ka FASTA file.
03:40	Ka write function ka shim 3 tylli ki argument
03:44	Ka ba nyngkong ka dei ka variable ba buh ia ka sequence record object.
03:49	Ka ba ar ka dei ka kyrteng file ban write ia ka FASTA file.
03:54	Ka ba lai ka dei ka file format ban write. Nion Enter.
03:58	Ka Output ka pyni kawei, kata ka dei, ngi la pynkylla kawei ka sequence record object sha ka FASTA file.
04:07	Ka file ha ka FASTA format la save ha ka home folder kum "example.fasta".
04:13	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	Ban peit ia ka file, leit sha ka file ha ka home folder.
04:24	Plie ia kane ka file ha ka text editor.
04:27	Ka protein sequence ka lah long mynta ha ka FASTA format.
04:31	Khang ia u text editor.
04:33	Bun ki bioinformatics tools ki shim bun jait ki input file formats.
04:38	Te, teng teng ngi hap ban inter-convert hapdeng ki sequence file formats.
04:44	Ngi lah ban pynkylla ia ki files da kaba pyndonkam convert function ha SeqIO module.
04:50	Ban pyni nuksa, ngan pynkylla ia u GenBank file sha ka FASTA file.
04:55	Nga don u GenBank file ha ka home folder jong nga.
04:59	To ngan plie ia une ha u text editor.
05:02	U file u don HIV genome ha GenBank format.
05:07	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	Nangta sa bud da u genome sequence ba pura.
05:18	Khang ia u text editor. Type ia ki line ha terminal kumne harum.
05:23	Hangne u convert function u pynkylla ia baroh ka genome sequence kiba don ha GenBank file sha FASTA file. Nion Enter.
05:33	Ka file ba thymmai ha ka FASTA format mynta la save kum HIV.fasta ha ka home folder.
05:39	Leit sha ka file bad plie ha u text editor.
05:46	Khang ia u text editor.
05:49	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	Ban write ia katto katne ki formats, donkam ia ki jingtip ba kiwei ki formats kim don.
06:02	kum Nuksa: Ngi lah ban pynkylla ia u GenBank file sha u FASTA file. Hynrei ngim lah ban leh da khongpong.
06:09	Kumjuh ruh, ngi lah ban pynkylla ia FASTQ file sha ka FASTA file hynrei ngim lah ban leh da khongpong pat.
06:15	Ban tip khap bniah shaphang ka convert function, type ia u help command.
06:21	Nion Enter.)
06:24	Nion 'q' ha ka keyboard ban ioh biang ia ka prompt.
06:28	Ngi lah ruh ban sei ia ki genesba shimet na ka HIV genome ha GenBank format.
06:35	Kine ki genes ba shimet lah ban save ruh ha FASTA lane kino kino ki formats.
06:41	Na bynta kane, type ia u code harum ha ka prompt.
06:47	Une u code un write ia baroh ki CDS gene sequences, ki id bad kyrteng jong ki gene ha ka file.
06:56	Ia kane ka file la save kum “HIV_geneseq.fasta” ha ka home folder jong phi. Nion Enter.
07:07	Da kaba pyndonkam u Biopython tools, ngi lah ban jied ia ki records jong ka file da ka jingjrong jong ka.
07:12	Hangne, nga lah plie ia u FASTA file “hemoglobin.fasta” uba don hynriew tylli ki records.
07:19	Kawei pa kawei ka record ki pher ha ka jingjrong.
07:23	Type iaki lain harum ban pynbeit nyngkong da ka record ba jrong tam.
07:27	Ka file ba thymmai kaba don u sequence ba la jied yn save kum "sorted_hemoglobin.fasta" ha ka home folder jong phi.
07:38	Ban ioh ia ki records ba lyngkot nyngkong, leh khongpong ia ki arguments ha ka records.sort command line.
07:45	To ngin batai lyngkot. Ha kane ka tutorial, ngi lah pule ban:* shna Sequence Record Objects
07:51	Write ia ki sequence files da kaba pyndonkam write function jongSequence Input/Output module.
07:58	Pynkylla hapdeng sequence file formats da kaba pyndonkamconvert function.
08:03	Bad, pynbeit ia ki records ha ka file da ka jingjrong.
08:07	Na ka bynta ka assignment:
08:09	Extract ia u gene "HIV1gp3" ha positions 4587 sha 5165 na ka genomic sequence jong HIV.
08:21	Ka file “HIV.gb” la kynthup lang ha ka code files jong kane ka tutorial.
08:28	Ka assignment ba lah dep jong phi kan don ia u code ba harum.
08:43	Ka video ha ka link harum ka batai lyngkot shaphang ka Spoken Tutorial project.
08:48	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.
08:57	Ban tip kham bniah, sngewbha thoh sha ngi.
09:00	Ia ka Spoken Tutorial Project la bei tyngka da ka NMEICT, MHRD, Government of India.
09:06	Khambun ki jingtip halor kane ka mission kadon haka link bala pyni.
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.

Contributors and Content Editors

Hezekiah2016