Biopython/C2/Parsing-Data/Khasi
From Script | Spoken-Tutorial
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| 00:01 | Khublei baroh. Ngi pdiang sngewbha ia phi sha kane ka tutorial halor ka Parsing Data. |
| 00:06 | Ha kane ka tutorial, ngin pule kumno ban download ia ki FASTA bad GenBank files na ka NCBI database website. |
| 00:14 | Bad ban Parseia ki data files da kaba pyndonkam ia ki functions ha ka Sequence Input/Output module. |
| 00:19 | Ban bud ia kane ka tutorial, phi dei ban tip bha ia ka undergraduate biochemistry lane bioinformatics. |
| 00:26 | bad ka basic Python programming. |
| 00:30 | Peit ia ka Python tutorials ha ka link ba la ai. |
| 00:34 | Ban record ia kane ka tutorial, nga pyndonkam da ka : * Ubuntu OS version 14.10 |
| 00:40 | Python version 2.7.8 |
| 00:44 | Ipython interpretor version 2.3.0 |
| 00:48 | Biopython version 1.64 bad * Mozilla Firefox browser 35.0. |
| 00:56 | 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 | Ia ki data files lah ban download na ka database websites. |
| 01:12 | Plie ia ka website link ba lah ai harum, da uno uno u web browser. |
| 01:17 | Ka web-page ka plie. |
| 01:19 | To ngin download iaka FASTA bad GenBank files na ka bynta ka human insulin gene. |
| 01:25 | Ha ka search box, type: "human insulin", click ha Search button. |
| 01:31 | Ka web-page ka pyni shibun tylli ki flies na ka bynta ka human insulin gene. |
| 01:35 | Ban pyni nuksa, ngan jied 4 tylli ki files kiba kyrteng “Homo sapiens Insulin mRNA”. |
| 01:43 | Ngan jied ia ki files ba duna ia ka 500 base pairs. |
| 01:48 | Click ha ka check-box ban jied ia ka file ban download. |
| 01:56 | Wanrah ia u cursor sha “Send to” option, kaba don ha kyndong khlieh ka mon jong ka page. |
| 02:02 | Click ha i selection button barit ba don u khnam ba kdew shapoh, ba don hajan ka “Send to” button. |
| 02:09 | Hapoh ka heading “Choose destination”, click ha File option. |
| 02:13 | Phi lah ban save ia kane ka file ha kano kano ka format, kiba don hapoh format drop-down list box. |
| 02:21 | Jied FASTA na ki options ba ai hapoh. |
| 02:25 | Nangta sa click ha Create file option. |
| 02:29 | Ka dialog-box kan sa mih ha ka screen. |
| 02:32 | Jied Open with, click ha OK. |
| 02:36 | Ka file ka plie ha ka text editor. |
| 02:39 | Kane ka file ka pyni 4 tylli ki records, namar ngi la jied 4 tylli ki files ban download. |
| 02:46 | U line banyngkong ha kawei pa kawei ka record u dei u identifier line. |
| 02:50 | U sdang da u “greater than >)” symbol. |
| 02:53 | Nangta la pynbud da usequence. |
| 02:56 | Save ia ka file ha homefolder jong phi kum ka“sequence.fasta'”. |
| 03:01 | Khang ia ka text editor. |
| 03:03 | Pynbud ki juh ki syn jam kum haneng ban download ia ki files ha GenBank format |
| 03:08 | na ka bynta ki files ba la jied hashwa. |
| 03:12 | Jied ia ka file format kum GenBank. |
| 03:16 | Shna ia ka file. Plie da u text editor. |
| 03:21 | Peit thuh ba ka sequence file ha GenBank format ka kham bun features ban ia ka FASTA file. |
| 03:27 | Save ia ka file kum "sequence.gb" ha ka home folder. Khang noh u text editor. |
| 03:34 | Ban peit nuksa, ngi donkam ia ka FASTA file ba don record tang iwei. |
| 03:39 | Na ka bynta kane, pynkhuid ia ki jingjied ba hashwa da kaba click biang ha ki check box. |
| 03:48 | Mynta, jied ia ka file “Human insulin gene complete cds”. |
| 03:54 | Click ha ka check-box. |
| 03:57 | Bad sa bud ia ki rukom kumba la pyni mynne ban save ia ka file ha ka home folder. |
| 04:01 | Save ia ka file kum "insulin.fasta". |
| 04:08 | Ia ki Biological data ba lah store ha kine ki files lah ban sei bad pynkylla da kaba pyndonkam da ka Biopython libraries. |
| 04:16 | Khang ia u text-editor. |
| 04:19 | Ban sei ia ki data na data files la khot Parsing. |
| 04:23 | Jan ia baroh ki file formats lah ban parsed da kaba pyndonkam functions kiba don ha SeqIO module. |
| 04:30 | Ki function jong ka SeqIO module kiba ju kham pyndonkam bha baroh ki long: parse, read, write bad convert. |
| 04:38 | Plie ia ka terminal da kaba nion lang ia Ctrl, Alt bad t keys. |
| 04:44 | Plie ia ka Ipython da kaba type "ipython" ha ka prompt. Nion Enter. |
| 04:51 | Nangta, import "SeqIO" module na Bio package. |
| 04:56 | Ha ka prompt, type: from Bio import SeqIO. Nion Enter. |
| 05:04 | Ngin ia sdang da ka function kaba kham donkam ka “parse”. |
| 05:07 | Na ka bynta ka nuksa, ngan pyndonkam ka FASTA file ka ba don bun records kaba ngi download hashwa na ka database. |
| 05:17 | Na ba bynta ka FASTA parsing ba kham suk, type kumne harum ha ka prompt. |
| 05:22 | Hangne, ngi pyndonkam ia ka parse function ban read ia ki contents jong ka sequence.fasta file. |
| 05:30 | Na ka bynta ka output, print record id, sequence kaba don ha ka record bad ruh ia ka jingjrong jong ka sequence. |
| 05:41 | Peit bha ruh ba ia ka parse function la pyndonkam ban read sequence data kum Sequence record objects. |
| 05:48 | La ju pyndonkam barabor bad ka for loop. |
| 05:52 | Ka pdiang ar tylli ki arguments, kaba nyngkong dei ka file name ban read ia ka data. |
| 05:59 | Ka ba ar ka batai shai ia ka format jong ka file. |
| 06:02 | Nion ia u Enter key ar sien ban ioh ia ka output. |
| 06:07 | 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 | Peit thuh ba ka FASTA format kam batai shai ia u alphabet. |
| 06:26 | Te, ka output kan nym pyni ia ka kum ka DNA sequence. |
| 06:31 | Ki juh ki synjam lah ban leh biang ban parse iaka GenBank file. |
| 06:36 | Ban pyni nuksa ngin pyndonkam ia ka GenBank file kaba ngi lah download mynne na ka database. |
| 06:43 | Nion ia u up-arrow key ban ioh ia ki lines jong ki code kiba ngi lah pyndonkam hashwa. |
| 06:49 | Pynkylla ia ka kyrteng jong ka file sha ka sequence.gb . |
| 06:53 | Pynkylla ia ka file format sha ka genbank. |
| 06:56 | Ki code ba sah kin neh kumjuh. |
| 06:58 | Nion ia u Enter key arsien ban ioh ia ka output. |
| 07:03 | 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 | Peit thuh ba ka GenBank format ka pyntikna ia ka sequence kum ka DNA sequence. |
| 07:19 | Kumjuh ruh, ia ki Swiss-prot bad ki file EMBL lah ban parse da kaba pyndonkam ia u juh u code kum haneng. |
| 07:27 | Lada ka file jong phi ka don uwei u record phi hap type ia ki line harum ban leh parsing. |
| 07:34 | Hangne, ngin pyndonkam iaka FASTA file ba lah save mynne, ba tang uwei u record, uta u dei insulin.fasta kum ka nuksa. |
| 07:43 | Peit thuh ba ngi lah dep pyndonkam ia ka read function ha jaka jong parse function. Nion Enter. |
| 07:50 | Ka output ka pyni ki contents na ka bynta ka file insulin.fasta. |
| 07:55 | Ka pyni ia ka sequence kum sequence record object. |
| 07:59 | Bad kiwei ki jinglong kum GI, accession number bad description. |
| 08:06 | Ngi lah ruh ban peit ia ki jinglong ba shimet jong kane ka record kumne harum. |
| 08:11 | Ha ka prompt, type: record dot seq. Nion Enter. |
| 08:18 | Ka output ka pyni ia ka sequence ba don ha ka file. |
| 08:22 | Ban peit ia ki identifiers jong kane ka record, type: record dot id. Nion Enter. |
| 08:29 | Ka output ka pyni ia u GI number bad accession number bad kumta ter ter. |
| 08:34 | Phi lah ban pyndonkam ia u function ba lah ong haneng ban parse ia ki data files kiba phi kwah. |
| 08:40 | Mynta to ngin batai lyngkot). |
| 08:42 | Ha kane ka tutorial, ngi lah pule ban: downloadFASTA bad GenBank files na ka NCBI database website bad pyndonkam iaka parse bad read functions na ka SeqIO module. |
| 08:55 | Ban sei ia ki data kum ki record ids, description bad sequences na FASTA bad GenBank files. |
| 09:03 | Mynta, na ka bynta ka assignment- |
| 09:06 | Download ia ki FASTA files na ka bynta ka nucleotide sequence haka jingjied jong phi na NCBI database. |
| 09:13 | Pynkylla ia ki file jong ki sequences sha ki reverse complements jong ki. |
| 09:17 | Ka assignment ba lah dep jong phi ka dei ban don ki lines of code kumne harum. |
| 09:22 | Pyndonkam ka parse function ban load ia nucleotide sequences na ka FASTA file. |
| 09:28 | Nangta, print ia ka reverse complements da kaba pyndonkam ia ka Sequence object’s built in reverse complement method. |
| 09:37 | Ka video ha ka link harum ka batai lyngkot ia kane ka spoken-tutorial project. |
| 09:42 | Sngewbha download bad peit ia ka. |
| 09:44 | 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 | Ban tip kham bniah, sngewbha thoh sha ngi. |
| 09:55 | Ia ka Spoken Tutorial Project la bei tyngka da ka NMEICT, MHRD, Sorkar India. |
| 10:01 | Khambun ki jingtip halor kane ka mission ka don ka ha link harum. |
| 10:06 | 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. |
