Difference between revisions of "Biopython/C2/Blast/Khasi"
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| '''Python''' version 2.7.8 | | '''Python''' version 2.7.8 | ||
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| 02:14 | | 02:14 | ||
− | | | + | |Hadien , ban '''run''' ia u BLAST lyngba ka internet, type ia kaba bud ha ka prompt.result= NCBIWWW.qblast("blastn","nt","186429". |
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|02:20 | |02:20 | ||
− | | | + | |Ngin pyndonkam da ka '''qblast function ''' ha ka '''NCBIWWW '''module. |
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| 02:25 | | 02:25 | ||
− | | | + | |'''qblast function''' ka shim lai tylli ki '''arguments''': |
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|02:29 | |02:29 | ||
− | | | + | |Ka '''argument''' ba nyngkong ka dei ka '''blast program''' ba pyndonkam haba wad. |
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|02:33 | |02:33 | ||
− | | | + | |Ba ar, ka pyntikna ia ka databases ban wad pyrshah. |
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|02:38 | |02:38 | ||
− | | | + | |Ka '''argument''' ba lai ka dei ka '''query sequence.''' jong phi |
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| 02:43 | | 02:43 | ||
− | | | + | | Ka input jong ka '''query sequence''' ka lah ban dei ha ka rukon jong ka '''GI''' number lane ka '''FASTA''' file. Lane, ka lah ban dei ka '''sequence record object'''. |
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| 02:53 | | 02:53 | ||
− | | | + | | Na ka bynta kane ka jingpyni, nga pyndonkam ia ka '''GI number''' na ka bynta ka '''nucleotide sequence'''. |
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|02:58 | |02:58 | ||
− | | | + | |Ka '''GI number''' ka dei na ka bynta ka '''nucleotide sequence''' jong ka '''insulin''' |
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| 03:03 | | 03:03 | ||
− | | | + | |Ka '''qblast function''' ka shim ruh ia kiwei ki jait option arguments . |
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|03:09 | |03:09 | ||
− | | | + | |Kine ki arguments ki long kiba syrïem ha ki parameters bapher bapher ba phi lah ban buh ha ka '''BLAST''' web page. |
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|03:15 | |03:15 | ||
− | | | + | |Ka '''qblast function''' kan pynphai ia ka '''BLAST''' results ha ka '''xml''' format. |
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| 03:20 | | 03:20 | ||
− | | | + | |To ngin ia phai biang sha ka '''terminal'''. |
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|03:22 | |03:22 | ||
− | | | + | |Ngi hap ban pyndonkam da ka '''Blast''' program, ba tikna. |
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|03:25 | |03:25 | ||
− | | | + | |ka shong ruh lada ka query sequence jong ngi ka dei ka '''nucleotide''' lane '''protein sequence'''. |
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|03:30 | |03:30 | ||
− | | | + | |Katba ka query jong ngi ka dei ka '''nucleotide''', ngin pyndonkam ka '''blastn '''program bad "nt" jong ka '''nucleotide''' database. |
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|03:39 | |03:39 | ||
− | | | + | |Ki jingtip ba kham bniah jong kine lah ban ioh na '''NCBI BLAST''' webpage. |
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| 03:45 | | 03:45 | ||
− | | | + | |Ia ka '''blast output''' la buh ha ka variable '''result''', ha ka rukom jong ka '''xml''' file. |
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|03:51 | |03:51 | ||
− | | | + | |Nion '''Enter'''. |
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| 03:53 | | 03:53 | ||
− | | | + | | Ka shong ha ka jingstet jong ka internet jong ngi ban pyndep ia ka jingwad jong ka '''BLAST''' |
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| 03:59 | | 03:59 | ||
− | | | + | | Ka long ruh kaba donkam ban save ia ka '''xml''' file ha ka disk shuwa ban iaid shakhmat. |
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|04:05 | |04:05 | ||
− | | | + | |Type ia ki line ba bud ban'''save''' iaka '''xml file. ''' |
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|04:09 | |04:09 | ||
− | | | + | |Kine ki lines jong ki code kin sa save ia ka jingwad kum '''blast.xml''' ha ka '''home''' folder. |
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| 04:18 | | 04:18 | ||
− | | | + | | Phai sha ka '''home''' folder jong ngi bad wad ia ka file. |
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|04:21 | |04:21 | ||
− | | | + | |Click ha ka file bad check ia ka contents (jingdon) jong ka file. |
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| 04:30 | | 04:30 | ||
− | | | + | | Pyndonkam ia u code ba pyni ha kane ka text file, lada phi kwah ban pyndonkam ia u '''FASTA''' file kum u '''query'''. |
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| 04:36 | | 04:36 | ||
− | | | + | | Hangne u don u code, lada phi kwah ban pyndonkam ia ka '''sequence record object''' na ka '''FASTA''' file kum ka query. |
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| 04:42 | | 04:42 | ||
− | | | + | |To ngin ia phai biang sha ka '''terminal'''. |
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|- | |- | ||
|04:44 | |04:44 | ||
− | | | + | |Ka bynta ba bud ka dei ban '''parse''' ia ka file sha ka '''extract''' data. |
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|04:48 | |04:48 | ||
− | | | + | |Ka bynta ba nyngkong jong ka parsing ka dei ban plie ia ka '''xml''' file na ka bynta ka input. |
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|04:53 | |04:53 | ||
− | | | + | |Type kumne harum ha ka prompt. Nion '''Enter'''. |
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| 04:57 | | 04:57 | ||
− | | | + | |Hadien , '''import''' ia ka module '''NCBIXML''' na "Bio.Blast" '''package'''. |
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|05:05 | |05:05 | ||
− | | | + | |Nion '''Enter'''. |
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| 05:07 | | 05:07 | ||
− | | | + | |Type ia ki lines ba bud sha ka '''parse''' ia ka '''Blast''' output. |
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|05:11 | |05:11 | ||
− | | | + | |Ka BLAST '''record''' ka don ia baroh ki jingpyntip ba phi kwah ban '''extract''' na ka '''BLAST''' output. |
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| 05:18 | | 05:18 | ||
− | | | + | |To ngin ia print khyndiat ia ki jingpyntip shaphang baroh ki '''hit'''s ha ki '''blast report''' jong ngi kiba kham heh ban ha ki jaka ba ki mih. |
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|05:27 | |05:27 | ||
− | | | + | |Type ia u code harum. |
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|05:30 | |05:30 | ||
− | | | + | |Khnang ba ka '''match''' kan long kaba tikna, peit ba u '''score''' u dei ban rit ia ka 0.01. |
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| 05:37 | | 05:37 | ||
− | | | + | | Na ka bynta uwei pa uwei u '''hsp''', kata ka mut, ki shijur ba heh score, ngi ioh ia ka '''title, length, hsp score, gaps''' bad '''expect value'''. |
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|05:49 | |05:49 | ||
− | | | + | |Ngin ia print ruh ia u '''string'''s uba don ia ka '''query''', ka database sequence ba la pynbeit bad u string ba pyntikna ia ka jingiadei bad jingbymiadei ki positions. |
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|06:02 | |06:02 | ||
− | | | + | |Nion ia u '''Enter''' key arsien ban ioh ia ka output. |
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| 06:05 | | 06:05 | ||
− | | | + | | Peit ia ka jingmih |
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|06:09 | |06:09 | ||
− | | | + | |Na ka bynta kawei pa kawei ka alignment, ngi don '''length, score, gaps, evalue''' bad '''strings'''. |
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| 06:16 | | 06:16 | ||
− | | | + | |Phi lah ban ioh ia ki jingpyntip ba donkam da kaba pyndonkam kiwei ki '''functions''', ki ba don ha '''Bio.Blast''' package. |
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|06:24 | |06:24 | ||
− | | | + | |Ngi lah poi sha kaba kut jong kane ka tutorial. |
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| 06:26 | | 06:26 | ||
− | | | + | | To ngin ia khmih ia kaei kaba ngi lah leh haneng . Ha kane ka tutorial, ngi lah tip kumno ban run ia ka '''BLAST''' na ka bynta ka query nucleotide sequence da kaba pyndonkam da u '''GI''' number. |
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|06:36 | |06:36 | ||
− | | | + | |Bad, ban parse ia u '''BLAST''' output da kaba pyndonkam da ka '''Bio.Blast.Record''' module. |
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| 06:43 | | 06:43 | ||
− | | | + | | Na ka bynta ka assignment, run ''' BLAST Search''' na ka bynta ka '''protein''' sequence kaba ngi kwah. |
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|06:50 | |06:50 | ||
− | | | + | |'''Save''' ia ka output file bad parse ia ka data kaba don ha ka file. |
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|06:55 | |06:55 | ||
− | | | + | |Ka assignment ba lah dep jong phi ka dei ban don ia ki lines ba don code , kumba lah pyni ha kane ka file. |
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|07:01 | |07:01 | ||
− | | | + | |Peit ia u code. Katba ka '''query''' jong ngi ka dei '''protein''' sequence, ngi lah pyndonkam '''blastp '''program and "nr", kata ka mut, ka protein database kaba donkam na ka bynta ka '''BLAST''' search. |
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| 07:16 | | 07:16 | ||
− | | | + | | Ka video kaba don ha ka link ba bud ka batai shai shaphang ka Spoken Tutorial project. |
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|07:20 | |07:20 | ||
− | | | + | |Sngewbha download bad peit ia ka. |
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| 07:22 | | 07:22 | ||
− | | | + | | Ka Spoken Tutorial Project team ka ju pynlong ia ki workshops bad ai ruh ki certificates ia kito kiba pass ia ka online test. |
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|07:30 | |07:30 | ||
− | | | + | |Na ka bynta ka jingtip ba kham bniah, sngewbha thoh sha ngi. |
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| 07:33 | | 07:33 | ||
− | | | + | | Ia ka Spoken Tutorial Project la bei tyngka da ka NMEICT, MHRD, Government of India. |
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|- | |- | ||
|07:40 | |07:40 | ||
− | | | + | |Ki jingtip ba kham pura ia kane ka mission lah ban ioh na link harum. |
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| 07:45 | | 07:45 | ||
− | | | + | | Ia kane ka script la pynkylla sha ka ktien khasi da u Yuwanki Kharlukhi bad ma Nga u Hezekiah Lyngdoh ngan pynkut noh. Khublei shibun . |
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|} | |} |
Revision as of 11:39, 29 May 2018
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00:01 | Ngi pdiang sngewbha ia phi sha kane ka tutorial shaphang u BLAST da kaba pyndonkam ki tools u Biopython |
00:06 | Ha kane ka jinghikai , ngin sa nang kumno ban: run "BLAST" na ka bynta ka query sequence da kaba pyndonkam ki tools u Biopython. |
00:13 | Bad, parse ia u BLAST output ban tip kham bniah . |
00:17 | Ban sngewthuh ia kane ka tutorial, phi dei ban long kiba shemphang ha ka undergraduate Biochemistry lane Bioinformatics. |
00:24 | Bad ka basic Python programming. |
00:27 | Pyndonkam da ka Python tutorials na ka link ba ai harum. |
00:31 | Ban record ia kane ka tutorial, nga pyndonkam da ka: * Ubuntu Operating System version 14.10 |
00:37 | Python version 2.7.8 |
00:41 | Ipython interpretor version 2.3.0 |
00:46 | Biopython version 1.64 bad ka internet ba trei kam. |
00:52 | BLAST ka dei ka acronym jong ka Basic Local Alignment Search Tool. |
00:57 | Ka dei ka algorithm ban pyniapher ki sequence information. |
01:02 | Kane ka program ka pyniapher ia ki nucleotide lane protein sequences sha ki sequences ha ki databases bad khein ia ka statistical significance jong ki matches . |
01:14 | Ki don artylli ki rukom ban run ia ka BLAST: |
01:17 | Ka Local BLAST ha ka machine jong phi lane run BLAST lyngba ka Internet jong ka NCBI servers. |
01:24 | Ki don ar tylli ki rukom ban pyndonkam ia ka BLAST ha ka Biopython |
01:28 | Nyngkong, run BLAST na ka bynta ka query sequence jong phi bad phin sa ioh output. |
01:33 | Ba ar, parse ka BLAST output na ka bynta ka jingkdew ba kham bniah hadien. |
01:38 | Ngin sa plie ia ka terminal bad run BLAST na ka bynta ka nucleotide sequence. |
01:43 | Plie ia ka terminal da kaba nion sah ia Ctrl, Alt bad T keys. |
01:48 | Ha ka prompt, type: ipython bad nion Enter. |
01:52 | Ha kane ka tutorial, ngan sa pyni kumno ban run ia ka BLAST lyngba ka internet da kaba pyndonkam da ka NCBI BLAST service. |
02:01 | Type kumne harum ha ka prompt: from Bio.Blast Import NCBIWWW Nion Enter. |
02:14 | Hadien , ban run ia u BLAST lyngba ka internet, type ia kaba bud ha ka prompt.result= NCBIWWW.qblast("blastn","nt","186429". |
02:20 | Ngin pyndonkam da ka qblast function ha ka NCBIWWW module. |
02:25 | qblast function ka shim lai tylli ki arguments: |
02:29 | Ka argument ba nyngkong ka dei ka blast program ba pyndonkam haba wad. |
02:33 | Ba ar, ka pyntikna ia ka databases ban wad pyrshah. |
02:38 | Ka argument ba lai ka dei ka query sequence. jong phi |
02:43 | Ka input jong ka query sequence ka lah ban dei ha ka rukon jong ka GI number lane ka FASTA file. Lane, ka lah ban dei ka sequence record object. |
02:53 | Na ka bynta kane ka jingpyni, nga pyndonkam ia ka GI number na ka bynta ka nucleotide sequence. |
02:58 | Ka GI number ka dei na ka bynta ka nucleotide sequence jong ka insulin |
03:03 | Ka qblast function ka shim ruh ia kiwei ki jait option arguments . |
03:09 | Kine ki arguments ki long kiba syrïem ha ki parameters bapher bapher ba phi lah ban buh ha ka BLAST web page. |
03:15 | Ka qblast function kan pynphai ia ka BLAST results ha ka xml format. |
03:20 | To ngin ia phai biang sha ka terminal. |
03:22 | Ngi hap ban pyndonkam da ka Blast program, ba tikna. |
03:25 | ka shong ruh lada ka query sequence jong ngi ka dei ka nucleotide lane protein sequence. |
03:30 | Katba ka query jong ngi ka dei ka nucleotide, ngin pyndonkam ka blastn program bad "nt" jong ka nucleotide database. |
03:39 | Ki jingtip ba kham bniah jong kine lah ban ioh na NCBI BLAST webpage. |
03:45 | Ia ka blast output la buh ha ka variable result, ha ka rukom jong ka xml file. |
03:51 | Nion Enter. |
03:53 | Ka shong ha ka jingstet jong ka internet jong ngi ban pyndep ia ka jingwad jong ka BLAST |
03:59 | Ka long ruh kaba donkam ban save ia ka xml file ha ka disk shuwa ban iaid shakhmat. |
04:05 | Type ia ki line ba bud bansave iaka xml file. |
04:09 | Kine ki lines jong ki code kin sa save ia ka jingwad kum blast.xml ha ka home folder. |
04:18 | Phai sha ka home folder jong ngi bad wad ia ka file. |
04:21 | Click ha ka file bad check ia ka contents (jingdon) jong ka file. |
04:30 | Pyndonkam ia u code ba pyni ha kane ka text file, lada phi kwah ban pyndonkam ia u FASTA file kum u query. |
04:36 | Hangne u don u code, lada phi kwah ban pyndonkam ia ka sequence record object na ka FASTA file kum ka query. |
04:42 | To ngin ia phai biang sha ka terminal. |
04:44 | Ka bynta ba bud ka dei ban parse ia ka file sha ka extract data. |
04:48 | Ka bynta ba nyngkong jong ka parsing ka dei ban plie ia ka xml file na ka bynta ka input. |
04:53 | Type kumne harum ha ka prompt. Nion Enter. |
04:57 | Hadien , import ia ka module NCBIXML na "Bio.Blast" package. |
05:05 | Nion Enter. |
05:07 | Type ia ki lines ba bud sha ka parse ia ka Blast output. |
05:11 | Ka BLAST record ka don ia baroh ki jingpyntip ba phi kwah ban extract na ka BLAST output. |
05:18 | To ngin ia print khyndiat ia ki jingpyntip shaphang baroh ki hits ha ki blast report jong ngi kiba kham heh ban ha ki jaka ba ki mih. |
05:27 | Type ia u code harum. |
05:30 | Khnang ba ka match kan long kaba tikna, peit ba u score u dei ban rit ia ka 0.01. |
05:37 | Na ka bynta uwei pa uwei u hsp, kata ka mut, ki shijur ba heh score, ngi ioh ia ka title, length, hsp score, gaps bad expect value. |
05:49 | Ngin ia print ruh ia u strings uba don ia ka query, ka database sequence ba la pynbeit bad u string ba pyntikna ia ka jingiadei bad jingbymiadei ki positions. |
06:02 | Nion ia u Enter key arsien ban ioh ia ka output. |
06:05 | Peit ia ka jingmih |
06:09 | Na ka bynta kawei pa kawei ka alignment, ngi don length, score, gaps, evalue bad strings. |
06:16 | Phi lah ban ioh ia ki jingpyntip ba donkam da kaba pyndonkam kiwei ki functions, ki ba don ha Bio.Blast package. |
06:24 | Ngi lah poi sha kaba kut jong kane ka tutorial. |
06:26 | To ngin ia khmih ia kaei kaba ngi lah leh haneng . Ha kane ka tutorial, ngi lah tip kumno ban run ia ka BLAST na ka bynta ka query nucleotide sequence da kaba pyndonkam da u GI number. |
06:36 | Bad, ban parse ia u BLAST output da kaba pyndonkam da ka Bio.Blast.Record module. |
06:43 | Na ka bynta ka assignment, run BLAST Search na ka bynta ka protein sequence kaba ngi kwah. |
06:50 | Save ia ka output file bad parse ia ka data kaba don ha ka file. |
06:55 | Ka assignment ba lah dep jong phi ka dei ban don ia ki lines ba don code , kumba lah pyni ha kane ka file. |
07:01 | Peit ia u code. Katba ka query jong ngi ka dei protein sequence, ngi lah pyndonkam blastp program and "nr", kata ka mut, ka protein database kaba donkam na ka bynta ka BLAST search. |
07:16 | Ka video kaba don ha ka link ba bud ka batai shai shaphang ka Spoken Tutorial project. |
07:20 | Sngewbha download bad peit ia ka. |
07:22 | Ka Spoken Tutorial Project team ka ju pynlong ia ki workshops bad ai ruh ki certificates ia kito kiba pass ia ka online test. |
07:30 | Na ka bynta ka jingtip ba kham bniah, sngewbha thoh sha ngi. |
07:33 | Ia ka Spoken Tutorial Project la bei tyngka da ka NMEICT, MHRD, Government of India. |
07:40 | Ki jingtip ba kham pura ia kane ka mission lah ban ioh na link harum. |
07:45 | Ia kane ka script la pynkylla sha ka ktien khasi da u Yuwanki Kharlukhi bad ma Nga u Hezekiah Lyngdoh ngan pynkut noh. Khublei shibun . |