UnixText2.pptx
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- たみえ なみこし
- 5 years ago
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1 Unix Unix! grep! sed! sort! cut! join! awk!
2 (grep)! grep ' ' [...]! grep 'GO' 1433B_HUMAN.sprot!! 1433B_HUMAN.sprot GO grep '^FT' 1433B_HUMAN.sprot!! 1433B_HUMAN.sprot FT! grep -v! grep -i! grep -w!!! grep!! File1 (File1!! [ ] File[1-3] (File1, File2, File3! \! \[abc\] ([abc] ) ' '
3 !.! a.c abc, adc a c! []!! [ad3@] a, d, [a-d] a, b, c, d! [^abd] a, b, d! ^, $! ^ID ID!! ;$ ;!! *! a.*m a m am, arm, alarm am am! grep E egrep! +! [a-z]+ [a-z][a-z]*!?! proteins? protein proteins!! {n,m} n m!! [1-9][0-9]{2,3} ( )!! [0-9]{5} 5 ( )!! OR! ( ) [ ]! tyrosine.*(kinase phosphatase) "#$%&'()*+,'(-&)!!"#$%&'()*+./%&./-"-&)!!! tyrosine.*kinase phosphatase "#$%&'()*+,'(-&)!!./%&./-"-&)!!
4 ! FASTA mouse.fas >mouse:q0vbh3 Olfr629 protein! MAGNATHHIASFFLVGIPGLENFHCWIGIPVCLLFALTLLGNSIILTTVKLEPSLHQPMY! FFLCMLAMNDMCLTCSTALKMLGIFWFDEHWINFDACLTQMFFIHTLCIMESAILVAMAF! DRFVAICIPLHYTSILTTPMVIKIGLVGLSRAILMIMPCPLLIKRLLYYTKYVIHHAYCE! HMAVVKMASGNTQVNRIYGILVALSVTIFDLGLIVTSYIKILQAVFRLSSQNARSKALGT! CVAHVCTILAFYTPALFSFLTHRFGKNVPASIHIIFAILYLLVSPTVNPLVYGAKTKQIR! DRVVSLLFSQKQKF! >mouse:q9jmi7 Testis-expressed protein 101! MGACRIQYVLLIFLLIASRWTLVQNTYCQVSQTLSLEDDPGRTFNWTSKAEQCNPGELCQ! ETVLLIKADGTRTVVLASKSCVSQGGEAVTFIQYTAPPGLVAISYSNYCNDSLCNNKDSL! ASVWRVPETTATSNMSGTRHCPTCVALGSCSSAPSMPCANGTTQCYQGRLEFSGGGMDAT! VQVKGCTTTIGCRLMAMIDSVGPMTVKETCSYQSFLQPRKAEIGASQMPTSLWVLELLFP! LLLLPLTHFP!! grep '^>' mouse.fas ' ' (sed) sed 's/ / /g' [ ]!!! sed 's/abc/xyz/g' file file abc xyz!! g! sed 's/:/ /' file :! sed ' '
5 FASTA mouse.fas FASTA > grep ^>' mouse.fas sed s/^>// sed 's/ /Tab/' > mouse.tit! >mouse:q0vbh3 Olfr629 protein! MAGNATHHIASFFLVGIPGLENFHCWIGIPVCLLFALTLLGNSIILTTVKLEPSLHQPMY! FFLCMLAMNDMCLTCSTALKMLGIFWFDEHWINFDACLTQMFFIHTLCIMESAILVAMAF! DRFVAICIPLHYTSILTTPMVIKIGLVGLSRAILMIMPCPLLIKRLLYYTKYVIHHAYCE! HMAVVKMASGNTQVNRIYGILVALSVTIFDLGLIVTSYIKILQAVFRLSSQNARSKALGT! CVAHVCTILAFYTPALFSFLTHRFGKNVPASIHIIFAILYLLVSPTVNPLVYGAKTKQIR! DRVVSLLFSQKQKF! >mouse:q9jmi7 Testis-expressed protein 101! MGACRIQYVLLIFLLIASRWTLVQNTYCQVSQTLSLEDDPGRTFNWTSKAEQCNPGELCQ! ETVLLIKADGTRTVVLASKSCVSQGGEAVTFIQYTAPPGLVAISYSNYCNDSLCNNKDSL! ASVWRVPETTATSNMSGTRHCPTCVALGSCSSAPSMPCANGTTQCYQGRLEFSGGGMDAT! VQVKGCTTTIGCRLMAMIDSVGPMTVKETCSYQSFLQPRKAEIGASQMPTSLWVLELLFP! LLLLPLTHFP! Tab Control-V Linux sed \t! mouse:q0vbh3!olfr629 protein! mouse:q9jmi7!testis-expressed protein 101!! ms_hm.bltab BLAST mouse human m 8 1. Query (mouse) 4. Alignment 6. Gap num. 8. Q.end 10. S.end 12. Bit-score length 2. Subject 5. Mismatches (human) 3. % identity 7. Q.start 9. S.start 11. E-value mouse:q0vbh3 human:q8nh e ! mouse:q0vbh3 human:q8ngk e ! mouse:q0vbh3 human:q9ukl e ! mouse:q0vbh3 human:q8ngj e ! mouse:q0vbh3 human:q8nh e ! mouse:q0vbh3 human:q8ngk e ! mouse:q0vbh3 human:q96rd e ! mouse:q0vbh3 human:q9h2c e ! mouse:q0vbh3 human:q8ngf e ! mouse:q0vbh3 human:q8ngh e !
6 (sort)! sort [ ] [!]!! -k FLD1,FLD2 (FLD1 FLD2! -k 2,2!!!!! Aoki S ! Hirano T ! Murton T ! Wada D ! Morino D ! Morino D ! Wada D ! Aoki S ! Hirano T ! Murton T !! -k 2,2 k 4,4nr (n) (r)! Aoki S ! Hirano T ! Murton T ! Wada D ! Morino D ! Wada D ! Morino D ! Aoki S ! Murton T ! Hirano T ! cut! cut f d [ ]!! cut f 1,2,11 ms_hs.bltab BLAST 1, 2, 11 ( E-value!! -f c cut c1-12 ms_hs.bltab 1 12
7 1. ms_hs.bltab human:q8nh57 Bit-score 12 Q8NH57.bltab! 2. E-value! grep human:q8nh57 ms_hs.bltab sort -k12,12nr > Q8NH57.bltab!! cut -f1,2,3,11 Q8NH57.bltab awk awk ' '!! { }! $1, $2,! $0 $NF awk ' '
8 awk!! awk '{print $1,$2,$11}' ms_hm.bltab!!!!! 11 (E-value) 0.001! awk '$11<0.001{print}' ms_hm.bltab!!! awk! 3 awk {sum+=$3} END{print sum}' ms_hm.bltab!! sum!! 2!! {sum+=$3}!!! sum!sum+=x sum x (sum=sum+x)!! END{print sum} END sum! BEGIN BEGIN{sum=0} {sum+=$3} END{print sum} sum 0
9 awk!,, *, /! =!! a=$1+$2 a!! +=, -=, *=, /=!! a+=($5-$4) a!! ++, --!! a++ a 1!! ==(,!=(, >, <, >=, <=!! $3== !! &&,!! a>=10 && a<20 a 10 20!! ~ / /,!~ / /!! a ~ /chr[1-3]/ a chr[1-3]!! length!! length(a) a!! awk ms_hm.bltab 3! (sum) (n) awk {a=1;b=2} ;! awk '{sum+=$3;n++} END{print sum/n}' ms_hm.bltab
10 ! Perl Ruby! 1 3 Perl (calc_mean.pl) #!/usr/bin/perl!#perl! # 1 <>! while(<>) {!!@F = += $F[2];!!# 0 3 $F[2]!!$n++;! }! #! $mean_identity = $sum / $n;! print "Mean identity: $mean_identity\n";!# \n!! ms_hm.bltab E-value 10-5! BLAST mouse:q0vbh3 human:q8nh e ! mouse:q0vbh3 human:q8ngk e ! mouse:q0vbh3 human:q9ukl e ! mouse:q0vbh3 human:q8ngj e ! mouse:q0vbh3 human:q8nh e ! mouse:q0vbh3 human:q8ngk e ! mouse:q0vbh3 human:q96rd e ! mouse:q0vbh3 human:q9h2c e ! mouse:q0vbh3 human:q e ! mouse:q0vbh3 human:q8ngg e ! mouse:q9jmi7 human:q9by e ! mouse:q9jmi7 human:q8n6q e ! mouse:q9jmi7 human:q8n6q e !
![Perl E-value 10-5 (calc_tophit_mean.pl) #!/usr/bin/perl! $EVAL_CUTOFF = 1e-5;!!# BLAST E-value! # 1! while(<>) {!!@F = split(/\t/);!!# @F!!#!!$query = $F[0];!!# 1!!$identity = $F[2];!!# 3!](/docs-images/87/97152433/images/11-0.jpg "!$evalue = $F[10];!!# E-value 11!!!# E-value!!next if ($evalue > $EVAL_CUTOFF);!!!#!!!!if ($prev_query ne $query) {!!!#!!!$sum += $identity;!!!$n ++;!!}!!$prev_query = $query;!#! }! #!")
11 Perl E-value 10-5 (calc_tophit_mean.pl) #!/usr/bin/perl! $EVAL_CUTOFF = 1e-5;!!# BLAST E-value! # 1! while(<>) {!!@F = = $F[0];!!# 1!!$identity = $F[2];!!# 3!!$evalue = $F[10];!!# E-value 11!!!# E-value!!next if ($evalue > $EVAL_CUTOFF);!!!#!!!!if ($prev_query ne $query) {!!!#!!!$sum += $identity;!!!$n ++;!!}!!$prev_query = $query;!#! }! #! $mean_identity = $sum / $n;! print "Number of Hits: $n\n";! print "Mean identity: $mean_identity\n";! join! ms_hm.top.bltab mouse:q0vbh3 human:q8nh ! mouse:q9jmi7 human:q9by ! mouse:e0cxa2 human:q8iz ! mouse:q8bkx7 human:q86vk ! mouse:q3uyp3 human:q9h ! mouse.tit mouse:q0vbh3 Olfr629 protein! mouse:q9jmi7 Testis-expressed protein 101! mouse:e0cxa2 MCG21550, isoform CRA_b! mouse:q8bkx7 Zinc finger protein 410! mouse:q3uyp3 Putative uncharacterized protein! mouse:q0vbh3 human:q8nh !Olfr629 protein! mouse:q9jmi7 human:q9by !Testis-expressed protein 101! mouse:e0cxa2 human:q8iz !MCG21550, isoform CRA_b! mouse:q8bkx7 human:q86vk !Zinc finger protein 410! mouse:q3uyp3 human:q9h !Putative uncharacterized protein!
12 Perl join ms_hm.top.bltab mouse.tit join #!/usr/bin/perl!! open(f1, "mouse.tit");!!# mouse.tit! while(<f1>) {!!chomp;!!!!!!#!!($ms_name, $title) = split(/\t/);!# $ms_name, $title!!$title{$ms_name} = $title;!!# %Title! }! close(f2);!! open(f2, "ms_hm.top.bltab");!# ms_hm.top.bltab! while(<f2>) {!!chomp;!!!!#!!@f = = $F[0];!!# $ms_name!!$title = $Title{$ms_name};!!#!!print $title),"\n";!# (@F) $title! }! close(f2);! (join_title.pl)!!!! mouse:q0vbh3!olfr629 protein! mouse:q9jmi7!testis-expressed protein 101! mouse:e0cxa2!mcg21550, isoform CRA_b! Unix join join [-t Delimitor] [ 1 FLD1 2 FLD2] [ o format] file1 file2!! File1 FLD1, File2 FLD2!! Format -o 1.1, 2.2, 2.3 file1 file2
13 Unix join! ms_hm.top.bltab mouse.tit ID 1. ms_hm.top.bltab ms_hm.top.bltab.sort sort k 1,1 ms_hm.top.bltab > ms_hm.top.bltab.sort! 2. mouse.tit mouse.tit.sort sort k 1,1 mouse.tit > mouse.tit.sort! 3. ms_hm.top.bltab.sort mouse.tit.sort join t 'Tab' ms_hm.top.bltab.sort mouse.tit.sort! Tab Control+v TAB! cut! cut -d! sort ( -t! awk ( -F! join ( -t
14 Unix Unix 1. SAM 2. SAM sample.sam Hint: 7 = 3. BED cpg_pred.txt CpG island GTF chr17partial.gtf (transcript) NM_ (1) (2)! 5. GTF chr17partial.gtf (transcript) hint: sort u man sort
15 Unix 1 1. grep -v grep -v '^@' sample.sam wc! 2. SAM 7 = awk '$7=="="{print}' sample.sam wc! 3. BED awk '$5>=500{print}' cpg_pred.txt! Unix 2 4. (1)GTF NM_ awk -F'Tab' '$9~/NM_007298/ && $3=="exon"{print}' chr17partial.gtf wc Tab Control-v GTF grep 'NM_007298' chr17partial.gtf grep 'exon' wc (2) awk -F'Tab' '$9~/NM_007298/&&$3=="exon"{print}' chr17partial.gtf > tmpf awk '{sum += ($5-$4+1)} END{print sum}' tmpf (tmpf) awk awk GTF(GFF) End-Start+1! 5. GTF sort -t'tab' -u -k 9,9 chr17partial.gtf wc!
_unix_text_command.pptx
Unix によるテキストファイル処理 2015/07/30 作業場所 以降の作業は 以下のディレクトリで行います ~/unix15/text/ cd コマンドを用いてディレクトリを移動し pwd コマンドを利用して カレントディレクトリが上記になっていることを確認してください 実習で使用するデータ 講習で使用するデータは以下のフォルダ内 ファイルがあることを確認してください ~/unix15/text/
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