菜鳥求助～如何獲取1條核苷酸翻譯后最長的那條蛋白序列

cxrfly

一條核苷酸序列，如U1，它對應的翻譯氨基酸序列具有53條(U1_1  to U1_53)；如另外一條U2，對應的氨基酸序列有18條(U2_1 to U2_'18')。類似這樣的核苷酸序列有2萬條，對應的氨基酸序列在一個文件里。現(xiàn)在我想提取每條核苷酸對應的可能氨基酸翻譯中最長的那條氨基酸序列及其ID號（即類似U1或者U2各自對應的最長氨基酸序列），如何實現(xiàn)阿？

菜鳥，剛學Perl，還不太會寫腳本阿。求好心大俠是否幫我寫一個？急阿~

>U1_1 [3 - 104]
VLDLFVAHHYIRRQRARHKIGQISHFWVITQLRI
>U1_2 [1 - 111]
KYSIFSLRIIIFEDSELATKSVRSAIFGSSLSFGSKK
>U1_3 [2 - 118]
STRSFRCASLYSKTASSPQNRSDQPFLGHHSASDLKSEA
>U1_4 [125 - 193]
SRRSTFELGLHPPWRTWNFGHQV
>U1_5 [108 - 215]
KVRRDDLAGRHSSWDCTLPGGHGILVIRFDEHMALL
>U1_6 [115 - 222]
GVMISQVDIRVGTAPSLEDMEFWSSGLMSTWLCSKK
>U1_7 [200 - 232]
AHGFALRNKRH
>U1_8 [219 - 314]
EINATDALVSEHEWFDVRVPDNNCAVAFNVSM
>U1_9 [226 - 330]
TPLTRSFPNMNGSMYAFQTITVRWPSTCRCKICCT
>U1_10 [287 - 364]
LCGGLQRVDVKSAARRTWPLCSPSRQ
>U1_11 [368 - 403]
IPSQNFLRLRRL
>U1_12 [318 - 536]
NLLHVERGRCVRHHVSEFQAKTFCDYVACSGFRALASVFIPVYPPCIASRTHVERQDMVV
EHFHAHTIHGITQ
>U1_13 [407 - 559]
WLQSFGLCIYSSVSTMHRQSHACRTARYGGRTLPCAYHSWHHAVGASGSSR
>U1_14 [334 - 606]
NVAVVFAITSVNSKPKLSAITSLVVASELWPLYLFQCIHHASPVARMSNGKIWWSNTSMR
IPFMASRSRGFWVISLIGTGLLVSTTTSAIR
>U1_15 [581 - 673]
FQPRLQQSDRSSPRQSTVRRRSALPSASDTQ
>U1_16 [677 - 718]
ESRYAVYEYFLPDT
>U1_17 [540 - 731]
GLLGHLVNRNGAVSFNHDFSNPIGVLHASRQFVEDQRCHLLQTPSRNLDTPCTSIFSQIH
DIPL
>U1_18 [722 - 826]
YPVVTGVGTAIFSGLGQLASPFHNPSSNAYFPARP
>U1_19 [610 - 843]
EFSTPVDSSSKISAAICFRHPVGISIRRVRVFSPRYMISRCDGCRYSNFLRPWTTCISLS
QPFFKCIFSRSALSRCSS
>U1_20 [735 - 872]
RVSVQQFSQALDNLHLPFTTLLQMHIFPLGPESLFQLTNTHLLPHH
>U1_21 [847 - 894]
RIHTSFHTTDIPLDIV
>U1_22 [830 - 940]
VVVPADEYTPPSTPLTYRWTLYDTIGLSYVVASSCLG
>U1_23 [944 - 976]
FATASTSSRAL
>U1_24 [898 - 1038]
HDRSFLRRGFFLPRMICNCFNFISSSLTSSRNSISWKRRSFLALFGS
>U1_25 [980 - 1042]
LRPATRSVGSDVHFLPCSDRS
>U1_26 [1084 - 1152]
VSVFVTSGAFTHWNGVTGSSSVP
>U1_27 [876 - 1193]
HTAGHCMTRSVFLTSWLLLASDDLQLLQLHLELFDFVPQLDQLEATFISCLVRIVVEFLL
LELRLCRLMSQRIRHIWCIYPLEWGYRQQFRAIVSDIVVHCAQKHL
>U1_28 [1156 - 1194]
SPISSSIALRSTS
>U1_29 [1061 - 1195]
VEVVQTHESAYSSHLVHLPTGMGLQAAVPCHSLRYRRPLRSEAPP
>U1_30 [1180 - 1133] (REVERSE SENSE)
AQWTTISETMARNCCL
>U1_31 [1194 - 1081] (REVERSE SENSE)
GGASERNGRRYRRLWHGTAACNPIPVGKCTRCDEYADS
>U1_32 [1077 - 1018] (REVERSE SENSE)
VCTTSTQEEETQLRSEQGKK
>U1_33 [1084 - 1001] (REVERSE SENSE)
LMSLHNLNSRRRNSTTIRTRQEMNVASN
>U1_34 [997 - 965] (REVERSE SENSE)
SSCGTKSKSSR
>U1_35 [1014 - 916] (REVERSE SENSE)
TSLPTDRVAGRSQRARDEVEAVANHPRQEEATT
>U1_36 [955 - 803] (REVERSE SENSE)
SSCKSSEARRSHDVRKTDRVIQCPAVCQWCGRRCVFVSWNNDSGPSGKICI
>U1_37 [912 - 790] (REVERSE SENSE)
ERPIVSYNVQRYVSGVEGGVYSSAGTTTQGRAGKYAFEEGL
>U1_38 [799 - 761] (REVERSE SENSE)
RRVVKGRCKLSKA
>U1_39 [757 - 665] (REVERSE SENSE)
ENCCTDTRHNGISCIWEKILVHGVSRFLLGV
>U1_40 [786 - 598] (REVERSE SENSE)
KGDASCPRPEKIAVPTPVTTGYHVSGRKYSYTAYRDSYWVSEADGSADLRRTVDWRGELL
SDC
>U1_41 [643 - 554] (REVERSE SENSE)
SSTNCRLAWRTPIGLLKSWLKLTAPFRLTR
>U1_42 [528 - 436] (REVERSE SENSE)
CHEWYAHGSVRPPYLAVRHACDWRCMVDTLE
>U1_43 [520 - 395] (REVERSE SENSE)
MVCAWKCSTTISCRSTCVRLAMHGGYTGINTEAKALKPLQAT
>U1_44 [411 - 364] (REVERSE SENSE)
SHYKRRNRRKFWLGIH
>U1_45 [391 - 359] (REVERSE SENSE)
SQKVLAWNSLT
>U1_46 [360 - 304] (REVERSE SENSE)
RDGEHNGHVLRAADFTSTR
>U1_47 [355 - 218] (REVERSE SENSE)
WRTQRPRSTCSRFYIDTLKATAQLLSGTRTSNHSCSETSASVAFIS
>U1_48 [300 - 190] (REVERSE SENSE)
RPPHSYCLERVHRTIHVRKRARQWRLFLRAKPCAHQT
>U1_49 [214 - 107] (REVERSE SENSE)
SKAMCSSNLMTKIPCPPGRVQSQLECRPARSSRLTF
>U1_50 [183 - 91] (REVERSE SENSE)
PKFHVLQGGCSPNSNVDLRDHHASLFRSEAE
>U1_51 [64 - 32] (REVERSE SENSE)
PILWRARCLRI
>U1_52 [1193 - 3] (REVERSE SENSE)
EVLLSAMDDDIGDYGTELLPVTPFQWVNAPDVTNTLTHESAQPQLKKKKLNYDPNKARNE
RRFQLIELRDEVKELEMKLKQLQIIRGKKKPRRKKDRSCHTMSSGMSVVWKEVCIRQLEQ
RLRAERENMHLKKGCEREMQVVQGLRKLLYRHPSQRDIMYLGENTRTRRIEIPTGCLKQM
AALIFDELSTGVENSYRIAEVVVETNSPVPINEMTQKPLLRDAMNGMRMEVFDHHILPFD
MRATGDAWWIHWNKYRGQSSEATTSDVIAESFGLEFTDVMANTTATFYVQQILHRHVEGH
RTVIVWNAYIEPFMFGNERVSGVYFLEQSHVLIKPDDQNSMSSREGAVPTRMSTCEIITP
HFLDPKLSDDPKMADLTDFVASSLSSNIMMRNEKIEY
>U1_53 [69 - 1] (REVERSE SENSE)
SDRFCGELAVFEYNDAQRKDRVL
>U2_1 [2 - 52]
FTEPTSIDELLASRFPQ
>U2_2 [3 - 56]
LQSQLLSMSSSHHVSLNK
>U2_3 [56 - 154]
ISTSAGSMYFRAKCSPFRVGCAKATRFLFTCMP
>U2_4 [28 - 159]
APRITFPSINKHLGWFHVFSRKVQPISCRLREGNEVLVHMHAVN
>U2_5 [163 - 213]
LFAHDGHHSGRNAFPAE
>U2_6 [60 - 245]
APRLVPCIFAQSAAHFVSAARRQRGSCSHACRKLTFRARRPPFGSQCFSCGMRGAPKSGR
CQ
>U2_7 [217 - 258]
GVHPNLADANNGGF
>U2_8 [249 - 356]
RRVLNRQTQSQHHSQLRRSPRPSSTAQSSSKWSCPE
>U2_9 [158 - 400]
IDFSRTTATIRVAMLFLRNEGCTQIWQMPITAGFESADAVTAPFAATEVSASEFDCTIQF
EVVLSRVKASVMRSVLTHPTT
>U2_10 [262 - 441]
IGRRSHSTIRSYGGLRVRVRLHNPVRSGLVQSKGFRDALRIDTSNDLMVLNVDKVAALQK
>U2_11 [387 - 443]
HIQRLDGPECRQSGCAAET
>U2_12 [443 - 297] (REVERSE SENSE)
RFCSAATLSTFRTIKSLDVSIRSASRKPLLWTRPLRTGLCSRTRTRRPP
>U2_13 [275 - 144] (REVERSE SENSE)
LRLPIQNPPLLASARFGCTPHSAGKALRPEWWPSCAKSQFTACM
>U2_14 [441 - 52] (REVERSE SENSE)
FLQRSHFVYIQDHQVVGCVNTERITEAFTLDKTTSNWIVQSNSDAETSVAANGAVTASAD
SKPAVIGICQIWVHPSFRRKSIATRMVAVVREKSIYGMHVNKNLVAFAQPTRNGLHFARK
YMEPAEVLIY
>U2_15 [442 - 41] (REVERSE SENSE)
VSAAQPLCLHSGPSSRWMCQYGAHHGSLYSGQDHFELDCAVELGRGDLRSCEWCCDCVCR
FKTRRYWHLPDLGAPLIPQEKHCDPNGGRRARKVNLRHACEQEPRCLRAADTKWAALCAK
IHGTSRGAYLLRET
>U2_16 [140 - 21] (REVERSE SENSE)
TRTSLPSRSRHEMGCTLRENTWNQPRCLFIEGNVMRGAHR
>U2_17 [37 - 2] (REVERSE SENSE)
CEELIDRSWLCK
>U2_18 [48 - 1] (REVERSE SENSE)
GKRDARSSSIEVGSVN

yestreenstars

不懂生物，看不懂

cxrfly

回復 2# yestreenstars


    會寫腳本就可以了，大俠留步

b114213903

你這些是一個序列相關(guān)的在一個文件里，還是全部都在一起？

yestreenstars

回復 3# cxrfly

看不懂你的需求
   

iamlimeng

今后請樓主自己先寫代碼再來問，不要總是伸手，那樣永遠不會有提高！

cxrfly

回復 4# b114213903


    所有2萬多個核苷酸序列對應的所有氨基酸翻譯都在一個文件（即一個氨基酸序列文件），想從這個文件里取出每個核苷酸對應的最長的氨基酸序列。

cxrfly

回復 6# iamlimeng


    大俠，我錯了，回頭努力提高自己。這次比較急切

b114213903

1. #!/usr/bin/perl
   
2. use Bio::SeqIO;
   
3. use strict;
   
4. 
   
5. my $file=shift @ARGV or die "Usage:\t$0\tseq_file\n";
   
6. my $SeqIO=Bio::SeqIO->new(-file=>"$file",-format=>"fasta") or die "Open seq_file failed!\n";
   
7. my ($flag,$length,%ids,@out)=();
   
8. while(my $seq=$SeqIO->next_seq()){
   
9.         (my $id= $seq->id)=~s/\_[\s\S]+$//;
   
10.         my $tag=$seq->id;
    
11.         my $len=$seq->length;
    
12.         if(! $ids{$id}){
    
13.                 $ids{$id}++;
    
14.                 if($length and $flag){
    
15.                         my $pos=$flag."\t".$length;
    
16.                         push @out,$pos;
    
17.                 }
    
18.                 $length=$len;
    
19.                 $flag=$tag;
    
20.         }else{
    
21.                 if($length<$len){
    
22.                         $length=$len;
    
23.                         $flag=$tag;
    
24.                 }
    
25.         }
    
26. }
    
27. my $pos=$flag."\t".$length;
    
28. push @out,$pos;
    
29. 
    
30. while(my $pos=shift @out){
    
31.         print $pos,"\n";
    
32. }

復制代碼

cxrfly

回復 9# b114213903


    能否一起把對應的氨基酸序列和ID一起生成一個文件阿？謝謝