菜鸟求助～如何获取1条核苷酸翻译后最长的那条蛋白序列

cxrfly

一条核苷酸序列，如U1，它对应的翻译氨基酸序列具有53条(U1_1  to U1_53)；如另外一条U2，对应的氨基酸序列有18条(U2_1 to U2_'18')。类似这样的核苷酸序列有2万条，对应的氨基酸序列在一个文件里。现在我想提取每条核苷酸对应的可能氨基酸翻译中最长的那条氨基酸序列及其ID号（即类似U1或者U2各自对应的最长氨基酸序列），如何实现阿？

菜鸟，刚学Perl，还不太会写脚本阿。求好心大侠是否帮我写一个？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

回复 2# yestreenstars


    会写脚本就可以了，大侠留步

b114213903

你这些是一个序列相关的在一个文件里，还是全部都在一起？

yestreenstars

回复 3# cxrfly

看不懂你的需求
   

iamlimeng

今后请楼主自己先写代码再来问，不要总是伸手，那样永远不会有提高！

cxrfly

回复 4# b114213903


    所有2万多个核苷酸序列对应的所有氨基酸翻译都在一个文件（即一个氨基酸序列文件），想从这个文件里取出每个核苷酸对应的最长的氨基酸序列。

cxrfly

回复 6# iamlimeng


    大侠，我错了，回头努力提高自己。这次比较急切

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. }

复制代码

cxrfly

回复 9# b114213903


    能否一起把对应的氨基酸序列和ID一起生成一个文件阿？谢谢