BioPython AlignIO序列长度必须相同[多个文件]

Question

当我尝试对齐多个文件时遇到了问题

这是我的剧本：

from Bio import AlignIO
from Bio.Align import MultipleSeqAlignment

from Bio.Align.Applications import ClustalOmegaCommandline


def divergence(fic1dna,fic2dna,fic1prot,fic2prot):

    from Bio import SeqIO


    seq1dna = list(SeqIO.parse(fic1dna, "fasta",alphabet=IUPAC.IUPACUnambiguousDNA()))
    seq2dna = list(SeqIO.parse(fic2dna, "fasta",alphabet=IUPAC.IUPACUnambiguousDNA()))
    seq1prot = list(SeqIO.parse(fic1prot, "fasta",alphabet=IUPAC.protein))
    seq2prot= list(SeqIO.parse(fic2prot, "fasta",alphabet=IUPAC.protein))

    u=0

    while u < len(seq1dna): # make an alignment betwen each element on 2 files for 2 paires files 


        nuc1=str(seq1dna[u].seq)
        nuc2=str(seq2dna[u].seq)
        prot1=str(seq1prot[u].seq)
        prot2=str(seq2prot[u].seq)


        prot1 = SeqRecord(Seq(prot1, alphabet=IUPAC.protein),id='pro1') 
        prot2 = SeqRecord(Seq(prot2, alphabet=IUPAC.protein),id='pro2')

        aln = MultipleSeqAlignment([prot1, prot2]) 

        print(aln)

        u+=1


print(divergence("concatenate_0035_fna_renamed.fst","concatenate_0042_fna_renamed.fst","concatenate_0035_faa_renamed.fst","concatenate_0042_faa_renamed.fst"))

所以，你可以看到我有4个文件，对应于来自2个物种的244个序列，我需要为它们中的每一个计算dN dS，所以，我需要在密码子比对中对齐每个配对的seq。

但是，当我试图调整我的244个蛋白质序列时，错误“ValueError（”序列必须都是相同的长度“）引发”

我不知道为什么脚本不接受具有不同长度的序列，因为所有其他程序都这样做。

短输入将是：

来自sp 1

的AA seq的一个文件

>EOG090X005Q
CEHNTAGRDCEKCLDFYNDAPWGRASPTNVHECKACNCNGFSNKCYFDKDLYERTGHGGHCIDCEENRDGANCERCKENFYQGMEDICLPCNCNPTGSRSLQCNAEGKCQCKPGVTGDKCDVCAPNYFEFTMHGCKPCDCNVSGSYGNTPQCDPQTGVCLCKQNVEGRRCRECKPGFFNLDVENEFGCTPCFCFGHSSQCSSAPKYQAHEISAHYIRDAEKWGAEDDQRKPVQLQFNANTQNIAVASKGSEILYFLASGQFLGDQRPSYNHDLKFTLRLGESGGYPSSQDIILEGARSSVSMNIYAQNNPEPSDVAQEYSFRLHEDPRYGWTPTLSNFEFMSILQNLTAIKIRGTYNKGGVGYLINFKLETAKIGREKGSAPANWVEKCSCPKAYVGDYCEECAPGYKHEPANGGPYSTCIPCDCNGHAHICDTATGFCICKHNTTGSNCELCAKGFYGNAIAGTADDCKPCPCPKDSGCIQLMDQSIVCTDCPVGYAGPRCEVCADAHFGDPTGQFGAPQECEECQCNGNVDPNAVGNCNRTTGECLKCIYNTAGEHCDKCLSGYFGDALDQKKKGDCKPCQCLEAGTVESPEGARKAPLCDGLTGFCSCRPHVIGRNCDKCEVDLNCIAVLKT
>EOG090X00BV
MNAHFPQNEIARSEAYNIMSVRKQYLVPKDGTPLSGLIQDHVISGVKMSIRGAFFTKADYQQLVFQALSNHKGEIKLLPPTILKPIMLWSGKQILSTIIINSIPKGKPYLSLTGKAKISSKAWQKEPARTWNAGGTPFTNPNSMSEAEVIIRKGELLCGVLDKTHYGATPYGLVHCMYELYGGDSSSALLSSFSKVFTFYLQWIGFTLGVKDILVVEEADKQRDNFINLVRKVGKVAAAKATELPVDVDELKLKETISEMLIKDPKFRANLDRQYKSLLDSYTNNINTVCLSEGLLEKFPYNNLQLMVQSGAKGSTVNTMQISCLLGQIELEGKRPPLMISGRSLPSFPPYDISPRAGGFIDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLSVAYDHTVRDSDSSVIQFAYGEDGLDVIKCQYFNKDQFEFLDVNSNAVISKSAIKKLKEDDKSKALAKSQKSLKKWKKKNGNPFEKVRYSPFTEFSAIAKNDIVLDDKPTDQTRDPNYWELEKMWRNLDADEKKQYARKRCPDPIPSKYSPEYKFGVINEQLNELTQNYLKNRKEHMYSDYTDKDKFTEIINAKYLASMAAPGEPVGLLAAQSIGEPSTQMTLNTFHFAGRGDMNVTLGIPRLREILMTASAKLKTPSMDIPFRSDLPDLNKKAERLRQKMNRVTVSDVLEKIDVHCEIVTNPNRQLKTVMRFSFLPHSQYKVQYTVKPAQIIKHMQNKFFSEMFSIIRKQAKTTCGVMWSTEKEKKRRAASDEDDEDGEGASPDVAEKAVNMDEDSSDEEGPNDDDDNTDVS

和另一个物种2：

>EOG090X005Q
MGGKIAAILLFAFFTSGSRSEPDFVDGQFNKINKNRVEVKCYDDFGAPQRCIPPFENAAFGVLMEATNTCGQDGRPTEFCRQTGVQRKPCEFCHPGDHPASFLTDRDNNDNATWWQSETMHEGIEYPNKVVLTLNLGKTYDITYVRVLFESPRPESWGIFRRRTEDSPWEPYQFYSATCRDTYGLPDRKDTVRGEDTRVLCTSEYSDISPLRRGTVAFSTLEGRPSAFQFDTNPALQSWVQATDLRLSLDRPNTFGDELFGDGQVLKSYYYAIADVAVGARCACNGHAGECINSPHTNGTTRRVCRCEHNTAGPDCNECLPFYNDAPWGRATTTDAHECKPCNCNGYSDRCYFDKDLYERSGHGGHCTDCRANRAGPNCERCRENFYQRLEDSYCVACNCNEIGSRSLQCNSEGKCQCKPGITGDKCDRCAANFFNFDSLGCTSCECSPKGSLDNEPNCDPVSGACVCKENVEGKRCRECRPGFFNLDLDNEFGCTPCFCYGHSSVCNLANGYSKLTIESMFGRGNEKWTASVAGNPIPLHYDAVTQTISVNAPDRDNVYFVAPERFLGDQRASYNQDLTFTLRIAENEPAPTARDVILEGGNGEQLTQPIFGQTNQLPNASPQVYKFRLNEHADYGWEPRVTSRAFMSVLSNLTAIKIRGTYTHQGRGFLDDVSLETAQRGAAGEPADWIEHCQCPHGYVGQFCESCAPGFHHDPPNGGPFSLCVPCNCNGHADICEAETGQCICHHNTAGSNCDLCSRGFYGYPLKGTPHDCKPCPCPDNGPCILLGNNPDPICSECPSGRTGARCETCSDGYFGNPDQGQACRLCDCNNNIDLNAVRNCNHETGECLKCVNNTAGFHCEDCLSGYWGDALSERKEDSCKLCQCYPPGTIELDDGSVAPCNQLTGHCACKPHVIGRNCDKCEDGYYQILSGDGCTACNCDPEGSYNRTCDATTGQCECRPGITGKRCDTCLPYQFGFGRDGCKHCDCDTIGSQELQCDASGQCPCLTNVEGRRCDRCKENKYNRQYGCIDCPPCYNLIQDSVNQHRRRLNELESTLRKINNSPTVMKDSDFEKELKNVENRVKSLLQVAKQGSGNENKTLVEQLDELRDQLNQIEKISQSVDATAEDARRTTNEGLTSIEEAERVLDQIYEQLTEAEDYLATDGARALAAAKKRADQVGQQNQQMTIIAQEARVLADLNTNEAKKIHVLAEQARNTSLEAYNLAKKAIAKYSNISDEIRGLENKLELLEDRFNEVKNLTAAAVAKSAAVDKEALQLLILDLRVPAVDTNELRILLETVSVDGSEIKEQAQLLLGQNEAWLNELANKARKSEELLERAQDQQAATADLLSEVDGANEKAKDALKRGNQTLVEAQETLKKLGEFDAEVQKERIKAQEALTVLEEIKDMVNEAIAKANETESVLKDAESNAIAAKDIAIQAQVSNNADEASANANLIRQEANKTKLDAVRLGNEADKLHLRVEITNSIAKKHEARVDKDVNATNEVNHQVGQARNSLNLAGQQVDKALAEVDEIIKELDVLPEIDDADLDRLEERLLAAEKEIEEANLEKRIRELTEAKNLQTQWVKNYEDEVSRLRLEVENIDDIRKALPSICYKRLRLEP
>EOG090X00BV
MFSIFTASDVRNLSVLKISTPLSFNILGHPLKGGLYDPALGPLNDRSDPCGTCGEGTIQCMGHFGHIELPVPVVNPLFHKVLTSLLKLSCLKCYTLQIPSYLKLLLNGKLRLMEEGFSNDIPGLEQEVGSAVAGMNRIAEGELEFISDIIEAYIEMTCNQRHHVQSGKSKESTSTRTLNMEWHHYIESVVKTCKASKLCINCRNPIPKMTILKNKILTNHVVNNEDTMMEDRVIHKLETSFMTPDQSKKHLRGLWQKEADILRIIIPCLGSVDLEFPTDVFFFEIIPVLPPITRPVNMLDNQLVEHPQSQVYKSIIQDCLVLRNIIQTIQDGDTTQLPEEGRAVFDEIRGDNAAEKLHHAWTTLQSNVDHLMDREMSKTTESANCHGLKQVIEKKEGIIRMHMMGKRVNYAARSVITPDPNLNIDEIGVPEAFALKLTYPVPVTPWNVTELRKLIINGPEIHPGAVMIEGEDGFVKLLRGDDKTQLEAIAKRLLTSSRKPFSGIKIVHRHLQNGDMLLLNRQPTLHKPSIMAHKARILKGEKTLRLHYANCKAYNADFDGDEMNAHFPQNELARSEGYFIANVSNQYLVPKDGTPLGGLIQDHVISGVRLTLRGNFFNRQDYMQLVYSAIADTTGDLILLPPTILKPVRLWSGKQIISTVIINLTPRGRAPINLKASAKISVKDWQVKKARKWKCGQEFTDQRTMSEAEVVIRGGELLSGVLDKTHYGATPYGLIHCLFELYGGTCSSKVLSAFGKLFQTYLQISGFTLGVEDILVVRKSDQKRREIIEACRQIGDQIQTATVELPPGTSEEQVKSKMEESYAKDPKFRAIVDRKYKSALDVFTNNINKTCLPAGLLKKFPHNNLQLMVQSGAKGSTVNTMQISCLLGQIELEGKRPPLMINGKSLPSFPAYDSSPRSGGFIDGRFMTGIQPQEFFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLTVNYDSTVRDSDGSLIQMSYGEDGLDIPNSRFLRKEELDFLVENRKAIVDPALVEHLKDETTEKIRKINKKIRKWRTKHGNGSTKWRNSEFAKFSEINRNSGSSKNRQINSNCGRTKAALSLMKKWIRADEEVKKKLKDECVRCPDPVTSIFRQDLQFGVLTEKMEALMEEYLDEKSRRFTTSIGKEEVRDLLCTKIMKSLCPPGEPVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMMASKNIKTPSMEIPFRTDLPNVENQATKLQLKLTKCYLSNILKNIKLDRKLEENPNRQLTFTLTVNCLPHKFYKNEYCVKPHNVLNEIERNFFKLFFRAIKKIGKATGTLLHIEEEKSSSREDDAMLDTGEPDETEAKPNRSDLGELHESSDEDEAAEDADATASRSIARHRENQEYEDPEEEEIEDAAPREPEDEENPQNPTNLPPEDEDDLDQPMCVADELITEQRKKDVVNMHPYALDYDYDSEKFLWCKLTFWLPLRMCRLDLPTILRTVAEKVVLWETPAIKRAFTFQNSEGETILKTDGLNIVEMFKYAQILDLHKLYTNDIYGVSRTYGIEAANRVILKEVKDVFKMYGITVDSRHLSLIADYMTFDGTFQPLSRKGMEDSASPLQQMSFEASLNFLKNATLQGKHDDLMSPSSRLMVGQPCKTGTGAFNVLFKMNNTAVSM

有人可以帮助我吗？ 谢谢你