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我有多个序列对齐的问题。我有两个序列如下，我正在尝试使用 biojava 方法对齐它们，我得到这样的错误。我不知道出了什么问题。我知道序列的长度不同，但没关系。

GSKTGTKITFYEDKNFQGRRYDCDCDCADFHTYLSRCNSIKVEGGTWAVYERPNFAGYMYILPQGEYPEYQRWMGLNDRLSSCRAVHLPSGGQYKIQIFEKGDFSGQMYETTEDCPSIMEQFHMREIHSCKVLEGVWIFYELPNYRGRQYLLDKKEYRKPIDWGAASPAVQSFRRIVE SMSAGPWKMVVWDEDGFQGRRHEFTAECPSVLELGFETVRSLKVLSGAWVGFEHAGFQGQQYILERGEYPSWDAWGGNTAYPAERLTSFRPAACANHRDSRLTIFEQENFLGKKGELSDDYPSLQAMGWEGNEVGSFHVHSGAWVCSQFPGYRGFQYVLECDHHSGDYKHFREWGSHAPTFQVQSIRRIQQ

线程“main”中的异常 java.lang.ArrayIndexOutOfBoundsException: 1 at org.forester.evoinference.distance.NeighborJoining.getValueFromD(NeighborJoining.java:150) at org.forester.evoinference.distance.NeighborJoining.execute(NeighborJoining.java:123 ) 在 org.biojava3.alignment.GuideTree.(GuideTree.java:88) 在 org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:183) 在 Fasta.main(Fasta.java:41)

public class Fasta {

    public static void main(String[] args) throws Exception{


        ArrayList<String> fileName = new ArrayList<String> ();
        fileName.add("2M3T.fasta.txt");
        fileName.add("3LWK.fasta.txt");
        ArrayList<ProteinSequence> al = new ArrayList<ProteinSequence>();
        //ArrayList<ProteinSequence> all =  new ArrayList<ProteinSequence>();
        for (String fn : fileName)
        {
        al = getProteinSequenceFromFasta(fn);
        //all.add(al.get(0));
        for  (ProteinSequence s : al)
        {
            System.out.println(s);
        }
        }
        Profile<ProteinSequence, AminoAcidCompound> profile = Alignments.getMultipleSequenceAlignment(al);
        System.out.printf("Clustalw:%n%s%n", profile);
        ConcurrencyTools.shutdown();
        }
        //for (int i=0;i<sequence.size();i++)
        //  System.out.println(sequence);


    public static ArrayList<ProteinSequence> getProteinSequenceFromFasta(String file) throws Exception{

        LinkedHashMap<String, ProteinSequence> a = FastaReaderHelper.readFastaProteinSequence(new File(file));
        //sztuczne
        ArrayList<ProteinSequence> sequence =  new ArrayList<ProteinSequence>(a.values());


        return sequence;
    }
}
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1 回答 1

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我的猜测是问题出在这一行：

for (String fn : fileName)
{
    al = getProteinSequenceFromFasta(fn);
...
 }

您正在覆盖a1每个文件的内容。（我假设您想将所有 fasta 记录添加到a1中。如果您的 fasta 文件每个只有 1 条记录，那么它不能对单个记录进行多重对齐。

你可能想要

for (String fn : fileName)
{
    al.addAll(getProteinSequenceFromFasta(fn) );
...
 }

当然，您使用的库可能应该首先检查以确保有超过 1 个序列......

于 2014-06-26T14:24:12.743 回答