Question

我有多个序列对齐的问题。我有两个序列如下，我试图使用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。我知道序列长度不一样但不重要。

GSKTGTKITFYEDKNFQGRRYDCDCDCADFHTYLSRCNSIKVEGGTWAVYERPNFAGYMYILPQGEYPEYQRWMGLNDRLSSCRAVHLPSGGQYKIQIFEKGDFSGQMYETTEDCPSIMEQFHMREIHSCKVLEGVWIFYELPNYRGRQYLLDKKEYRKPIDWGAASPAVQSFRRIVE SMSAGPWKMVVWDEDGFQGRRHEFTAECPSVLELGFETVRSLKVLSGAWVGFEHAGFQGQQYILERGEYPSWDAWGGNTAYPAERLTSFRPAACANHRDSRLTIFEQENFLGKKGELSDDYPSLQAMGWEGNEVGSFHVHSGAWVCSQFPGYRGFQYVLECDHHSGDYKHFREWGSHAPTFQVQSIRRIQQ

线程中的异常＆＃34; main＆＃34; java.lang.ArrayIndexOutOfBoundsException：1 在 org.forester.evoinference.distance.NeighborJoining.getValueFromD（NeighborJoining.java:150）在 org.forester.evoinference.distance.NeighborJoining.execute（NeighborJoining.java:123）在org.biojava3.alignment.GuideTree。（GuideTree.java:88）at 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;
    }
}

Answer 1

我的猜测是问题在于这一行：

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

您正在覆盖每个文件的a1内容。（我假设您要将所有fasta记录添加到a1。如果您的fasta文件每个只有1条记录，那么它就无法对单条记录进行多重对齐。

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....

biojava线程“main”中的异常java.lang.ArrayIndexOutOfBoundsException：

1 个答案: