[Biojava-l] SeqIOTools.readSwissprot API

[Fard, Payam (NIH/NCI)]

Hi all,

I am using the following program to read a swissProt file, but I am getting
"Could not read sequence exception". I am using jdk 1.4.2_04-b05 and bioJava
1.4pre1. Any ideas what I am doing wrong?

import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;
import java.io.*;
import org.biojava.bio.*;
import java.util.*;

public class ReadSwiss {
  public static void main(String[] args) {
    BufferedReader br = null;

    try {

      //create a buffered reader to read the sequence file specified by
args[0]
      br = new BufferedReader(new FileReader(args[0]));

    }
    catch (FileNotFoundException ex) {
      //can't find the file specified by args[0]
      ex.printStackTrace();
      System.exit(-1);
    }

    //read the SwissProt File
    SequenceIterator sequences = SeqIOTools.readSwissprot(br);

    //iterate through the sequences
    while(sequences.hasNext()){
      try {

        Sequence seq = sequences.nextSequence();
        //do stuff with the sequence

                System.out.println("Sequence length is : " + seq.length());
                System.out.println("Sequence name is : " + seq.getName());

      }
      catch (BioException ex) {
        //not in SwissProt format
        ex.printStackTrace();
      }catch (NoSuchElementException ex) {
        //request for more sequence when there isn't any
        ex.printStackTrace();
      }
    }
  }
}

I am getting the following exception:

     [java] org.biojava.bio.BioException: Could not read sequence
     [java]     at
org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader
.java:104)
     [java]     at ReadSwiss.main(ReadSwiss.java:30)
     [java]     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
Method)
     [java]     at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAcces
sorImpl.java:39)
     [java]     at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMet
hodAccessorImpl.java:25)
     [java]     at java.lang.reflect.Method.invoke(Method.java:324)
     [java]     at
org.apache.tools.ant.taskdefs.ExecuteJava.run(ExecuteJava.jav
a:208)
     [java]     at
org.apache.tools.ant.taskdefs.ExecuteJava.execute(ExecuteJava
.java:150)
     [java]     at org.apache.tools.ant.taskdefs.Java.run(Java.java:443)
     [java]     at
org.apache.tools.ant.taskdefs.Java.executeJava(Java.java:163)

     [java]     at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108)
     [java]     at org.apache.tools.ant.Task.perform(Task.java:341)
     [java]     at org.apache.tools.ant.Target.execute(Target.java:309)
     [java]     at org.apache.tools.ant.Target.performTasks(Target.java:336)
     [java]     at
org.apache.tools.ant.Project.executeTarget(Project.java:1339)

     [java]     at
org.apache.tools.ant.Project.executeTargets(Project.java:1255
)
     [java]     at org.apache.tools.ant.Main.runBuild(Main.java:609)
     [java]     at org.apache.tools.ant.Main.start(Main.java:196)
     [java]     at org.apache.tools.ant.Main.main(Main.java:235)
     [java] Caused by: java.io.IOException: Premature end of stream or
missing e
nd tag '//' for EMBL
     [java]     at
org.biojava.bio.seq.io.EmblLikeFormat.readSequence(EmblLikeFo
rmat.java:267)
     [java]     at
org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader
.java:101)

Thanks,
Payam.

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