[Biojava-l] readFasta problem

xyz mitlox at op.pl
Thu Apr 8 11:30:52 UTC 2010


Hello,
I would like to read fasta file without to specify whether it is DNA,
RNA or Protein in code and I wrote this code

import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import org.biojava.bio.BioException;
import org.biojavax.SimpleNamespace;
import org.biojavax.bio.seq.RichSequence;
import org.biojavax.bio.seq.RichSequenceIterator;

public class SortFasta {

  public static void main(String[] args) throws FileNotFoundException,
  BioException {


    BufferedReader br = new BufferedReader(new
    FileReader("sortFasta.fasta")); 
    SimpleNamespace ns = new SimpleNamespace("biojava");

    // You can use any of the convenience methods found in the BioJava 1.6 API 
    //RichSequenceIterator rsi = RichSequence.IOTools.readFastaDNA(br,  ns); 
    RichSequenceIterator rsi = RichSequence.IOTools.readFasta(br, null, ns);

    // Since a single file can contain more than a sequence, you need
    // to iterate over rsi to get the information.
    while (rsi.hasNext()) {
      RichSequence rs = rsi.nextRichSequence();
      System.out.println(rs.getComments());
      System.out.println(rs.seqString());
    }
  }
}
but unfortunately it I have got following error:
it the details that follow to biojava-l at biojava.org or post a bug
    report to http://bugzilla.open-bio.org/ 

Format_object=org.biojavax.bio.seq.io.FastaFormat
Accession=
Id=
Comments=problem parsing symbols
Parse_block=atccccc
Stack trace follows ....


        at
        org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:222)
        at
        org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:110) ...
        1 more Caused by: java.lang.NullPointerException at
        org.biojava.bio.symbol.SimpleSymbolList.<init>(SimpleSymbolList.java:165)
        at
        org.biojavax.bio.seq.io.FastaFormat.readRichSequence(FastaFormat.java:213) ...
        2 more Java Result: 1

What did I wrong?

Thank you in advance.

Best regards,



More information about the Biojava-l mailing list