Are you using the latest source from the CVS? We should have recently cleaned up a lot of the genbank and msf parsing code. -Robin
-----Original Message----- From: Neill White [mailto:[EMAIL PROTECTED]] Sent: Monday, July 29, 2002 6:30 PM To: [EMAIL PROTECTED] Subject: [Biojava-l] Genbank SeqIO question Hello- I'm a new user of biojava and have a small problem that I'm hoping someone can help me with - that is, I'm trying to read in and write out genbank files such that what I write out is somewhat close to what I read in (it's acceptable if some info is lost - not all parsers are perfect). The problem is that some information (the annotation) is lost after the first iteration. Not a huge problem, but if I now modify the program to read in this freshly created genbank file ('file.dat'), and write it out again - it's now missing the feature table. Any advice would be greatly appreciated. Thanks- neill my program: import java.io.FileOutputStream; import java.io.PrintStream; import java.io.BufferedReader; import java.io.FileReader; import org.biojava.bio.*; import org.biojava.bio.seq.*; import org.biojava.bio.seq.impl.*; import org.biojava.bio.seq.io.*; import org.biojava.bio.symbol.*; public class SimpleBioJava{ public static void main(String args[]) throws Exception{ // First, make, or read in a simple DNA sequence //Sequence sequence = nwSequence( "gattaca", "DNA" ); // This line reads in the first sequence from a fasta file //Sequence sequence = nwReadFastaSequence( "test.fa" ); // This line reads in the first sequence from a genbank file Sequence sequence = nwReadGenbankSequence( "gi20537285.gbk" ); // Phew, now that that's done, let's write it to a file SequenceFormat seqFormat = new GenbankFormat(); PrintStream stream = new PrintStream( new FileOutputStream( "test.dat" ) ); seqFormat.writeSequence( sequence, stream ); } public static Sequence nwReadGenbankSequence( String fileName ) throws Exception{ Sequence sequence = null; BufferedReader br = new BufferedReader( new FileReader( fileName ) ); SequenceIterator stream = SeqIOTools.readGenbank( br ); if ( stream.hasNext() ){ sequence = stream.nextSequence(); } return sequence; } } __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
