[Biojava-l] Genbank SeqIO question

[Neill White]

Thanks Robin - 

I was using the latest (1.21) binary.  Updating to the 
current code was a marked improvement.  The input and
output genbank files nearly match.  There is a slight issue
with an accumulation of '/JoinType="join"' feature table
qualifiers on CDS and mRNA records (i.e., if you read in
and print out the same genbank record n times, you'll get
n '/JoinType="join"' qualifiers for each feature that has
a join.  This probably won't break anyone's parser though
and is more cosmetic than vital.

neill

--- "Emig, Robin" <Robin.Emig@maxygen.com> wrote:
> 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:nk_white@yahoo.com]
> Sent: Monday, July 29, 2002 6:30 PM
> To: biojava-l@biojava.org
> 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;
>     }
> }
> 
> 
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