Hi Ulrik, Can you send me your .gb file off list?
Thanks, Andreas On Sat, Sep 7, 2013 at 11:42 AM, Ulrik Stervbo <[email protected]>wrote: > Hello Everyone, > > I am new to Biojava and quite new to java it sel (have not worked with it > in years). > > I am trying to figure out how to read and later write a genbank file. > > It seems that writing genbank is not supported? > > What about all the different features annotated in the genbank file? When I > use getFeatures() I have 0 elements? > > How can I access each sequence annotation/feature? > > The genbank file is attached, and my code below. > > Thanks > Ulrik > > import java.io.File; > import java.util.LinkedHashMap; > import java.util.List; > > import org.biojava3.core.sequence.DNASequence; > import org.biojava3.core.sequence.compound.NucleotideCompound; > import org.biojava3.core.sequence.features.FeatureInterface; > import org.biojava3.core.sequence.io.GenbankReaderHelper; > import org.biojava3.core.sequence.template.AbstractSequence; > > > public class bioTest{ > > /** > * @param args > * @throws Exception > */ > public static void main(String[] args) throws Exception{ > > File dnaFile = new File("test-genbank.gb"); > LinkedHashMap<String, DNASequence> dnaSequences = > GenbankReaderHelper.readGenbankDNASequence( dnaFile ); > for (DNASequence sequence : dnaSequences.values()) { > System.out.println( sequence.getSequenceAsString() ); > > System.out.println("Length: " + sequence.getLength()); > > List<FeatureInterface<AbstractSequence<NucleotideCompound>,NucleotideCompound>> > features = sequence.getFeatures(); > > System.out.println(features.size()); > } > } > > } > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
