[Biojava-l] Extracting information from Genbank

Orest Kozyar orest.kozyar at gmail.com
Wed Jun 6 19:30:04 UTC 2007

I should also add that for some reason, the bytecode folder is not
present in my BioJava 1.5b2 package.


On 6/6/07, Orest Kozyar <orest.kozyar at gmail.com> wrote:
> I've been trying to figure out how to use Biojava to extract
> information from Genbank.  It seems that the following code would work
> according to the API docs:
> GenbankRichSequenceDB db = new GenbankRichSequenceDB();
> RichSequence rs = db.getRichSequence("'NM_177408");
> I've also tried variations on the ID (such as gi:NNNNNN) with and
> without the gi: annotation where the number corresponds to the record
> of interest, but no luck so far.  I keep getting the following error:
> Exception in thread "main" java.lang.NoClassDefFoundError:
> org/biojava/utils/bytecode/CodeException
>         at org.biojava.bio.seq.FeatureFilter$OnlyChildren.<clinit>(FeatureFilter.java:1270)
>         at org.biojava.bio.seq.FeatureFilter.<clinit>(FeatureFilter.java:1813)
>         at org.biojava.bio.seq.SimpleFeatureHolder.<init>(SimpleFeatureHolder.java:54)
>         at org.biojavax.bio.seq.RichFeature$Tools.makeEmptyFeature(RichFeature.java:167)
>         at org.biojavax.bio.seq.io.RichSeqIOAdapter.<init>(RichSeqIOAdapter.java:61)
>         at org.biojavax.bio.seq.io.SimpleRichSequenceBuilder.<init>(SimpleRichSequenceBuilder.java:100)
>         at org.biojavax.bio.seq.io.SimpleRichSequenceBuilderFactory.makeSequenceBuilder(SimpleRichSequenceBuilderFactory.java:70)
>         at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109)
>         at org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:154)
>         at Test.main(Test.java:58)
> Java Result: 1
> Perhaps I am just not formatting the string properly?  Any guidance
> you can provide will greatly be appreciated!
> Thanks,
> Orest

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