[Biojava-l] Tr: Retrieve Information from GenBank file

[Scooter Willis]

Jean-Charles

I have it on my list to do a GenBank parser but haven't had the time. I
can't promise anything in the next couple weeks. Can you send some details
about what a typical use case is for your purpose? Are you trying to get the
sequence data or are you more interested in the features?

Thanks

Scooter

On Wed, Oct 27, 2010 at 4:11 AM, jc.lucky <jc.lucky at laposte.net> wrote:

>
> I tried once again with the new version of BioJava but without succeding.
> Any idea or suggestion?
>
> Thanks in advance
> Regards,
>
> Jean-Charles Ferrières
>
>
> > Message du 22/10/10 10:11
> > De : "jc.lucky"
> > A : biojava-l at lists.open-bio.org
> > Copie à :
> > Objet : [Biojava-l] Retrieve Information from GenBank file
> >
> >
> > Hi
> >
> > I'm trying to convert a GenBank file into a rdf file. The gene of
> interest can be found a t : http://www.ncbi.nlm.nih.gov/protein/284794945
> >
> > With the below code I can read the GenBank file and I manage to retrieve
> information and convert them in a rdf format. However I don't succeed in
> retrieving some information such as Title, protein or product. According to
> this page (http://www.biojava.org/wiki/BioJava:BioJavaXDocs#GenBan)it is
> possible to do so.
> > Please help me find what I do wrong or what should be done to achieve my
> goal.
> >
> > //read the GeneBank File
> > public static RichSequenceIterator readFile(String input,
> > RichSequenceBuilderFactory seqFactory,
> > Namespace ns)
> > throws IOException, NoSuchElementException, BioException
> > {
> > ns = null;
> > InputStream stream = new FileInputStream(input);
> > BufferedReader rdfFile = new BufferedReader(new
> InputStreamReader(stream));
> > RichSequenceIterator seqs =
> RichSequence.IOTools.readGenbankDNA(rdfFile,ns);
> > return seqs;
> > }
> >
> > //Retrieve information and convert them in rdf format
> > public void writeToRDFFile(RichSequenceIterator rsi, String output)
> > throws IOException, NoSuchElementException, BioException {
> > //create model for the ontology
> > OntModel model = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM,
> null);
> > OntClass parents;
> > String URI = "http://pbr.wur.nl/#";
> >
> > while(rsi.hasNext())
> > {
> > RichSequence seq = rsi.nextRichSequence();
> > String id = seq.getName();
> > parents = model.createClass(URI + id);
> > Set author = seq.getRankedDocRefs();//code to clean up Set&convert
> toString
> > String definition = seq.getDescription(); //code to clean up String
> > //Add to model
> > parents.addProperty(DC.description, definition);
> > parents.addProperty(DC.publisher, authors);
> > parents.addComment(taxonomy, "EN");
> > parents.addProperty(DC.type, organism);
> > //print in rdf format
> > model.write(out, "RDF/XML");
> > out.close(); }
> > }
> >
> >
> > Thanks,
> > Jean-Charles Ferrières
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