[Biojava-l] add Source Organism to genbank

[Richard Holland]

It only knows the display name if you've told it what it is. Therefore you either have to load up the NCBI taxonomy in memory or via a BioSQL database.

cheers,
Richard

On 12 Jun 2011, at 21:01, Khalil El Mazouari wrote:

> Hi,
> 
> I am trying to set Organism to RichSequence via:
> 
> richSequence.setTaxon(new SimpleNCBITaxon(taxid)); //ncbi tax id
> 
> the genbank ouptut:
> 
> SOURCE      
>  ORGANISM  
>            .
> FEATURES             Location/Qualifiers
>     source          1..394
>                     /mol_type="genomic DNA"
>                     /strand="+"
>                     /organism=""
>                     /db_xref="taxon:10090"
> 
> How to add Organism display name to the Source Field and to the annotation organism?
> 
> Thanks
> 
> khalil
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--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/