[Biojava-l] add Source Organism to genbank

[Richard Holland]

If you investigate the SimpleNCBITaxon class, you'll see that it has a addName() function. By using that on the instance you passed to richSequence.setTaxon() before doing the Genbank export then you'll get the name appearing correctly.

(The name classes are defined as constants in the parent NCBITaxon interface - COMMON or SCIENTIFIC are the two most commonly used.)

cheers,
Richard

On 12 Jun 2011, at 21:30, Khalil El Mazouari wrote:

> Could you please show me how to set "Mus musculus" organism to RichSequence?
> 
> many thanks.
> 
> Khalil
> On 12 Jun 2011, at 22:19, Richard Holland wrote:
> 
>> 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
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>> 
>> --
>> 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/
>> 
> 

--
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/