[Biojava-l] Can I get the additional information, such as chromosome number from "source" feature from genbank file?

[Richard Holland]

It's in the RichAnnotation object associated with the RichFeature inside
the parsed RichSequence object (if you're using the BioJavaX
GenbankFormat parser). The RichAnnotation is a key/value map - the keys
are term objects, which you can find by requesting the term for
"chromosome" from the default ontology. You can then search the map for
the matching key/value pair.

cheers,
Richard

On Sun, 2009-07-19 at 11:41 +0800, pprun wrote:
> Hi,
> 
> Given a genbank file with feature as this:
> 
> FEATURES             Location/Qualifiers
>       source          1..412
>                       /chromosome="12"
>                       /map="12q22-qter"
>                       /organism="Homo sapiens"
>                       /db_xref="taxon:9606"
> 
> 
> How can I get the chromosome="12" information? I need it to sort out the 
> sequence by chromosome.
> 
> Appreciate your help.
> Pprun
> 
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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/