[Biojava-l] Parsing an EMBL flatfile

[mark.schreiber at group.novartis.com]

Hi Anna,

I think that information is probably ending up in an Annotation object. 
You can use the example TreeView program to interactively find out how a 
file is parsed and which features and Annotations end up where in the 
object model (http://www.biojava.org/docs/bj_in_anger/treeView.htm)

Let me know if this doesn't help.

Regards,

Mark Schreiber
Principal Scientist (Bioinformatics)

Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com

phone +65 6722 2973
fax  +65 6722 2910





"Anna Henricson" <Anna.Henricson at cgb.ki.se>
Sent by: biojava-l-bounces at portal.open-bio.org
11/30/2004 06:06 PM

 
        To:     <biojava-l at biojava.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Parsing an EMBL flatfile


Hi,
I'm a new beginner at Biojava and I'm trying to parse an EMBL flatfile, 
it's
especially info in the CDS section of the Feature Table that I want to
retrieve. I have looked at the examples and tutorials on the Biojava 
website
and tried using the FeatureFilter.ByType("CDS"), however, that only gives 
me
the exons to join and not the info that follow, such as protein_id, 
db_xref,
the amino acid sequence etc.
Instead, I have been trying to use the EmblLikeFormat class, 
EmblProcessor,
FeatureTableParser and EmblLikeLocationParser, but I can't really put it
together.
I would really appreciate some help, since I'm the only one around here 
that
is using Biojava.
Thanks!
/Anna

--------------------------------------------
Anna Henricson, MSc, PhD student
Center for Genomics and Bioinformatics (CGB)
Karolinska Institutet
S-171 77 Stockholm
Sweden
Phone: +46 (0)8 524 87296
Fax: +46 (0)8 337983


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