[Biojava-l] Exporting accessions to Genbank files

[Hoebeke Mark]

Hi all,

In the context of importing/exporting genbank files into/from a database
I stumbled across an oddity :
 - when building a Sequence instance from a genbank file
(SeqIOTools.readGenbank()), the accession is available through the
"ACCESSION" property of its Annotation
 - when exporting a Sequence instance into a genbank file
(SeqIOTools.writeGenBank()), after having intialized the accession
through the "ACCESSION" property, no ACCESSION line is generated.

Wading through the code (stable 1.3 or 1.4pre1) I noticed the following
comment in  GenBankFormat.java :
(...)
 * Added GenBank header	info to	the sequence annotation. The ACCESSION
header
 * tag is not included.	Stored in sequence.getName().
(...)

which I interpreted as "the ACCESSION property is not written to the
file".

To solve my problem I has to resort to the ugly line below :

	annot.setProperty(GenbankProcessor.PROPERTY_GENBANK_ACCESSIONS,acces);

I'm sure there must be a better way. If anyone has a pointer related to
this issue, I'll gladly adopt a cleaner way of coding this.

Thanks 

Mark

-- 
--------------------------Mark.Hoebeke at jouy.inra.fr----------------------
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