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
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