[Biojava-l] read DBLINK field from genbank file
George Waldon
gwaldon at geneinfinity.org
Fri Mar 4 17:16:25 UTC 2011
Hi Bart,
DBLINK is a recent addition to Genbank format and unfortunately bj1
parser does not read it. You can check yourself in
org.biojavax.bio.seq.io.GenbankFormat.
Regards,
George
Quoting Bart Mesuere <bart.mesuere at ugent.be>:
> Hi,
>
> I'm trying to read some genbank files using the 1.7 legacy code. All works
> fine but I'm having trouble extracting the projectid located in the DBLINK
> field (in bold in the example):
>
> LOCUS NC_009926 374161 bp DNA circular BCT
>> 25-JUL-2008
>> DEFINITION Acaryochloris marina MBIC11017 plasmid pREB1, complete
>> sequence.
>> ACCESSION NC_009926
>> VERSION NC_009926.1 GI:158339488
>> *DBLINK Project: 58167*
>
>
> I already inspected the SimpleRichSequence object with a debugger but
> couldn't find anything useful. Is it possible to read this field using
> biojava 1.7?
>
> Kind regards,
> Bart Mesuere
> _______________________________________________
> Biojava-l mailing list - Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
More information about the Biojava-l
mailing list