[Biojava-l] Parsing INSDseq Sequences (1.3 & 1.4)

[Richard Holland]

Yesterday I think I said I was going to add other-seqids but I forgot to
do it, so I did it just now. Try it and see. Use the new
INSDseqFormat.Terms.getOtherSeqIdTerm() term to find them.

cheers,
Richard

On Wed, 2006-06-07 at 19:48 -0400, Seth Johnson wrote:
> Hi Richard,
> 
> I still cannot locate the GI number for the main sequence.  After I
> parse it with readINSDseqDNA, I then use:
> 
>                 Note [] myAccs = ((RichAnnotation)rs.getAnnotation
> ()).getProperties(Terms.getAdditionalAccessionTerm ());
> 
> However, the 'myAccs' appears to be empty.  Am I on the wrong track to
> get to other-seqids???
> 
> On 6/6/06, Richard Holland <richard.holland at ebi.ac.uk> wrote:
>         GenBank has a separate line for GI number, so it can be parsed
>         out 
>         nicely. INSDseq does not, so you have to rely on the other-
>         seqids tag
>         and hope that one of them is the GI number. However it seems I
>         have not
>         included that tag in the parser, so I will include it. This
>         will make 
>         the other-seqids values available through the notes with the
>         term
>         Terms.getAdditionalAccessionTerm(), but getIdentifier() will
>         remain
>         null.
>         
>         For your second question, the tutorial makes the mistake in
>         several 
>         places of saying getNoteSet(Terms.blahblah()). This was
>         shorthand for:
>         
>         rs.getAnnotation().getProperty(Terms.blahblah())
>                 (for single values)
>         
>         or
>         
>         ((RichAnnotation)rs.getAnnotation()).getProperties
>         ( Terms.blahblah())
>                 (for multiple values)
>         
>         but never got expanded. Maybe someone can fix that one
>         day... :)ded...
>         
>         I'm just updating INSDseq to 1.4 now. The guys next door gave
>         me the
>         details of the changes, and told me that 1.3 is actually no
>         longer
>         supported by them after Friday this week! So I'll make it 1.4
>         only.
>         
>         cheers,
>         Richard
>         
-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416