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 <[EMAIL PROTECTED]> 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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
