On Wed, 29 Jan 2003, Stein Aerts wrote: > Hi Ewan, > I know of Mart (and I like it) but it is not suited for automated > sequence retrieval using gene_stable_id's (a SOAP web service for the > export data function would be nice). Anyway, the Mart output would have > currently the same faults I guess. Do you reckon that the fixing of the > Ensembl bugs is a short term matter?
(a) we know that people want to script against Mart and are working towards this - Arek might be able to fill you in (over to Arek) (b) Scripting against the core is best done probably with a specific ensembl script (perl) that doesn't bounce through genbank format - tell us what you want and I suspect Arne or Graham can whip up a (perl) script quickly (c) If you don't like Perl ( ... this is the biojava mailing list...) then there is a pretty complete and stable Java binding to Ensembl - it doesn't use BioJava - it is more just a vanilla Java binding to Ensembl. Craig melsopp is the lead on that. The web page is http://www.ensembl.org/java/ (d) Almost certainly, parsing GenBank/EMBL format is one of the worst ways to get information out of Ensembl - there is lots of stuff inside Ensembl which we can't dump due to format and/or space issues; we don't consider it to be a primary route of information... ... it doesn't change the fact there are bugs on our side ;) and we will fix those. k _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
