From: Lincoln S. <ls...@cs...> - 2006-01-04 16:33:29
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Great fun! I'll have a look at this. I've been working on the updated Bio::DB::GFF on and off for the past couple of weeks. Lincoln On Wednesday 04 January 2006 11:27 am, Jason Stajich wrote: > I noticed that NCBI is providing GFF3 dumps which is from some sort > of ASN1 -> GFF3 dumping program. Has anyone tackled loading it in? > I don't think the output is quite loadable to gbrowse, and I have > found it still easier to write a Genbank->GFF3 massager script to > generate loadable data than play with this GFF yet. > I think since the loaders don't really respect GFF3 (Id vs Parent as > the Group tag for a CDS feature) and whether or not the Group tag has > to be the 1st part of the ninth column. > > Scott are there definitive plans on full GFF3 support, the new schema > for Bio::DB::GFF, etc in 2006? > > An example file: > ftp://ftp.ncbi.nih.gov:/genomes/Fungi/Schizosaccharomyces_pombe/ > NC_003424.gff > > I know i am not being particularly helpful in that I didn't actually > take the time to try and load this but just seeing whether anyone > else has tried. > I think this is "almost" there and I would like to see if we could > share any sort of intermediate processing script so that we can more > easily pipeline this data into our Gbrowses. > > -jason > -- > Jason Stajich > Duke University > http://www.duke.edu/~jes12 > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse -- Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 FOR URGENT MESSAGES & SCHEDULING, PLEASE CONTACT MY ASSISTANT, SANDRA MICHELSEN, AT mic...@cs... |