[DAS] das-ensembl question
Tom Fahland
tfahland@dgt.com
Fri, 19 Jul 2002 11:26:00 -0700
Hi
I posted this to the ensembl thread, but have not got any help.
I have an internal copy of ensembl installed locally and also a DAS
server running locally.
I was able to get DAS to work with an older version of ensembl, but the
newer version of ensembl seems to require a different format of the
data. I was using the standard my_feature table format, ie:
CREATE TABLE my_feature (
contig_id varchar(40) NOT NULL default '',
start int(10) NOT NULL default '0',
end int(10) NOT NULL default '0',
strand int(2) NOT NULL default '0',
id varchar(40) NOT NULL default '',
score double(16,4) NOT NULL default '0.0000',
gff_feature varchar(40) default NULL,
gff_source varchar(40) default NULL,
name varchar(40) default NULL,
hstart int(11) NOT NULL default '0',
hend int(11) NOT NULL default '0',
hid varchar(40) NOT NULL default '',
evalue varchar(40) default NULL,
perc_id int(10) default NULL,
phase int(11) NOT NULL default '0',
end_phase int(11) NOT NULL default '0',
KEY id_contig (contig_id),
KEY id_pos (id,start,end)
) TYPE=MyISAM;
but I noticed that the only external DAS sources that work with the
newer version have a METHOD varible (when doing mouse over on
contigview), thus the table above does not have METHOD, thus the format
has seemed to change. I can't find any docs about the new table format??
Any help would be great.
Tom Fahland