[DAS] das-ensembl question

[James Freeman]

Hi Tom,

Look at some old postings on the das and ensembl mailing lists, and it 
should help you out:

http://www.ensembl.org/Dev/Lists/dev/msg07618.html
http://www.ensembl.org/Dev/Lists/das/msg01056.html
http://www.ensembl.org/Dev/Lists/das/msg01042.html
http://www.ensembl.org/Dev/Lists/dev/msg07627.html
http://www.ensembl.org/Dev/Lists/dev/msg07524.html
http://www.ensembl.org/Dev/Lists/das/msg00940.html

Good luck,

Jim

Tom Fahland wrote:

>Hi James
>
>I am setting up an Ldas server and had a couple quick questions. If I
>want to keep things as simple as possible, can I only load one section
>of data ,the annotation section? 
>If I am used to using a simple line like
>AB000381.1.1.35863      1       57      -1      Alu
>
>to load (normal das description) data, what is the simplest I can use to
>load the ldas table? Also, is it possible to add a link to another area
>(when its viewed in contigview and you are on mouseover)
>
>Thanks
>Tom
>
>
>
>-----Original Message-----
>From: James Freeman [mailto:jmfreeman@attbi.com]
>Sent: Tuesday, July 23, 2002 4:59 PM
>To: Tom Fahland
>Subject: Re: [DAS] das-ensembl question
>
>
>Hi Tom,
>
>If you set up the database correctly in mysql and have an apache server,
>
>the new sources server should appear in the add DAS sources option in 
>Ensembl.  The plus side is it is a trivial upload script of  tab 
>delimited files and if you use the big goldenpath file off the fasta/dna 
>directory of current_human in Ensembl the coordinates will be understood
>
>by ensembl.  Add the ability to give it a link back to your data sources
>
>and you are all set.
>
>
>Try it out and let me know if you run into any snags,
>
>Jim Freeman
>Bioinformatics Consultant at Biogen
>james_freeman@biogen.com
>
>Tom Fahland wrote:
>
>>Hi James
>>
>>Just a couple quick questions. Does this work more or less the same
>>
>way,
>
>>store data in a database and then viewable from contigview? i'll read
>>
>up
>
>>on it.
>>Tom
>>
>>-----Original Message-----
>>From: James Freeman [mailto:jmfreeman@attbi.com]
>>Sent: Monday, July 22, 2002 4:58 PM
>>To: Tom Fahland
>>Subject: Re: [DAS] das-ensembl question
>>
>>
>>Hi Tom,
>>
>>This might be a good time to try an LDAS server, I found it to be 
>>excellent and not directly tied to Ensembl.
>>
>>If you have any problem doing that please send details,
>>
>>--
>>Jim Freeman
>>Bioinformatics Consultant at Biogen
>>jmfreeman@attbi.com
>>
>>
>>
>>Tom Fahland wrote:
>>
>>>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
>>>
>>>
>>>
>>>_______________________________________________
>>>DAS mailing list
>>>DAS@biodas.org
>>>http://biodas.org/mailman/listinfo/das
>>>
>>
>>
>>
>
>
>
>