Yup that did it. Thanks!
I'm using an older version which doesn't quite as a full a description
of the build_types() method.
Sorry for not replying earlier - been having webserver and database
issues that needed fixing first.
Cheers,
Chris
On 07/02/11 14:56, Andy Jenkinson wrote:
The SourceAdaptor POD documents the build_types method. Just return an array
containing a hash per type. For example:
return ( { 'type' => 'expression_tag', 'category' => 'experimental' } );
A more complete implementation would also include an ontology term and the
'count' for each type (i.e. the number of features of each type). Note that the
build_types command takes segment parameters like the build_features method,
except the segment is optional for build_types:
/das/yoursource/types
/das/yoursource/types?segment=X:1,100
Just make sure the content matches the types and categories used by the
features command.
See the spec for more details:
http://www.biodas.org/documents/spec-1.6.html#types
On 7 Feb 2011, at 14:48, Chris Cole wrote:
Hi Andy,
Thanks for the help. Looks like I was close...
I now get an error regarding the 'types' command. I haven't implemented it so
that's not a surprise. However, I'm struggling to find documentation on the
build_types() function and what data it should return. My source data only has
one type: 'expression_tag' so how should I return that?
Cheers,
Chris
On 07/02/11 11:40, Andy Jenkinson wrote:
Hi Chris,
The 'reference' Ensembl sources are suitable for use as mapmasters, as they
provide sequence information:
http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/entry_points
http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/sequence?segment=1:1,100
So, barring any particular nuance of IGB, the correct mapmaster URL would be:
http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference
(assuming thaliana)
The reason for all this is I guess that IGB does not support the DAS 1.53E/1.6
sources command, which provides species and coordinate information directly.
Cheers,
Andy
On 7 Feb 2011, at 10:34, Chris Cole wrote:
Hi,
I have a functioning ProServer install that works fine with Ensembl, but I'd
like to get it working with IGB as well. However, it fails to load as it has a
'Missing MAPMASTER element'. I see I need to specify a URI to a known MAPMASTER
source, but I've no idea how.
The server is for Arabidopsis data and I've found the Ensembl DAS sources for
plants, but which can I use as a mapmaster?
http://plants.ensembl.org/das/dsn
Or am I barking up the wrong tree?
Any pointers much appreciated.
Cheers,
Chris
_______________________________________________
DAS mailing list
[email protected]
http://lists.open-bio.org/mailman/listinfo/das
--
Dr Chris Cole
Senior Bioinformatics Research Officer
College of Life Sciences
University of Dundee
Dow Street
Dundee
DD1 5EH
Scotland, UK
url: http://network.nature.com/profile/drchriscole
e-mail: [email protected]
Tel: +44 (0)1382 388 721
The University of Dundee is a registered Scottish charity, No: SC015096
--
Dr Chris Cole
Senior Bioinformatics Research Officer
College of Life Sciences
University of Dundee
Dow Street
Dundee
DD1 5EH
Scotland, UK
url: http://network.nature.com/profile/drchriscole
e-mail: [email protected]
Tel: +44 (0)1382 388 721
The University of Dundee is a registered Scottish charity, No: SC015096
_______________________________________________
DAS mailing list
[email protected]
http://lists.open-bio.org/mailman/listinfo/das
