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
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