[DAS] Configuring a valid MAPMASTER?

[Chris Cole]

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
>>>>
>>>>
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>>>
>>
>>
>> --
>> 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: chris at compbio.dundee.ac.uk
>> 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: chris at compbio.dundee.ac.uk
Tel: +44 (0)1382 388 721

The University of Dundee is a registered Scottish charity, No: SC015096