Hi Eric

There is already a genbank format in the EMBOSS datatypes
(although there is talk of defining this and others in a set of
smaller repositories defined as its dependencies for more
modularity). Note it uses "genbank" not "gb" as the name!

https://toolshed.g2.bx.psu.edu/view/devteam/emboss_datatypes

However that doesn't answer your question :(

Peter

On Mon, Jul 14, 2014 at 7:31 PM, Eric Rasche <rasche.e...@yandex.ru> wrote:
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> I'm trying to add a new datatype to my galaxy instance for genbank
> files, however I'm running into various issues. I've followed the
> tutorial (https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes)
>
> however that example subclasses tabular, and I'd like to subclass Text
> as they're plain text files, and I'd like to be able to define a sniffer
> for them (not possible if your type=galaxy.datatypes.data:Text)
>
> I figured the call ought to be something like
>
> <datatype extension="gb" type="galaxy.datatypes.data:Genbank"
> subclass="True" />
>
> however, everything I try fails with
>
>> Error importing datatype module galaxy.datatypes.data: 'module' object has 
>> no attribute 'Genbank'
>
> To avoid this particular issue, I tried writing a separate datatype just
> for genbank files (type="galaxy.datatypes.genbank:Genbank"), however
> that fails with the same error:
>
>> galaxy.datatypes.registry ERROR 2014-07-14 13:23:23,100 Error importing 
>> datatype module galaxy.datatypes.genbank: 'module' object has no attribute 
>> 'genbank'
>> Traceback (most recent call last):
>>   File "/home/hxr/work/galaxy-central/lib/galaxy/datatypes/registry.py", 
>> line 206, in load_datatypes
>>     module = getattr( module, mod )
>> AttributeError: 'module' object has no attribute 'genbank'
>
> Here's my lib/galaxy/datatypes/genbank.py looks like:
>
>> import pkg_resources
>> pkg_resources.require( "bx-python" )
>> import logging
>> from galaxy.datatypes import data
>> log = logging.getLogger(__name__)
>>
>> class Genbank( data.Text ):
>>     file_ext = "gb"
>>
>>     def sniff( self, filename ):
>>         header = open(filename).read(5)
>>         return header == 'LOCUS'
>
> To debug this, I've tried copying the tabular data type completely,
> removed all the classes other than Tabular, and renamed it "Genbank",
> however this fails too with the same error.
>
> Can anyone offer some insight?
>
> Cheers,
> Eric
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