[Bioperl-pipeline] Annotation+Transformers (fwd)

[Shawn Hoon]

On Thursday, March 20, 2003, at 12:51 PM, kiran wrote:

>
>
>> This is still work in progess.  Transformers(Converter) works with
>> RepeatMasker but not for blast yet.
>> A small annoying problem. Converter objects need a RawContig obj to
>> attach to the feature. So for RepeatMasker,
>> I include as an input to the transformer INPUTOBJ which the input to
>> the RepeatMasker analysis. Problem with blast
>> is that I'm using ->get_repeat_maskedseq which is a BIo::PrimarySeqI
>> ..grr..DnaAlignFeatureAdaptor  doesn't like it
>>
>> So either I over kill the problem by attaching an iohandler to the
>> Transformer and fetch the RawContig or attach a RawContigAdaptor to 
>> the
>> converter
>> and fetch it using the original input id...any feelings?
>
>
>
> can you pass in ensembl db information (dbname, host, etc) and contig 
> name
> as arguments to the transformer (converter) as arguments and the 
> converter
> would contain the code to fetch the rawcontig (using the rawcontig
> adaptor) and attaches it as required.
>

Frankly hints of BioToEns but heck, I just want to get it working so it 
works for me.
Unless Juguang objects, let just make it so, since it really is a small 
part of it. And we should
hold things up just so we can find the most elegant solution to passing 
a contig around.
Also I desperately wanna tag biopipe but am working on something else 
this week.


shawn

>
> kiran
>
>
>
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