[Bioperl-pipeline] Annotation+Transformers (fwd)

[kiran]

> 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.  


kiran