[Bioperl-pipeline] Annotation+Transformers

[Shawn Hoon]

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?



code is committed..test passed so far...
Bala and Juguang can check it out.


shawn




On Thursday, March 13, 2003, at 04:18 PM, Elia Stupka wrote:

>> Oh, I am late a bit to mention that I also would like to give a 
>> 10-min talk about cigar string. :) But maybe next time is also ok for 
>> me.
>
> Yes, best is if tomorrow you, Shawn and Bala sort out the 
> converter-transfomer-cigar problem once and for all, then next week 
> you can talk about it.
>
>> Including temp illegal worker me, right? hehe
>
> Of course :)
>
> Elia
>