[Bioperl-l] Re: Proposed bioperl submission

[Donald G. Jackson]

Ewan,

thanks for the feedback; your comments were very helpful.  I'll go ahead 
and implement your suggestions a-c, plus work over the POD (which has 
lagged behind a bit... mea culpa).  Should I send the revised code to 
you or to someone else?

Regarding your suggestion for a to_FTHelper method:

I'd be glad to add this, but am fuzzy on how this method would be used 
in the display of SiRNA feature objects.  I read over the 
Bio::SeqIO::FTHelper docs but that didn't help...  Could you give me a 
clearer picture of why/how this method would be used?  That would help 
me make sure it does the right things.

Thanks for the feedback!

Don Jackson
BMS Bioinformatics

Ewan Birney wrote:

>[cc'ing in Bioperl for this submission of siRNA objects]
>
>Looks very cool. The basic flow if I have got it right is:
>
>
>   Bio::Tools::SiRNA ----> make a set of Bio::SeqFeature::SiRNAs which is
>made from two oligo object, and has a ranking.
>
>
>   Bio::Tools::SiRNA tries to dodge SNPs and repeats and uses the MDust
>module as well... 
>
(detailed comments truncated)