[Bioperl-l] trunc and Features?

[Charles Tilford]

Ewan Birney wrote:
> 
> Charles - welcome to one of the more frustrating parts of bioperl.
> 
> Bioperl doesn't do this not because this is a bad thing (it would be
> great) but because it is a real implementation challenge.

...snip...

I think I have a general understanding of the problem as you describe
it, but suspect that much of my remaining confusion is due to the fact
that I'm only just now learning object-oriented Perl. I have added
"autoload" to my spell check dictionary, but that's about the extent
of my knowledge of it ;) I'll consult the cookbook to figure out what
it's about...
 
> Re: your immeadaite problem -
> 
> I would love to see an attempt at solving this with either (a) adding a
> deep clone method on seqfeature::generic and working from there or
> (b) trying out the Proxy idea.

We decided to tackle the problem for the time being by generating
pruned genbank source files that only contain features from the area
of interest, and then loading those through SeqIO. If I get time I'll
look later into clone routines (it might be a good way to learn more
about autoloading), but right now I have a lot of BSML bells and
whistles I want to code up.

> Apologies that we haven't solved this already.

Apologies are hardly needed, the Bio:: hierarchy is extraordinarily
useful as it is! Thanks for taking the time to explain the issue to me
though, it's helped me to better understand some of the threads in the
past week.

-Charles

-- 
Charles Tilford, Bioinformatics-Applied Genomics
Bristol-Myers Squibb PRI, Hopewell 3A039
P.O. Box 5400, Princeton, NJ 08543-5400, (609) 818-3213
charles.tilford@bms.com