[Bioperl-l] trunc and Features?

[Charles Tilford]

Hi all,

I've just started working with Bio objects, so please let me know if
there is an obvious place I should have checked to find answers to any
of my questions. I've checked the list archives but am uncertain if
there are other resources as well.

I'd like to take a large, featured-decorated sequence and get from
that a subsequence decorated with any features that were overlapping
it. I tried ->trunc, which generated the appropriate subsequence, but
no features.

I also tried manually extracting any Features that had ->overlaps() to
the appropriate Range, but aside from the fact that I could not get it
to work (how does one deep-clone Bio objects? new( -OBJ =>
$parentObject ) appeared to fail), I also became worried about
propogation of base numbering (i.e. even if I adjusted the base
positions for the feature, what about those of underlying Locations or
References? Seemed like much work to check them all).

Does code exist for generating truncated sequences with all the
assorted children objects attached?

Also, is there any way to specify 'custom' numbering for a sequence
(i.e. starting from something other than '1')?

While I'm here... is there a way to generate a Seq object with a
specified length but no underlying sequence data?
$theSeq->length($desiredLength) did not work for me...

Thanks,
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