[Bioperl-l] location binner object

[Lincoln Stein]

It's would be easy to use the GFF binning system and store it in a
temporary BDB "B-tree".  The B-tree implementation will be as fast or
faster than the MySQL MyISAM index.  The implementation is trivial --
feel free to steal the bin methods from Bio::DB::GFF.

Lincoln

Jason Stajich writes:
 > I'm generating a bunch of Bio::LocationI objects and would like to test if
 > some are within some specified distance away from each other.  I want to
 > be able to do fast lookups to see if a location is within some range.
 > This seems pretty similar to Lincoln's binning in GFF for locations, but
 > would it be possible to do this in-memory/BDB file as I am generating a
 > lot of these and don't need to keep them once I've processed and
 > identified the best choices?
 > 
 > Essentially I want to be able to take a location from list A and see if
 > any locations in list B fall in the range of X bp downstream of A.
 > Plenty of implementation options, probably the fastes and easiest to
 > implement would be a single vector of length of the full range covered by
 > all the locations and have ptrs to the objects in the slots where the
 > location overlaps, but this is a memory hog.  I could map to a BDB file
 > and just eat the disk space since this is essentially generating a
 > tempfile
 > 
 > Anyways, Lincoln do you have any input here - is it just going to be
 > easier to slap everything into an sql backend with DB:GFF rather than
 > reinventing the wheel or can I basically just run everything through the
 > Bio::DB::GFF binning but store in a BDB file?  I'm happy to adapt this to
 > some sort of location aggregator/binner object for everyone's use.
 > 
 > Thanks.
 > 
 > -jason
 > -- 
 > Jason Stajich
 > Duke University
 > jason at cgt.mc.duke.edu
 > 
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 > Bioperl-l@bioperl.org
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
Positions available at my lab: see http://stein.cshl.org/#hire
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