NAME¶
Bio::DB::GFF::Util::Binning - binning utility for Bio::DB::GFF index
SYNOPSIS¶
use Bio::DB::GFF::Util::Binning qw(bin bin_bot bin_top);
my $tier = bin($start,$stop,$min);
DESCRIPTION¶
This is a utility module that exports the functions
bin(),
bin_bot() and
bin_top(). These functions translate a range on
the genome into a named bin that is used as an index in the Bio::DB::GFF
schema. The index makes certain range retrieval queries much faster.
API¶
The remainder of the document describes the function calls. No calls are
exported by default, but must be imported explicitly.
- $bin_name = bin($start,$stop,$bin_size)
- Given a start, stop and bin size on the genome, translate this location
into a bin name. In a list context, returns the bin tier name and the
position that the bin begins.
- $bottom = bin_bot($tier,$start)
- Given a tier name and a range start position, returns the lower end of the
bin range.
- $top = bin_top($tier,$end)
- Given a tier name and the end of a range, returns the upper end of the bin
range.
BUGS¶
None known yet.
SEE ALSO¶
Bio::DB::GFF,
AUTHOR¶
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2001 Cold Spring Harbor Laboratory.
This library is free software; you can redistribute it and/or modify it under
the same terms as Perl itself.