Bio::DB::GFF::Util::Binning

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 <[email protected]>. 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.