Christopher Fields > BioPerl-1.6.901 > Bio::DB::GFF::Util::Binning

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Module Version: 1.006901   Source   Latest Release: BioPerl-1.6.924

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.

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