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Summary

Bio::DB::GFF::Util::Binning - binning utility for Bio::DB::GFF index

Package variables

Inherit

Exporter

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.

Methods

Methods description

None available.

Methods code

sub bin {

  my ($start,$stop,$min) = @_;
  my $tier = $min;
  my ($bin_start,$bin_end);
  while (1) {
    $bin_start = int $start/$tier;
    $bin_end   = int $stop/$tier;
    last if $bin_start == $bin_end;
    $tier *= 10;
  }
  return wantarray ? ($tier,$bin_start) : bin_name($tier,$bin_start);

}

sub bin_bot {

  my $tier = shift;
  my $pos  = shift;
  bin_name($tier,int($pos/$tier));

}

sub bin_name {

 sprintf("%d.%06d",@_)

}

sub log10 {

  my $i = shift;
  log($i)/log(10);
}

1;

}

General documentation

The remainder of the document describes the function calls. No calls
are exported by default, but must be imported explicitly.

None known yet.

Bio::DB::GFF,

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.