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1 =head1 NAME
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2
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3 Bio::DB::GFF::Util::Binning - binning utility for Bio::DB::GFF index
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4
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5 =head1 SYNOPSIS
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6
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7 use Bio::DB::GFF::Util::Binning qw(bin bin_bot bin_top);
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8 my $tier = bin($start,$stop,$min);
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9
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10 =head1 DESCRIPTION
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11
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12 This is a utility module that exports the functions bin(), bin_bot()
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13 and bin_top(). These functions translate a range on the genome into a
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14 named bin that is used as an index in the Bio::DB::GFF schema. The
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15 index makes certain range retrieval queries much faster.
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16
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17 =head1 API
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18
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19 The remainder of the document describes the function calls. No calls
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20 are exported by default, but must be imported explicitly.
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21
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22 =over 4
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23
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24 =cut
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25
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26 package Bio::DB::GFF::Util::Binning;
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27
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28 use strict;
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29 require Exporter;
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30 use vars qw($VERSION @ISA @EXPORT @EXPORT_OK);
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31 @ISA = 'Exporter';
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32 @EXPORT_OK = qw(bin bin_bot bin_top);
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33 @EXPORT = @EXPORT_OK;
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34
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35 =item $bin_name = bin($start,$stop,$bin_size)
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36
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37 Given a start, stop and bin size on the genome, translate this
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38 location into a bin name. In a list context, returns the bin tier
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39 name and the position that the bin begins.
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40
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41 =cut
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42
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43 sub bin {
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44 my ($start,$stop,$min) = @_;
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45 my $tier = $min;
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46 my ($bin_start,$bin_end);
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47 while (1) {
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48 $bin_start = int $start/$tier;
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49 $bin_end = int $stop/$tier;
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50 last if $bin_start == $bin_end;
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51 $tier *= 10;
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52 }
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53 return wantarray ? ($tier,$bin_start) : bin_name($tier,$bin_start);
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54 }
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55
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56 =item $bottom = bin_bot($tier,$start)
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57
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58 Given a tier name and a range start position, returns the lower end of
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59 the bin range.
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60
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61 =cut
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62
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63 sub bin_bot {
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64 my $tier = shift;
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65 my $pos = shift;
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66 bin_name($tier,int($pos/$tier));
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67 }
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68
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69 =item $top = bin_top($tier,$end)
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70
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71 Given a tier name and the end of a range, returns the upper end of the
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72 bin range.
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73
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74 =cut
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75
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76 *bin_top = \&bin_bot;
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77
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78 sub bin_name { sprintf("%d.%06d",@_) }
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79
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80 sub log10 {
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81 my $i = shift;
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82 log($i)/log(10);
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83 }
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84
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85 1;
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86
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87 =back
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88
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89 =head1 BUGS
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90
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91 None known yet.
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92
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93 =head1 SEE ALSO
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94
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95 L<Bio::DB::GFF>,
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96
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97 =head1 AUTHOR
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98
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99 Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
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100
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101 Copyright (c) 2001 Cold Spring Harbor Laboratory.
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102
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103 This library is free software; you can redistribute it and/or modify
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104 it under the same terms as Perl itself.
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105
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106 =cut
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