1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
|
=head1 NAME
Bio::DB::GFF::Util::Binning - binning utility for Bio::DB::GFF index
=head1 SYNOPSIS
use Bio::DB::GFF::Util::Binning qw(bin bin_bot bin_top);
my $tier = bin($start,$stop,$min);
=head1 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.
=head1 API
The remainder of the document describes the function calls. No calls
are exported by default, but must be imported explicitly.
=over 4
=cut
package Bio::DB::GFF::Util::Binning;
use strict;
require Exporter;
use vars qw(@EXPORT @EXPORT_OK);
use base qw(Exporter);
@EXPORT_OK = qw(bin bin_bot bin_top);
@EXPORT = @EXPORT_OK;
use Bio::Root::Version;
=item $bin_name = bin($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.
=cut
sub bin {
my ($start,$stop,$min) = @_;
$start = abs($start); # to allow negative coordinates
$stop = abs($stop);
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);
}
=item $bottom = bin_bot($tier,$start)
Given a tier name and a range start position, returns the lower end of
the bin range.
=cut
sub bin_bot {
my $tier = shift;
my $pos = shift;
bin_name($tier,int(abs($pos)/$tier));
}
=item $top = bin_top($tier,$end)
Given a tier name and the end of a range, returns the upper end of the
bin range.
=cut
sub bin_top {
my $tier = shift;
my $pos = shift;
bin_name($tier,int(abs($pos)/$tier)); # bin_name($tier,int($pos/$tier),+1);
}
sub bin_name {
my ($tier, $int, $fudge) = @_;
my $pos = abs($int) + ($fudge || 0);
$pos = 0 if $pos < 0;
sprintf("%d.%06d",$tier, $pos);
}
sub log10 {
my $i = shift;
log($i)/log(10);
}
1;
=back
=head1 BUGS
None known yet.
=head1 SEE ALSO
L<Bio::DB::GFF>,
=head1 AUTHOR
Lincoln Stein E<lt>lstein@cshl.orgE<gt>.
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.
=cut
|
