File Coverage

blib/lib/GenOO/Intron.pm
Criterion Covered Total %
statement 6 6 100.0
branch n/a
condition n/a
subroutine 2 2 100.0
pod n/a
total 8 8 100.0


line stmt bran cond sub pod time code
1             # POD documentation - main docs before the code
2              
3             =head1 NAME
4              
5             GenOO::Intron - Intron object
6              
7             =head1 SYNOPSIS
8              
9             # This object represents an intron of a transcript
10             # It extends the L<GenOO::GenomicRegion> object
11            
12             # To initialize
13             GenOO::Intron->new(
14             species => undef,
15             strand => undef, #required
16             chromosome => undef, #required
17             start => undef, #required
18             stop => undef, #required
19             part_of => reference to a transcript object
20             );
21              
22             =head1 DESCRIPTION
23              
24             The intron class describes an intron of a transcript.
25             It requires a strand (1,-1), a chromosome name, a genomic start and stop position (start is always the
26             smallest coordinate in the genome and NOT the 5p of the intron - i.e. if the intron is in the -1 strand
27             the start coordinate will be the 3p of the intron)
28             See L<GenOO::Region> and for more available methods
29              
30             =head1 EXAMPLES
31              
32             my $intron = GenOO::Intron->new(
33             strand => 1, #required
34             chromosome => 'chr11', #required
35             start => 8893144, #required
36             stop => 8911139, #required
37             );
38             my $intron_start = $intron->start; #8893144
39              
40             =cut
41              
42             # Let the code begin...
43              
44             package GenOO::Intron;
45             $GenOO::Intron::VERSION = '1.5.2';
46 1     1   8 use Moose;
  1         2  
  1         10  
47 1     1   7181 use namespace::autoclean;
  1         3  
  1         11  
48              
49             extends 'GenOO::GenomicRegion';
50              
51             has 'part_of' => (is => 'rw', weak_ref => 1);
52              
53              
54             __PACKAGE__->meta->make_immutable;
55              
56             1;