File Coverage

blib/lib/GenOO/Transcript/Part.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::Transcript::Part - A functional region within a transcript consisting of spliceable elements
6              
7             =head1 SYNOPSIS
8              
9             # This is the main region object.
10             # Represents a functional region within
11             # a transcript eg 3'UTR, CDS or 5'UTR
12             # It supports splicing.
13            
14             # To initialize
15             my $region = GenOO::Transcript::Part->new({
16             species => undef,
17             strand => undef, #required
18             chromosome => undef, #required
19             start => undef, #required
20             stop => undef, #required
21             name => undef,
22             sequence => undef,
23             transcript => undef, #backreference to a L<GenOO::Transcript> object
24             splice_starts => undef, #reference to an array of splice starts
25             splice_stops => undef, #reference to an array of splice stops
26             });
27              
28             =head1 DESCRIPTION
29              
30             A transcript part can be any functional part of a transcript. It is usually used for the 3'UTR
31             5'UTR, coding region (CDS) etc. It has a genomic location (start, stop, chromosome, strand),
32             it is spliceable (splice_starts, splice_stops, exons, introns etc) and is connected to a
33             transcript object.
34              
35             =head1 EXAMPLES
36              
37             Not provided yet
38              
39             =cut
40              
41             # Let the code begin...
42              
43             package GenOO::Transcript::Part;
44             $GenOO::Transcript::Part::VERSION = '1.5.2';
45 1     1   712 use Moose;
  1         2  
  1         6  
46 1     1   7065 use namespace::autoclean;
  1         3  
  1         9  
47              
48             extends 'GenOO::GenomicRegion';
49              
50             has 'transcript' => (isa => 'GenOO::Transcript',is => 'rw', weak_ref => 1);
51              
52             with 'GenOO::Spliceable';
53              
54             __PACKAGE__->meta->make_immutable;
55              
56             1;