File Coverage

Bio/DB/GFF/Aggregator/processed_transcript.pm
Criterion Covered Total %
statement 9 9 100.0
branch n/a
condition n/a
subroutine 5 5 100.0
pod 3 3 100.0
total 17 17 100.0


line stmt bran cond sub pod time code
1             =head1 NAME
2              
3             Bio::DB::GFF::Aggregator::processed_transcript -- Sequence Ontology Transcript
4              
5             =head1 SYNOPSIS
6              
7             use Bio::DB::GFF;
8              
9             # Open the sequence database
10             my $db = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
11             -dsn => 'dbi:mysql:elegans42',
12             -aggregator => ['processed_transcript'],
13             );
14              
15             ------------------------------------------------------------------------
16             Aggregator method: processed_transcript
17             Main method: mRNA
18             Sub methods: CDS exon five_prime_UTR three_prime_UTR transcription_start_site polyA_site 5'-UTR 3'-UTR
19             ------------------------------------------------------------------------
20              
21             =head1 DESCRIPTION
22              
23             Bio::DB::GFF::Aggregator::processed_transcript is one of the default
24             aggregators, and was written to be compatible with the Sequence
25             Ontology canonical gene. It aggregates raw "exon," "CDS",
26             "five_prime_UTR", "three_prime_UTR", "transcription_start_site" and
27             "polyA_site" features into "mRNA" features. The UTRs may also be
28             named "untranslated_region," "five_prime_untranslated_region,"
29             "three_prime_untranslated_region,", "5'-UTR," and other synonyms.
30              
31             =cut
32              
33             package Bio::DB::GFF::Aggregator::processed_transcript;
34              
35 3     3   12 use strict;
  3         3  
  3         75  
36              
37 3     3   9 use base qw(Bio::DB::GFF::Aggregator);
  3         3  
  3         351  
38              
39             =head2 method
40              
41             Title : method
42             Usage : $aggregator->method
43             Function: return the method for the composite object
44             Returns : the string "processed_transcript"
45             Args : none
46             Status : Public
47              
48             =cut
49              
50 211     211 1 365 sub method { 'processed_transcript' }
51              
52             =head2 part_names
53              
54             Title : part_names
55             Usage : $aggregator->part_names
56             Function: return the methods for the sub-parts
57             Returns : the list CDS 5'-UTR 3'-UTR transcription_start_site polyA_site
58             Args : none
59             Status : Public
60              
61             =cut
62              
63             sub part_names {
64 106     106 1 326 return qw(CDS 5'-UTR 3'-UTR transcription_start_site
65             polyA_site UTR five_prime_untranslated_region
66             three_prime_untranslated_region
67             five_prime_UTR three_prime_UTR exon);
68             }
69              
70             =head2 main_name
71              
72             Title : main_name
73             Usage : $aggregator->main_name
74             Function: return the method for the main component
75             Returns : the string "mRNA"
76             Args : none
77             Status : Public
78              
79             =cut
80              
81             sub main_name {
82 182     182 1 358 return 'mRNA';
83             }
84              
85             1;
86             __END__