File Coverage

blib/lib/GenOO/Data/File/BED/Record.pm
Criterion Covered Total %
statement 8 17 47.0
branch 0 12 0.0
condition n/a
subroutine 3 4 75.0
pod 0 2 0.0
total 11 35 31.4


line stmt bran cond sub pod time code
1             # POD documentation - main docs before the code
2              
3             =head1 NAME
4              
5             GenOO::Data::File::BED::Record - Object representing a record of a bed file
6              
7             =head1 SYNOPSIS
8              
9             # Object representing a record of a bed file
10              
11             # To initialize
12             my $record = GenOO::Data::File::BED::Record->new({
13             rname => undef,
14             start => undef,
15             stop_1based => undef,
16             name => undef,
17             score => undef,
18             strand_symbol => undef,
19             thick_start => undef,
20             thick_stop_1based => undef,
21             rgb => undef,
22             block_count => undef,
23             block_sizes => undef,
24             block_starts => undef,
25             copy_number => undef,
26             });
27              
28              
29             =head1 DESCRIPTION
30              
31             This object represents a record of a bed file and offers methods for accessing the different attributes.
32             It implements several additional methods that transform original attributes in more manageable attributes.
33              
34             =head1 EXAMPLES
35              
36             # Return strand
37             my $strand = $record->strand; # -1
38             my $strand_symbol = $record->strand_symbol; # -
39            
40             # Return stop position
41             my $stop = $record->stop; #10
42             my $stop_1based = $record->stop_1based; #11
43            
44             # Return location
45             my $location = $record->location;
46              
47             =cut
48              
49             # Let the code begin...
50              
51             package GenOO::Data::File::BED::Record;
52             $GenOO::Data::File::BED::Record::VERSION = '1.5.1';
53 1     1   6 use Moose;
  1         3  
  1         7  
54 1     1   7144 use namespace::autoclean;
  1         4  
  1         9  
55              
56             # Define the attributes
57             has 'rname' => (isa => 'Str', is => 'ro', required => 1);
58             has 'start' => (isa => 'Int', is => 'ro', required => 1);
59             has 'stop' => (isa => 'Int', is => 'ro', required => 1);
60             has 'name' => (isa => 'Str', is => 'ro', required => 1);
61             has 'score' => (isa => 'Num', is => 'ro', required => 1);
62             has 'strand' => (isa => 'Int', is => 'ro', required => 1);
63             has 'thick_start' => (isa => 'Int', is => 'ro');
64             has 'thick_stop_1based' => (isa => 'Int', is => 'ro');
65             has 'rgb' => (isa => 'Str', is => 'ro');
66             has 'block_count' => (isa => 'Int', is => 'ro');
67             has 'block_sizes' => (
68             traits => ['Array'],
69             is => 'ro',
70             isa => 'ArrayRef[Int]',
71             default => sub { [] },
72             handles => {
73             all_block_sizes => 'elements',
74             add_block_size => 'push',
75             map_block_sizes => 'map',
76             filter_block_sizes => 'grep',
77             find_block_size => 'first',
78             get_block_size => 'get',
79             join_block_sizes => 'join',
80             count_block_sizes => 'count',
81             has_block_sizes => 'count',
82             has_no_block_sizes => 'is_empty',
83             sorted_block_sizes => 'sort',
84             },
85             );
86             has 'block_starts' => (
87             traits => ['Array'],
88             is => 'ro',
89             isa => 'ArrayRef[Int]',
90             default => sub { [] },
91             handles => {
92             all_block_starts => 'elements',
93             add_block_start => 'push',
94             map_block_starts => 'map',
95             filter_block_starts => 'grep',
96             find_block_start => 'first',
97             get_block_start => 'get',
98             join_block_starts => 'join',
99             count_block_starts => 'count',
100             has_block_starts => 'count',
101             has_no_block_starts => 'is_empty',
102             sorted_block_starts => 'sort',
103             },
104             );
105             has 'extra' => (is => 'rw');
106             has 'copy_number' => (isa => 'Int', is => 'ro', default => 1, lazy => 1);
107              
108             # Consume roles
109             with 'GenOO::Region';
110              
111             # Before object creation edit the hash with the arguments to resolve 1 based and strand symbol
112             around BUILDARGS => sub {
113             my $orig = shift;
114             my $class = shift;
115            
116             my $argv_hash_ref = $class->$orig(@_);
117            
118             if (exists $argv_hash_ref->{stop_1based}) {
119             $argv_hash_ref->{stop} = $argv_hash_ref->{stop_1based} - 1;
120             }
121             if (exists $argv_hash_ref->{strand_symbol}) {
122             if ($argv_hash_ref->{strand_symbol} eq '+') {
123             $argv_hash_ref->{strand} = 1;
124             }
125             elsif ($argv_hash_ref->{strand_symbol} eq '-') {
126             $argv_hash_ref->{strand} = -1;
127             }
128             }
129            
130             return $argv_hash_ref;
131             };
132              
133             #######################################################################
134             ######################## Interface Methods ########################
135             #######################################################################
136             sub stop_1based {
137 1     1 0 736 my ($self) = @_;
138 1         31 return $self->stop + 1;
139             }
140              
141             sub to_string {
142 0     0 0   my ($self) = @_;
143            
144 0           my @fields = (
145             $self->rname,
146             $self->start,
147             $self->stop_1based,
148             $self->name,
149             $self->score,
150             $self->strand_symbol);
151            
152 0 0         push @fields, $self->thick_start if defined $self->thick_start;
153 0 0         push @fields, $self->thick_stop_1based if defined $self->thick_stop_1based;
154 0 0         push @fields, $self->rgb if defined $self->rgb;
155 0 0         push @fields, $self->block_count if defined $self->block_count;
156 0 0         push @fields, $self->join_block_sizes(",") if $self->has_block_sizes;
157 0 0         push @fields, $self->join_block_starts(",") if $self->has_block_starts;
158            
159 0           return join("\t", @fields);
160             }
161              
162             #######################################################################
163             ############################ Finalize #############################
164             #######################################################################
165             __PACKAGE__->meta->make_immutable;
166              
167             1;