File Coverage

lib/Bio/Tradis/TradisPlot.pm
Criterion Covered Total %
statement 12 12 100.0
branch n/a
condition n/a
subroutine 4 4 100.0
pod 0 1 0.0
total 16 17 94.1


line stmt bran cond sub pod time code
1             package Bio::Tradis::TradisPlot;
2             $Bio::Tradis::TradisPlot::VERSION = '1.3.2';
3             # ABSTRACT: Generate plots as part of a tradis analysis
4              
5              
6 3     3   98943 use Moose;
  3         385231  
  3         21  
7 3     3   19953 use Bio::Tradis::Analysis::InsertSite;
  3         10  
  3         336  
8              
9             has 'mappedfile' => ( is => 'rw', isa => 'Str', required => 1 );
10             has 'outfile' =>
11             ( is => 'rw', isa => 'Str', required => 1, default => 'tradis.plot' );
12             has 'mapping_score' =>
13             ( is => 'rw', isa => 'Int', required => 1, default => 30 );
14              
15             sub plot {
16 1     1 0 3 my ($self) = @_;
17              
18 1         24 Bio::Tradis::Analysis::InsertSite->new(
19             filename => $self->mappedfile,
20             output_base_filename => $self->outfile,
21             mapping_score => $self->mapping_score
22             )->create_plots;
23              
24 1         9 return 1;
25             }
26              
27             __PACKAGE__->meta->make_immutable;
28 3     3   21 no Moose;
  3         6  
  3         15  
29             1;
30              
31             __END__
32              
33             =pod
34              
35             =encoding UTF-8
36              
37             =head1 NAME
38              
39             Bio::Tradis::TradisPlot - Generate plots as part of a tradis analysis
40              
41             =head1 VERSION
42              
43             version 1.3.2
44              
45             =head1 SYNOPSIS
46              
47             Generate insertion plots for Artemis from a mapped fastq file and a reference
48             in GFF format
49              
50             use Bio::Tradis::TradisPlot;
51            
52             my $pipeline = Bio::Tradis::TradisPlot->new(mappedfile => 'abc');
53             $pipeline->plot();
54              
55             =head1 PARAMETERS
56              
57             =head2 Required
58              
59             C<mappedfile> - mapped and sorted BAM file
60              
61             =head2 Optional
62              
63             =over
64              
65             =item * C<outfile> - base name to assign to the resulting insertion site plot. Default = tradis.plot
66              
67             =item * C<mapping_score> - cutoff value for mapping score. Default = 30
68              
69             =back
70              
71             =head1 METHODS
72              
73             C<plot> - create insertion site plots for reads in `mappedfile`. This file will be readable by the L<Artemis genome browser|http://www.sanger.ac.uk/resources/software/artemis/>
74              
75             =head1 AUTHOR
76              
77             Carla Cummins <path-help@sanger.ac.uk>
78              
79             =head1 COPYRIGHT AND LICENSE
80              
81             This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
82              
83             This is free software, licensed under:
84              
85             The GNU General Public License, Version 3, June 2007
86              
87             =cut