/usr/share/perl5/Bio/Tradis/TradisPlot.pm is in bio-tradis 1.3.3+dfsg-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 | package Bio::Tradis::TradisPlot;
# ABSTRACT: Generate plots as part of a tradis analysis
=head1 SYNOPSIS
Generate insertion plots for Artemis from a mapped fastq file and a reference
in GFF format
use Bio::Tradis::TradisPlot;
my $pipeline = Bio::Tradis::TradisPlot->new(mappedfile => 'abc');
$pipeline->plot();
=head1 PARAMETERS
=head2 Required
C<mappedfile> - mapped and sorted BAM file
=head2 Optional
=over
=item * C<outfile> - base name to assign to the resulting insertion site plot. Default = tradis.plot
=item * C<mapping_score> - cutoff value for mapping score. Default = 30
=back
=head1 METHODS
C<plot> - create insertion site plots for reads in `mappedfile`. This file will be readable by the L<Artemis genome browser|http://www.sanger.ac.uk/resources/software/artemis/>
=cut
use Moose;
use Bio::Tradis::Analysis::InsertSite;
has 'mappedfile' => ( is => 'rw', isa => 'Str', required => 1 );
has 'outfile' =>
( is => 'rw', isa => 'Str', required => 1, default => 'tradis.plot' );
has 'mapping_score' =>
( is => 'rw', isa => 'Int', required => 1, default => 30 );
sub plot {
my ($self) = @_;
Bio::Tradis::Analysis::InsertSite->new(
filename => $self->mappedfile,
output_base_filename => $self->outfile,
mapping_score => $self->mapping_score
)->create_plots;
return 1;
}
__PACKAGE__->meta->make_immutable;
no Moose;
1;
|