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lib/Bio/ViennaNGS/Bed.pm  view on Meta::CPAN

# -*-CPerl-*-
# Last changed Time-stamp: <2017-06-10 18:20:26 michl>

package Bio::ViennaNGS::Bed;

use Bio::ViennaNGS;
use Carp;
use Moose;
use namespace::autoclean;
use Data::Dumper;
use version; our $VERSION = version->declare("$Bio::ViennaNGS::VERSION");

extends 'Bio::ViennaNGS::Feature';

has '+strand' => (
		  required => 1,
		 );

has 'thickStart' => (
		     is => 'rw',
		     isa => 'Int',
		     predicate => 'has_thickStart',
		    );

has 'thickEnd' => (
		   is => 'rw',
		   isa => 'Int',
		   predicate => 'has_thickEnd',
		  );

has 'itemRgb' => ( 
		  is => 'rw',
		  isa => 'Str',
		  lazy => 1,
		  default => '0',
		 );

has 'blockCount' => (
		     is => 'rw',
		     isa => 'Int',
		     predicate => 'has_blockCount',
		    );

has 'blockSizes' => (
		     is => 'rw',
		     isa => 'Value',
		    );

has 'blockStarts' => (
		      is => 'rw',
		      isa => 'Value',
		     );

has 'length' => (
		 is => 'rw',
		 isa => 'Int',
		 builder => '_build_length',
		 lazy => 1,
		 predicate => 'has_length',
		);


sub _build_length {
  my ($self) = @_;
  my ($i,$len) = (0)x2;
  my $this_function = (caller(0))[3];
  my @blockSizes = split (/,/ ,$self->blockSizes);
  my $bc = scalar @blockSizes;
  croak "ERROR [$this_function] invalid blockSount in BED12 line"

lib/Bio/ViennaNGS/Bed.pm  view on Meta::CPAN

  use Bio::ViennaNGS::Bed;

  my $bedobject = Bio::ViennaNGS::Bed->new();

  # compute the length of a BED12 block
  $bedobject->_build_length();

  # dump an object as BED12 line
  $bedobject->as_bed_line(12);

=head1 DESCRIPTION

This module provides a L<Moose> interface for storage and manipulation
of genomic interval data. It is primarily used as a convenience
wrapper for BED data with more generic L<Bio::ViennaNGS> classes for
feature annotation, such as L<Bio::ViennaNGS::FeatureInterval>,
L<Bio::ViennaNGS::MinimalFeature>, L<Bio::ViennaNGS::Feature>,
L<Bio::ViennaNGS::FeatureChain> and L<Bio::ViennaNGS::FeatureLine>.

=head1 METHODS

=over

=item _build_length

Title   : _build_length

Usage   : C<$obj-E<gt>_build_length();>

Function: Compute the length of a BED12 interval block / line, i.e.
          the sum over the lengths of all intervals that make up a
          BED12 entry.

Args    :

Returns :

=item as_bed_line

Title   : as_bed_line

Usage   : C<$obj-E<gt>as_bed_line($bedtype);>

Function: Dump the contents of the object as BED6 or BED12 line.

Args    : C<$bedtype> can either be 6 or 12, determining BED6 or BED12
          output.

Returns : A (tab-separated) BED6 or BED12 line as string.

=back

=head1 DEPENDENCIES

=over

=item L<Moose>

=item L<Carp>

=item L<namespace::autoclean>

=back

=head1 AUTHORS

Michael T. Wolfinger E<lt>michael@wolfinger.euE<gt>

=head1 COPYRIGHT AND LICENSE

Copyright (C) 2015-2017 Michael T. Wolfinger E<lt>michael@wolfinger.euE<gt>

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.10.0 or,
at your option, any later version of Perl 5 you may have available.

This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.


=cut