NAME

Bio::ViennaNGS::FeatureChain - Generic Moose wrapper class for combined/linked genomic intervals, eg BED12 elements

SYNOPSIS

  use Bio::ViennaNGS::Feature;
  use Bio::ViennaNGS::FeatureChain;

  # get some new sequence features as instances of Bio::ViennaNGS::Feature
  my $start1 = 1100; my $start2 = 2345; my $start3 = 2987;
  my $end1 = 1346; my $end2 = 2544; my $end3 = 3076;
  my $name1 = "feat1"; my $name2 = "feat2"; my $name3 = "feat3";
  my $strand = "+";
  my $chr = "chr1";
  my $feat1 = Bio::ViennaNGS::Feature->(chromosome => $chr,
                                        start => $start1,
                                        end => $end1,
                                        name => $name1,
                                        strand => $strand,
                                        );
   my $feat2 = Bio::ViennaNGS::Feature->(chromosome => $chr,
                                        start => $start2,
                                        end => $end2,
                                        name => $name2,
                                        strand => $strand,
                                        );
   my $feat3 = Bio::ViennaNGS::Feature->(chromosome => $chr,
                                        start => $start3,
                                        end => $end3,
                                        name => $name3,
                                        strand => $strand,
                                        );

  # initialize a FeatureChain for two of these intervals
  my $fc = Bio::ViennaNGS::FeatureChain->new(type => "exon",
                                             chain => [$feat1,$feat3],
                                            );

  # append a genomic intervald to the chain
  $fc->add($feat2);

  # sort the chain in ascending order by start coordinates 
  $fc->sort_chain_ascending();

  # get the number of elements in the chain
  $fc->count_entries();

DESCRIPTION

METHODS

sort_chain_ascending

as_bed12_line

as_bed6_array

DEPENDENCIES

Carp

AUTHORS

Michael T. Wolfinger <michael@wolfinger.eu>

COPYRIGHT AND LICENSE

Copyright (C) 2014-2017 Michael T. Wolfinger <michael@wolfinger.eu>

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.