Bio-ViennaNGS

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META.json  view on Meta::CPAN

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         "Path::Class" : "0",
         "PerlIO::gzip" : "0",
         "Pod::Usage" : "0",
         "Template" : "0",
         "Test::Deep" : "0",
         "Test::File::Contents" : "0",
         "Test::Files" : "0",
         "Tie::Hash::Indexed" : "0",
         "constant" : "0",
         "lib" : "0",
         "namespace::autoclean" : "0",
         "perl" : "5.010",
         "strict" : "0",
         "version" : "0",
         "warnings" : "0"
      }
   }
},
"release_status" : "stable",
"version" : "v0.19.2",
"x_serialization_backend" : "JSON::PP version 2.97001"

META.yml  view on Meta::CPAN

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  Path::Class: '0'
  PerlIO::gzip: '0'
  Pod::Usage: '0'
  Template: '0'
  Test::Deep: '0'
  Test::File::Contents: '0'
  Test::Files: '0'
  Tie::Hash::Indexed: '0'
  constant: '0'
  lib: '0'
  namespace::autoclean: '0'
  perl: '5.010'
  strict: '0'
  version: '0'
  warnings: '0'
version: v0.19.2
x_serialization_backend: 'CPAN::Meta::YAML version 0.018'

Makefile.PL  view on Meta::CPAN

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"File::Temp"                   => '0',
"File::Slurp"                  => '0',
"FindBin"                      => '0',
"IPC::Cmd"                     => '0',
"lib"                          => '0',
"List::Util"                   => '0',
"Moose"                        => '0',
"MooseX::Clone"                => '0',
"Moose::Util::TypeConstraints" => '0',
"Moose::Role"                  => '0',
"namespace::autoclean"         => '0',
"Path::Class"                  => '0',
"Math::Round"                  => '0',
"Params::Coerce"               => '0',
"Pod::Usage"                   => '0',
"PerlIO::gzip"                 => '0',
"POSIX"                        => '0',
"strict"                       => '0',
"Template"                     => '0',
"Test::Files"                  => '0',
"Test::File::Contents"         => '0',

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

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# -*-CPerl-*-
# Last changed Time-stamp: <2017-06-10 18:18:45 michl>
 
package Bio::ViennaNGS::AnnoC;
use Bio::ViennaNGS;
use Bio::ViennaNGS::Util qw(sortbed);
use Bio::Tools::GFF;
use Path::Class;
use Carp;
use Moose;
use namespace::autoclean;
use version; our $VERSION = version->declare(eval($Bio::ViennaNGS::VERSION));
 
has 'accession' => (
                    is => 'rw',
                    isa => 'Str',
                    predicate => 'has_accession',
                   );
 
has 'features' => (
                   is => 'ro',

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

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# -*-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 'https://metacpan.org/pod/Bio::ViennaNGS::Feature">Bio::ViennaNGS::Feature';
 
has '+strand' => (
                  required => 1,
                 );
 
has 'thickStart' => (

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

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# -*-CPerl-*-
# Last changed Time-stamp: <2018-07-03 12:59:06 mtw>
 
package Bio::ViennaNGS::FeatureIntervalN;
 
use version; our $VERSION = version->declare("$Bio::ViennaNGS::VERSION");
use namespace::autoclean;
use Moose;
 
extends 'https://metacpan.org/pod/Bio::ViennaNGS::FeatureInterval">Bio::ViennaNGS::FeatureInterval';
 
has 'name' => (
               is  => 'rw',
               isa => 'Str',
               required => '1',
               predicate => 'has_name',
              );

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

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# -*-CPerl-*-
# Last changed Time-stamp: <2017-06-10 19:03:07 michl>
 
package Bio::ViennaNGS::FeatureLine;
 
use Bio::ViennaNGS;
use Moose;
use namespace::autoclean;
use version; our $VERSION = version->declare("$Bio::ViennaNGS::VERSION");
 
extends 'https://metacpan.org/pod/Bio::ViennaNGS::MinimalFeature">Bio::ViennaNGS::MinimalFeature';
 
has 'id' => (
             is => 'rw',
             isa => 'Str', # e.g. a transcript ID
             required => '1',
            );

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

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# -*-CPerl-*-
# Last changed Time-stamp: <2018-01-09 23:56:32 mtw>
 
package Bio::ViennaNGS::MinimalFeature;
 
use Bio::ViennaNGS;
use namespace::autoclean;
use Moose;
use Bio::ViennaNGS::Subtypes;
use version; our $VERSION = version->declare("$Bio::ViennaNGS::VERSION");
 
extends 'https://metacpan.org/pod/Bio::ViennaNGS::FeatureInterval">Bio::ViennaNGS::FeatureInterval';
 
has 'strand' => (
                 is      => 'rw',
                 isa     => 'Bio::ViennaNGS::PlusOrMinus',
                 default => '.',

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

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package Bio::ViennaNGS::Peak;
 
use Bio::ViennaNGS;
use Moose;
use Carp;
use Data::Dumper;
use Path::Class;
use List::Util qw(sum sum0 min max first);
use Bio::ViennaNGS::Util qw(sortbed);
use namespace::autoclean;
use File::Temp qw(tempfile);
use version; our $VERSION = version->declare("$Bio::ViennaNGS::VERSION");
 
has 'data' => (
               is => 'ro',
               isa => 'HashRef',
               predicate => 'has_data',
               default => sub { {} },
              );

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