Bio-RNA-RNAaliSplit

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META.json  view on Meta::CPAN

            "Path::Class" : "0",
            "Path::Class::Dir" : "0",
            "Path::Class::File" : "0",
            "Pod::Usage" : "0",
            "RNA" : "v2.3.4",
            "Storable" : "0",
            "Test::Script" : "1.25",
            "constant" : "0",
            "diagnostics" : "0",
            "lib" : "0",
            "namespace::autoclean" : "0",
            "perl" : "5.01",
            "strict" : "0",
            "version" : "0",
            "warnings" : "0"
         }
      },
      "test" : {
         "requires" : {
            "Test2::V0" : "0.000060",
            "Test::More" : "0",

META.yml  view on Meta::CPAN

  Path::Class: '0'
  Path::Class::Dir: '0'
  Path::Class::File: '0'
  Pod::Usage: '0'
  RNA: v2.3.4
  Storable: '0'
  Test::Script: '1.25'
  constant: '0'
  diagnostics: '0'
  lib: '0'
  namespace::autoclean: '0'
  perl: '5.01'
  strict: '0'
  version: '0'
  warnings: '0'
resources:
  bugtracker: https://github.com/mtw/Bio-RNA-RNAaliSplit/issues
  homepage: https://github.com/mtw/Bio-RNA-RNAaliSplit
  repository: https://github.com/mtw/Bio-RNA-RNAaliSplit.git
version: v0.11
x_serialization_backend: 'CPAN::Meta::YAML version 0.018'

Makefile.PL  view on Meta::CPAN

				     "Moose::Util::TypeConstraints" => '0',
				     "Params::Coerce" => 0,
				     "Path::Class" => '0',
				     "Path::Class::Dir" => '0',
				     "Path::Class::File" => '0',
				     "Pod::Usage" => '0',
				     "RNA" => "2.3.4",
				     "Storable" => '0',
				     "Test::Script" => '1.25',
				     "FileDirUtil" => '0',
				     "namespace::autoclean" => '0',
				    },
	      'EXE_FILES'        => [ map { "scripts/$_" } @scripts ],
	      'META_MERGE'       => {
				     'meta-spec' => { version => 2 },
				     resources => {
						   repository => {
								  type => 'git',
								  url  => "https://github.com/mtw/Bio-RNA-RNAaliSplit.git",
								  web  => "https://github.com/mtw/Bio-RNA-RNAaliSplit",
								 },

lib/Bio/RNA/RNAaliSplit/AliFeature.pm  view on Meta::CPAN

# -*-CPerl-*-
# Last changed Time-stamp: <2019-04-24 00:47:47 mtw>
#
#  Derive features of an alignment, in particular scores to compare
#  different alignments of the same sequences

package Bio::RNA::RNAaliSplit::AliFeature;

use Moose;
use namespace::autoclean;
use version; our $VERSION = qv('0.11');
use diagnostics;
use Data::Dumper;
use Carp;

extends 'Bio::RNA::RNAaliSplit::AliHandler';

has 'sop' => ( # sum of pairs score
	      is => 'rw',
	      isa => 'Int',

lib/Bio/RNA/RNAaliSplit/AliHandler.pm  view on Meta::CPAN

# -*-CPerl-*-
# Last changed Time-stamp: <2019-04-24 00:49:39 mtw>
#
# This a base class for handling alignment files in different formats

package Bio::RNA::RNAaliSplit::AliHandler;

use Moose;
use Bio::RNA::RNAaliSplit::Subtypes;
use namespace::autoclean;
use Data::Dumper;
use diagnostics;
use version; our $VERSION = qv('0.11');

has 'format' => (
                 is => 'ro',
                 isa => 'Str',
                 predicate => 'has_format',
                 default => 'ClustalW',
                 required => 1,

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