Bio-Protease

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Build.PL  view on Meta::CPAN

  "recommends" => {},
  "recursive_test_files" => 1,
  "requires" => {
    "Cache::Ref::LRU" => 0,
    "Carp" => 0,
    "Moose" => "1.23",
    "Moose::Role" => 0,
    "MooseX::ClassAttribute" => 0,
    "MooseX::Types" => 0,
    "MooseX::Types::Moose" => 0,
    "namespace::autoclean" => 0
  },
  "script_files" => []
);


my $build = Module::Build->new(%module_build_args);

$build->create_build_script;

META.json  view on Meta::CPAN

      },
      "runtime" : {
         "requires" : {
            "Cache::Ref::LRU" : 0,
            "Carp" : 0,
            "Moose" : "1.23",
            "Moose::Role" : 0,
            "MooseX::ClassAttribute" : 0,
            "MooseX::Types" : 0,
            "MooseX::Types::Moose" : 0,
            "namespace::autoclean" : 0
         }
      },
      "test" : {
         "requires" : {
            "Cache::Ref::Null" : 0,
            "Modern::Perl" : 0,
            "Test::Exception" : 0,
            "Test::More" : 0,
            "Time::HiRes" : 0,
            "YAML::Any" : 0,

lib/Bio/Protease.pm  view on Meta::CPAN

package Bio::Protease;
{
  $Bio::Protease::VERSION = '1.112980';
}

# ABSTRACT: Digest your protein substrates with customizable specificity

use Moose 1.23;
use MooseX::ClassAttribute;
use Bio::Protease::Types qw(ProteaseRegex ProteaseName);
use namespace::autoclean;

with qw(
    Bio::ProteaseI
    Bio::Protease::Role::Specificity::Regex
    Bio::Protease::Role::WithCache
);

has '+regex' => ( init_arg => 'specificity' );

has specificity => (

lib/Bio/Protease/Role/WithCache.pm  view on Meta::CPAN

package Bio::Protease::Role::WithCache;
{
  $Bio::Protease::Role::WithCache::VERSION = '1.112980';
}

# ABSTRACT: A role that adds optional memoization of ProteaseI methods

use Moose::Role;
use MooseX::Types::Moose 'Bool';
use namespace::autoclean;

has use_cache => ( is => 'ro', isa => Bool, default => 0 );

has cache => (
    is        => 'ro',
    lazy      => 1,
    does      => 'Cache::Ref::Role::API',
    predicate => '_has_cache',
    default =>
      sub { require Cache::Ref::LRU; Cache::Ref::LRU->new( size => 5000 ) },

lib/Bio/Protease/Types.pm  view on Meta::CPAN

package Bio::Protease::Types;
{
  $Bio::Protease::Types::VERSION = '1.112980';
}

# ABSTRACT: Specific types for Bio::Protease

use MooseX::Types::Moose qw(Str ArrayRef RegexpRef Any);
use MooseX::Types -declare => [qw(ProteaseName ProteaseRegex)];
use namespace::autoclean;
use Carp qw(croak);

subtype ProteaseName, as Str;

subtype ProteaseRegex, as ArrayRef;

coerce ProteaseRegex,
    from Str,       via { _str_to_prot_regex($_) },
    from RegexpRef, via { [ $_ ] };

lib/Bio/ProteaseI.pm  view on Meta::CPAN

package Bio::ProteaseI;
{
  $Bio::ProteaseI::VERSION = '1.112980';
}

# ABSTRACT: A role to build your customized Protease

use Moose::Role;
use Carp 'croak';
use namespace::autoclean;

requires '_cuts';

sub cut {
    my ( $self, $substrate, $pos ) = @_;

    croak "Incorrect substrate argument"
        unless ( defined $substrate and _looks_like_string($substrate) );

    unless ( defined $pos and $pos > 0 and $pos <= length $substrate ) {

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