Bio-MUST-Core
31 results

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META.yml  view on Meta::CPAN 

  Test::Files: '0'
  Test::Most: '0'
  Tie::IxHash: '0'
  Try::Tiny: '0'
  Try::Tiny::Warnings: '0'
  XML::Bare: '0.53'
  YAML::XS: '0'
  aliased: '0'
  autodie: '0'
  feature: '0'
  namespace::autoclean: '0'
  perl: '5.013002'
  strict: '0'
  warnings: '0'
version: '0.250380'
x_generated_by_perl: v5.26.3
x_serialization_backend: 'YAML::Tiny version 1.76'
x_spdx_expression: 'Artistic-1.0-Perl OR GPL-1.0-or-later'

Makefile.PL  view on Meta::CPAN 

    "Test::Files" => 0,
    "Test::Most" => 0,
    "Tie::IxHash" => 0,
    "Try::Tiny" => 0,
    "Try::Tiny::Warnings" => 0,
    "XML::Bare" => "0.53",
    "YAML::XS" => 0,
    "aliased" => 0,
    "autodie" => 0,
    "feature" => 0,
    "namespace::autoclean" => 0,
    "strict" => 0,
    "warnings" => 0
  },
  "TEST_REQUIRES" => {
    "Test::Deep" => 0
  },
  "VERSION" => "0.250380",
  "test" => {
    "TESTS" => "t/*.t"
  }

lib/Bio/MUST/Core/Ali/Stash.pm  view on Meta::CPAN 

package Bio::MUST::Core::Ali::Stash;
# ABSTRACT: Thin wrapper for an indexed Ali read from disk
$Bio::MUST::Core::Ali::Stash::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments;

use Carp;

use Bio::MUST::Core::Types;
use Bio::MUST::Core::Constants qw(:seqids);

lib/Bio/MUST/Core/Ali/Temporary.pm  view on Meta::CPAN 

package Bio::MUST::Core::Ali::Temporary;
# ABSTRACT: Thin wrapper for a temporary mapped Ali written on disk
$Bio::MUST::Core::Ali::Temporary::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Path::Class qw(file);

use Bio::MUST::Core::Types;

# Note: tried to implement it as a subclass of Bio::MUST::Core::Ali but this
# led to issues: (1) coercions became a nightmare and (2) the temp_fasta was

lib/Bio/MUST/Core/GeneticCode.pm  view on Meta::CPAN 

package Bio::MUST::Core::GeneticCode;
# ABSTRACT: Genetic code for conceptual translation
$Bio::MUST::Core::GeneticCode::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Bio::MUST::Core::Constants qw(:gaps);
use aliased 'Bio::MUST::Core::Seq';


has 'ncbi_id' => (
    is       => 'ro',

lib/Bio/MUST/Core/GeneticCode/Factory.pm  view on Meta::CPAN 

package Bio::MUST::Core::GeneticCode::Factory;
# ABSTRACT: Genetic code factory based on NCBI gc.prt file
$Bio::MUST::Core::GeneticCode::Factory::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

# AUTOGENERATED CODE! DO NOT MODIFY THIS FILE!

use autodie;
use feature qw(say);

use Carp;
use Const::Fast;
use File::Spec;
use List::AllUtils qw(uniq);

lib/Bio/MUST/Core/IdList.pm  view on Meta::CPAN 

package Bio::MUST::Core::IdList;
# ABSTRACT: Id list for selecting specific sequences
$Bio::MUST::Core::IdList::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

# use Smart::Comments;

use Carp;

use Bio::MUST::Core::Types;
use Bio::MUST::Core::Constants qw(:files);

lib/Bio/MUST/Core/IdMapper.pm  view on Meta::CPAN 

package Bio::MUST::Core::IdMapper;
# ABSTRACT: Id mapper for translating sequence ids
$Bio::MUST::Core::IdMapper::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Carp;
use List::AllUtils qw(mesh uniq each_array);

use Bio::MUST::Core::Types;
use Bio::MUST::Core::Constants qw(:files);
use aliased 'Bio::MUST::Core::SeqId';

lib/Bio/MUST/Core/PostPred.pm  view on Meta::CPAN 

package Bio::MUST::Core::PostPred;
# ABSTRACT: Posterior predictive tests for sequences
$Bio::MUST::Core::PostPred::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

# use Smart::Comments;

use Statistics::Descriptive;
use Tie::IxHash;

use Bio::MUST::Core::Types;

lib/Bio/MUST/Core/PostPred/Composition.pm  view on Meta::CPAN 

package Bio::MUST::Core::PostPred::Composition;
# ABSTRACT: Posterior predictive test for compositional bias
$Bio::MUST::Core::PostPred::Composition::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

# use Smart::Comments;

use List::AllUtils qw(sum);
use Tie::IxHash;

use Bio::MUST::Core::Types;

lib/Bio/MUST/Core/Seq.pm  view on Meta::CPAN 

package Bio::MUST::Core::Seq;
# ABSTRACT: Nucleotide or protein sequence
# CONTRIBUTOR: Catherine COLSON <ccolson@doct.uliege.be>
# CONTRIBUTOR: Arnaud DI FRANCO <arnaud.difranco@gmail.com>
# CONTRIBUTOR: Valerian LUPO <valerian.lupo@doct.uliege.be>
$Bio::MUST::Core::Seq::VERSION = '0.250380';
use Moose;
use MooseX::SemiAffordanceAccessor;
use namespace::autoclean;

# use Smart::Comments '###';

use autodie;
use feature qw(say);

use Carp;

use Bio::MUST::Core::Types;
use Bio::MUST::Core::Constants qw(:seqtypes :seqids :gaps);

lib/Bio/MUST/Core/SeqId.pm  view on Meta::CPAN 

package Bio::MUST::Core::SeqId;
# ABSTRACT: Modern and legacy MUST-compliant sequence id
# CONTRIBUTOR: Mick VAN VLIERBERGHE <mvanvlierberghe@doct.uliege.be>
$Bio::MUST::Core::SeqId::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

# AUTOGENERATED CODE! DO NOT MODIFY THIS FILE!

use autodie;
use feature qw(say);

# use Smart::Comments;

use Carp;
use Const::Fast;

lib/Bio/MUST/Core/SeqId/Filter.pm  view on Meta::CPAN 

package Bio::MUST::Core::SeqId::Filter;
# ABSTRACT: Helper class for filtering seqs according to SeqId components
$Bio::MUST::Core::SeqId::Filter::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments '###';

use Bio::MUST::Core::Types;
with 'Bio::MUST::Core::Roles::Filterable';

lib/Bio/MUST/Core/SeqMask.pm  view on Meta::CPAN 

package Bio::MUST::Core::SeqMask;
# ABSTRACT: Sequence mask for selecting specific sites
# CONTRIBUTOR: Catherine COLSON <ccolson@doct.uliege.be>
# CONTRIBUTOR: Raphael LEONARD <rleonard@doct.uliege.be>
$Bio::MUST::Core::SeqMask::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

# use Smart::Comments '###';

use Carp;
use File::Basename;
use IPC::System::Simple qw(system);
use List::AllUtils 0.08 qw(uniq max sum natatime first_index last_index pairmap mesh bundle_by);

lib/Bio/MUST/Core/SeqMask/Freqs.pm  view on Meta::CPAN 

package Bio::MUST::Core::SeqMask::Freqs;
# ABSTRACT: Arbitrary frequencies for sequence sites
$Bio::MUST::Core::SeqMask::Freqs::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use List::AllUtils qw(sum);

use Bio::MUST::Core::Types;
use aliased 'Bio::MUST::Core::SeqMask::Rates';

lib/Bio/MUST/Core/SeqMask/Pmsf.pm  view on Meta::CPAN 

package Bio::MUST::Core::SeqMask::Pmsf;
# ABSTRACT: Posterior mean site frequencies (PMSF) for sequence sites
$Bio::MUST::Core::SeqMask::Pmsf::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Carp;
use List::AllUtils qw(sum each_arrayref);

extends 'Bio::MUST::Core::SeqMask';

use Bio::MUST::Core::Types;

lib/Bio/MUST/Core/SeqMask/Profiles.pm  view on Meta::CPAN 

package Bio::MUST::Core::SeqMask::Profiles;
# ABSTRACT: Evolutionary profiles for sequence sites
$Bio::MUST::Core::SeqMask::Profiles::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Carp;
use Const::Fast;
use Tie::IxHash;

extends 'Bio::MUST::Core::SeqMask';

lib/Bio/MUST/Core/SeqMask/Rates.pm  view on Meta::CPAN 

package Bio::MUST::Core::SeqMask::Rates;
# ABSTRACT: Evolutionary rates for sequence sites
$Bio::MUST::Core::SeqMask::Rates::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

# use Smart::Comments;

use Carp;
use Const::Fast;
use List::AllUtils qw(each_arrayref);
use POSIX;

lib/Bio/MUST/Core/SeqMask/Weights.pm  view on Meta::CPAN 

package Bio::MUST::Core::SeqMask::Weights;
# ABSTRACT: Random weights for resampling sequence sites
$Bio::MUST::Core::SeqMask::Weights::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

# use Smart::Comments;

use List::AllUtils qw(sample);
use POSIX;

extends 'Bio::MUST::Core::SeqMask';

lib/Bio/MUST/Core/Taxonomy.pm  view on Meta::CPAN 

package Bio::MUST::Core::Taxonomy;
# ABSTRACT: NCBI Taxonomy one-stop shop
# CONTRIBUTOR: Loic MEUNIER <loic.meunier@doct.uliege.be>
# CONTRIBUTOR: Mick VAN VLIERBERGHE <mvanvlierberghe@doct.uliege.be>
$Bio::MUST::Core::Taxonomy::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments '###';

use MooseX::Storage;
with Storage('io' => 'StorableFile');

use Moose::Util::TypeConstraints;

lib/Bio/MUST/Core/Taxonomy/Category.pm  view on Meta::CPAN 

package Bio::MUST::Core::Taxonomy::Category;
# ABSTRACT: Helper class for multiple-criterion classifier based on taxonomy
$Bio::MUST::Core::Taxonomy::Category::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use Bio::MUST::Core::Types;


has 'label' => (
    is       => 'ro',
    isa      => 'Str',
    required => 1,
);

lib/Bio/MUST/Core/Taxonomy/Classifier.pm  view on Meta::CPAN 

package Bio::MUST::Core::Taxonomy::Classifier;
# ABSTRACT: Helper class for multiple-criterion classifier based on taxonomy
$Bio::MUST::Core::Taxonomy::Classifier::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

# use Smart::Comments;

use Const::Fast;
use List::AllUtils qw(indexes mesh partition_by pairmap);

use Bio::MUST::Core::Types;
use aliased 'Bio::MUST::Core::IdList';
use aliased 'Bio::MUST::Core::SeqMask';

lib/Bio/MUST/Core/Taxonomy/ColorScheme.pm  view on Meta::CPAN 

package Bio::MUST::Core::Taxonomy::ColorScheme;
# ABSTRACT: Helper class providing color scheme for taxonomic annotations
# CONTRIBUTOR: Valerian LUPO <valerian.lupo@doct.uliege.be>
$Bio::MUST::Core::Taxonomy::ColorScheme::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use Smart::Comments '###';

use autodie;
use feature qw(say);

use Carp;
# use Color::Spectrum::Multi;
use Const::Fast;
use Graphics::ColorNames;

lib/Bio/MUST/Core/Taxonomy/Criterion.pm  view on Meta::CPAN 

package Bio::MUST::Core::Taxonomy::Criterion;
# ABSTRACT: Helper class for multiple-criterion classifier based on taxonomy
$Bio::MUST::Core::Taxonomy::Criterion::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use List::AllUtils qw(sum count_by);

use Bio::MUST::Core::Types;


has 'tax_filter' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::Taxonomy::Filter',
    required => 1,

lib/Bio/MUST/Core/Taxonomy/Filter.pm  view on Meta::CPAN 

package Bio::MUST::Core::Taxonomy::Filter;
# ABSTRACT: Helper class for filtering seqs according to taxonomy
$Bio::MUST::Core::Taxonomy::Filter::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments '###';

use List::AllUtils;

use Bio::MUST::Core::Types;
use aliased 'Bio::MUST::Core::IdList';

lib/Bio/MUST/Core/Taxonomy/Labeler.pm  view on Meta::CPAN 

package Bio::MUST::Core::Taxonomy::Labeler;
# ABSTRACT: Helper class for simple labeler based on taxonomy
$Bio::MUST::Core::Taxonomy::Labeler::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use Carp;

use Bio::MUST::Core::Types;
with 'Bio::MUST::Core::Roles::Taxable';


has 'labels' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::IdList',

lib/Bio/MUST/Core/Taxonomy/MooseNCBI.pm  view on Meta::CPAN 

package Bio::MUST::Core::Taxonomy::MooseNCBI;
# ABSTRACT: Wrapper class for serializing Bio::LITE::Taxonomy::NCBI object
$Bio::MUST::Core::Taxonomy::MooseNCBI::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use MooseX::NonMoose;

use Bio::LITE::Taxonomy::NCBI 0.10;         # for handling synonyms
extends 'Bio::LITE::Taxonomy::NCBI';

use Smart::Comments;


## no critic (ProhibitBuiltinHomonyms)

lib/Bio/MUST/Core/Tree.pm  view on Meta::CPAN 

package Bio::MUST::Core::Tree;
# ABSTRACT: Thin wrapper around Bio::Phylo trees
# CONTRIBUTOR: Valerian LUPO <valerian.lupo@doct.uliege.be>
$Bio::MUST::Core::Tree::VERSION = '0.250380';
use Moose;
# use MooseX::SemiAffordanceAccessor;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments '###';

use Carp;
use Const::Fast;
use File::Basename;
use List::AllUtils qw(uniq max_by);

lib/Bio/MUST/Core/Tree/Forest.pm  view on Meta::CPAN 

package Bio::MUST::Core::Tree::Forest;
# ABSTRACT: Collection of (bootstrap) trees
$Bio::MUST::Core::Tree::Forest::VERSION = '0.250380';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Bio::Phylo::IO qw(parse);

use Bio::MUST::Core::Types;
use aliased 'Bio::MUST::Core::Tree';

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