Bio-MUST-Apps-FortyTwo

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META.yml  view on Meta::CPAN

  Sort::Naturally: '0'
  Template: '0'
  Term::Completion::Path: '0'
  Test::Deep::NoTest: '0'
  Test::Most: '0'
  Tie::IxHash: '0'
  aliased: '0'
  autodie: '0'
  experimental: '0'
  feature: '0'
  namespace::autoclean: '0'
  perl: '5.013002'
version: '0.213470'
x_generated_by_perl: v5.26.3
x_serialization_backend: 'YAML::Tiny version 1.73'
x_spdx_expression: 'Artistic-1.0-Perl OR GPL-1.0-or-later'

Makefile.PL  view on Meta::CPAN

    "Sort::Naturally" => 0,
    "Template" => 0,
    "Term::Completion::Path" => 0,
    "Test::Deep::NoTest" => 0,
    "Test::Most" => 0,
    "Tie::IxHash" => 0,
    "aliased" => 0,
    "autodie" => 0,
    "experimental" => 0,
    "feature" => 0,
    "namespace::autoclean" => 0
  },
  "TEST_REQUIRES" => {
    "Test::Files" => 0,
    "Test::Most" => 0
  },
  "VERSION" => "0.213470",
  "test" => {
    "TESTS" => "t/*.t"
  }
);

lib/Bio/MUST/Apps/Debrief42/OrgReport.pm  view on Meta::CPAN

package Bio::MUST::Apps::Debrief42::OrgReport;
# ABSTRACT: Internal class for tabular tax-report parser
# CONTRIBUTOR: Mick VAN VLIERBERGHE <mvanvlierberghe@doct.uliege.be>
$Bio::MUST::Apps::Debrief42::OrgReport::VERSION = '0.213470';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Bio::MUST::Core;
use aliased 'Bio::MUST::Core::SeqId';
use aliased 'Bio::MUST::Apps::Debrief42::TaxReport';


has 'org' => (

lib/Bio/MUST/Apps/Debrief42/RunReport.pm  view on Meta::CPAN

package Bio::MUST::Apps::Debrief42::RunReport;
# ABSTRACT: Internal class for tabular tax-report parser
# CONTRIBUTOR: Mick VAN VLIERBERGHE <mvanvlierberghe@doct.uliege.be>
$Bio::MUST::Apps::Debrief42::RunReport::VERSION = '0.213470';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Path::Class qw(file);
use Tie::IxHash;

use Bio::MUST::Core;
use aliased 'Bio::MUST::Core::SeqId';
use aliased 'Bio::MUST::Apps::Debrief42::TaxReport';

lib/Bio/MUST/Apps/Debrief42/TaxReport.pm  view on Meta::CPAN

package Bio::MUST::Apps::Debrief42::TaxReport;
# ABSTRACT: Front-end class for tabular tax-report parser
# CONTRIBUTOR: Mick VAN VLIERBERGHE <mvanvlierberghe@doct.uliege.be>
$Bio::MUST::Apps::Debrief42::TaxReport::VERSION = '0.213470';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use List::AllUtils qw(mesh);

extends 'Bio::FastParsers::Base';

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(change_suffix);

lib/Bio/MUST/Apps/Debrief42/TaxReport/NewSeq.pm  view on Meta::CPAN

package Bio::MUST::Apps::Debrief42::TaxReport::NewSeq;
# ABSTRACT: Internal class for tabular tax-report parser
# CONTRIBUTOR: Mick VAN VLIERBERGHE <mvanvlierberghe@doct.uliege.be>
$Bio::MUST::Apps::Debrief42::TaxReport::NewSeq::VERSION = '0.213470';
use Moose;
use namespace::autoclean;


# public attributes

has $_ => (
    is       => 'ro',
    isa      => 'Maybe[Str]',
    required => 1,
) for qw( seq_id contam_org lca lineage acc seq );

lib/Bio/MUST/Apps/FortyTwo.pm  view on Meta::CPAN

package Bio::MUST::Apps::FortyTwo;
# ABSTRACT: Main class for forty-two tool
# CONTRIBUTOR: Mick VAN VLIERBERGHE <mvanvlierberghe@doct.uliege.be>
$Bio::MUST::Apps::FortyTwo::VERSION = '0.213470';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments -ENV;

use aliased 'Bio::MUST::Apps::FortyTwo::RunProcessor';

with 'Bio::MUST::Apps::Roles::Configable';

lib/Bio/MUST/Apps/FortyTwo/AliProcessor.pm  view on Meta::CPAN

package Bio::MUST::Apps::FortyTwo::AliProcessor;
# ABSTRACT: Internal class for forty-two tool
$Bio::MUST::Apps::FortyTwo::AliProcessor::VERSION = '0.213470';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments -ENV;

use Carp;
use Const::Fast;
use File::Basename;
use List::AllUtils qw(first part partition_by pairmap);

lib/Bio/MUST/Apps/FortyTwo/OrgProcessor.pm  view on Meta::CPAN

package Bio::MUST::Apps::FortyTwo::OrgProcessor;
# ABSTRACT: Internal class for forty-two tool
$Bio::MUST::Apps::FortyTwo::OrgProcessor::VERSION = '0.213470';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments -ENV;

use Carp;
use Const::Fast;
use List::AllUtils qw(each_array pairmap);
use Path::Class qw(file);

lib/Bio/MUST/Apps/FortyTwo/RunProcessor.pm  view on Meta::CPAN

package Bio::MUST::Apps::FortyTwo::RunProcessor;
# ABSTRACT: Internal class for forty-two tool
$Bio::MUST::Apps::FortyTwo::RunProcessor::VERSION = '0.213470';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments;                    # logging always enabled here

use Carp;
use List::AllUtils;
use Path::Class qw(dir file);

lib/Bio/MUST/Apps/Leel.pm  view on Meta::CPAN

package Bio::MUST::Apps::Leel;
# ABSTRACT: Main class for leel tool
$Bio::MUST::Apps::Leel::VERSION = '0.213470';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments -ENV;

use aliased 'Bio::MUST::Apps::Leel::RunProcessor';

with 'Bio::MUST::Apps::Roles::Configable';

lib/Bio/MUST/Apps/Leel/AliProcessor.pm  view on Meta::CPAN

package Bio::MUST::Apps::Leel::AliProcessor;
# ABSTRACT: Internal class for leel tool
$Bio::MUST::Apps::Leel::AliProcessor::VERSION = '0.213470';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments -ENV;

use Carp;
use File::Basename;
use List::AllUtils 'uniq';
use Path::Class qw(file);

lib/Bio/MUST/Apps/Leel/OrgProcessor.pm  view on Meta::CPAN

package Bio::MUST::Apps::Leel::OrgProcessor;
# ABSTRACT: Internal class for leel tool
$Bio::MUST::Apps::Leel::OrgProcessor::VERSION = '0.213470';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments -ENV;

use Carp;
use Path::Class qw(file);
use Tie::IxHash;

lib/Bio/MUST/Apps/Leel/RunProcessor.pm  view on Meta::CPAN

package Bio::MUST::Apps::Leel::RunProcessor;
# ABSTRACT: Internal class for leel tool
$Bio::MUST::Apps::Leel::RunProcessor::VERSION = '0.213470';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments;                    # logging always enabled here

use Path::Class qw(dir);

use Parallel::Batch;

lib/Bio/MUST/Apps/SlaveAligner/Local.pm  view on Meta::CPAN

package Bio::MUST::Apps::SlaveAligner::Local;
# ABSTRACT: Internal class for slave-aligner
$Bio::MUST::Apps::SlaveAligner::Local::VERSION = '0.213470';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say switch);
use experimental qw(smartmatch);        # to suppress warnings about 'when'

use Smart::Comments -ENV;

use List::AllUtils qw(max);
use Sort::Naturally;

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