Bio-FastParsers

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META.yml  view on Meta::CPAN

  Path::Class: '0'
  Smart::Comments: '0'
  Sort::Naturally: '0'
  Test::Most: '0'
  Tie::IxHash: '0'
  Try::Tiny: '0'
  XML::Bare: '0.53'
  aliased: '0'
  autodie: '0'
  feature: '0'
  namespace::autoclean: '0'
  perl: v5.10.0
  strict: '0'
  warnings: '0'
version: '0.221230'
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

    "Path::Class" => 0,
    "Smart::Comments" => 0,
    "Sort::Naturally" => 0,
    "Test::Most" => 0,
    "Tie::IxHash" => 0,
    "Try::Tiny" => 0,
    "XML::Bare" => "0.53",
    "aliased" => 0,
    "autodie" => 0,
    "feature" => 0,
    "namespace::autoclean" => 0,
    "strict" => 0,
    "warnings" => 0
  },
  "TEST_REQUIRES" => {
    "Test::Most" => 0
  },
  "VERSION" => "0.221230",
  "test" => {
    "TESTS" => "t/*.t"
  }

lib/Bio/FastParsers/Blast/Table.pm  view on Meta::CPAN

package Bio::FastParsers::Blast::Table;
# ABSTRACT: Front-end class for tabular BLAST parser
$Bio::FastParsers::Blast::Table::VERSION = '0.221230';
use Moose;
use namespace::autoclean;

use autodie;

use List::AllUtils qw(mesh);

extends 'Bio::FastParsers::Base';

use Bio::FastParsers::Constants qw(:files);
use aliased 'Bio::FastParsers::Blast::Table::Hsp';

lib/Bio/FastParsers/Blast/Table/Hsp.pm  view on Meta::CPAN

package Bio::FastParsers::Blast::Table::Hsp;
# ABSTRACT: Internal class for tabular BLAST parser
$Bio::FastParsers::Blast::Table::Hsp::VERSION = '0.221230';
use Moose;
use namespace::autoclean;


# public attributes

has $_ => (
    is       => 'ro',
    isa      => 'Str',
    required => 1,
) for qw(query_id hit_id);

lib/Bio/FastParsers/Blast/Xml.pm  view on Meta::CPAN

package Bio::FastParsers::Blast::Xml;
# ABSTRACT: Front-end class for XML BLAST parser
# CONTRIBUTOR: Aymeric NAOME <aymeric.naome@gmail.com>
$Bio::FastParsers::Blast::Xml::VERSION = '0.221230';
use Moose;
use namespace::autoclean;

use Carp;
use XML::Bare;

extends 'Bio::FastParsers::Base';

use aliased 'Bio::FastParsers::Blast::Xml::BlastOutput';

# TODO: check behavior with single iterations, hits or hsps

lib/Bio/FastParsers/Blast/Xml/BlastOutput.pm  view on Meta::CPAN

package Bio::FastParsers::Blast::Xml::BlastOutput;
# ABSTRACT: NCBI BLAST DTD-derived internal class
$Bio::FastParsers::Blast::Xml::BlastOutput::VERSION = '0.221230';
use Moose;
use namespace::autoclean;

# AUTOGENERATED CODE! DO NOT MODIFY THIS FILE!

use XML::Bare qw(forcearray);

use aliased 'Bio::FastParsers::Blast::Xml::Iteration';
use aliased 'Bio::FastParsers::Blast::Xml::Statistics';
use aliased 'Bio::FastParsers::Blast::Xml::Parameters';

lib/Bio/FastParsers/Blast/Xml/Hit.pm  view on Meta::CPAN

package Bio::FastParsers::Blast::Xml::Hit;
# ABSTRACT: NCBI BLAST DTD-derived internal class
$Bio::FastParsers::Blast::Xml::Hit::VERSION = '0.221230';
use Moose;
use namespace::autoclean;

# AUTOGENERATED CODE! DO NOT MODIFY THIS FILE!

use XML::Bare qw(forcearray);

use aliased 'Bio::FastParsers::Blast::Xml::Hsp';


# private attributes

lib/Bio/FastParsers/Blast/Xml/Hsp.pm  view on Meta::CPAN

package Bio::FastParsers::Blast::Xml::Hsp;
# ABSTRACT: NCBI BLAST DTD-derived internal class
$Bio::FastParsers::Blast::Xml::Hsp::VERSION = '0.221230';
use Moose;
use namespace::autoclean;

# AUTOGENERATED CODE! DO NOT MODIFY THIS FILE!

use XML::Bare qw(forcearray);



# private attributes

has '_root' => (

lib/Bio/FastParsers/Blast/Xml/Iteration.pm  view on Meta::CPAN

package Bio::FastParsers::Blast::Xml::Iteration;
# ABSTRACT: NCBI BLAST DTD-derived internal class
$Bio::FastParsers::Blast::Xml::Iteration::VERSION = '0.221230';
use Moose;
use namespace::autoclean;

# AUTOGENERATED CODE! DO NOT MODIFY THIS FILE!

use XML::Bare qw(forcearray);

use aliased 'Bio::FastParsers::Blast::Xml::Hit';
use aliased 'Bio::FastParsers::Blast::Xml::Statistics';


# private attributes

lib/Bio/FastParsers/Blast/Xml/Parameters.pm  view on Meta::CPAN

package Bio::FastParsers::Blast::Xml::Parameters;
# ABSTRACT: NCBI BLAST DTD-derived internal class
$Bio::FastParsers::Blast::Xml::Parameters::VERSION = '0.221230';
use Moose;
use namespace::autoclean;

# AUTOGENERATED CODE! DO NOT MODIFY THIS FILE!

use XML::Bare qw(forcearray);



# private attributes

has '_root' => (

lib/Bio/FastParsers/Blast/Xml/Statistics.pm  view on Meta::CPAN

package Bio::FastParsers::Blast::Xml::Statistics;
# ABSTRACT: NCBI BLAST DTD-derived internal class
$Bio::FastParsers::Blast::Xml::Statistics::VERSION = '0.221230';
use Moose;
use namespace::autoclean;

# AUTOGENERATED CODE! DO NOT MODIFY THIS FILE!

use XML::Bare qw(forcearray);



# private attributes

has '_root' => (

lib/Bio/FastParsers/CdHit.pm  view on Meta::CPAN

package Bio::FastParsers::CdHit;
# ABSTRACT: Front-end class for CD-HIT parser
# CONTRIBUTOR: Amandine BERTRAND <amandine.bertrand@doct.uliege.be>
$Bio::FastParsers::CdHit::VERSION = '0.221230';
use Moose;
use namespace::autoclean;

use autodie;

use Tie::IxHash;

extends 'Bio::FastParsers::Base';


# public attributes (inherited)

lib/Bio/FastParsers/Hmmer/DomTable.pm  view on Meta::CPAN

package Bio::FastParsers::Hmmer::DomTable;
# ABSTRACT: Front-end class for tabular HMMER domain parser
# CONTRIBUTOR: Arnaud DI FRANCO <arnaud.difranco@gmail.com>
$Bio::FastParsers::Hmmer::DomTable::VERSION = '0.221230';
use Moose;
use namespace::autoclean;

use autodie;

use List::AllUtils qw(mesh);

extends 'Bio::FastParsers::Base';

use Bio::FastParsers::Constants qw(:files);
use aliased 'Bio::FastParsers::Hmmer::DomTable::Hit';

lib/Bio/FastParsers/Hmmer/DomTable/Hit.pm  view on Meta::CPAN

package Bio::FastParsers::Hmmer::DomTable::Hit;
# ABSTRACT: Internal class for tabular HMMER domain parser
# CONTRIBUTOR: Arnaud DI FRANCO <arnaud.difranco@gmail.com>
$Bio::FastParsers::Hmmer::DomTable::Hit::VERSION = '0.221230';
use Moose;
use namespace::autoclean;

# public attributes

has $_ => (
    is       => 'ro',
    isa      => 'Str',
    required => 1,
) for qw(target_name query_name);

has $_ => (

lib/Bio/FastParsers/Hmmer/Model.pm  view on Meta::CPAN

package Bio::FastParsers::Hmmer::Model;
# ABSTRACT: Internal class for HMMER parser
# CONTRIBUTOR: Arnaud DI FRANCO <arnaud.difranco@gmail.com>
$Bio::FastParsers::Hmmer::Model::VERSION = '0.221230';
use Moose;
use namespace::autoclean;

use autodie;

use Carp;
use Path::Class;

use Smart::Comments;
use List::AllUtils qw(firstidx);

extends 'Bio::FastParsers::Base';

lib/Bio/FastParsers/Hmmer/Standard.pm  view on Meta::CPAN

package Bio::FastParsers::Hmmer::Standard;
# ABSTRACT: Front-end class for standard HMMER parser
# CONTRIBUTOR: Arnaud DI FRANCO <arnaud.difranco@gmail.com>
$Bio::FastParsers::Hmmer::Standard::VERSION = '0.221230';
use Moose;
use namespace::autoclean;

# TODO: check if autodie is actually needed here
use autodie;

use List::AllUtils qw(indexes firstidx mesh);

extends 'Bio::FastParsers::Base';

use Bio::FastParsers::Constants qw(:files);
use aliased 'Bio::FastParsers::Hmmer::Standard::Iteration';

lib/Bio/FastParsers/Hmmer/Standard/Domain.pm  view on Meta::CPAN

package Bio::FastParsers::Hmmer::Standard::Domain;
# ABSTRACT: Internal class for standard HMMER parser
# CONTRIBUTOR: Arnaud DI FRANCO <arnaud.difranco@gmail.com>
$Bio::FastParsers::Hmmer::Standard::Domain::VERSION = '0.221230';
use Moose;
use namespace::autoclean;

use List::AllUtils qw(mesh);


# public attributes

has $_ => (
    is       => 'ro',
    isa      => 'Str',
    required => 1,

lib/Bio/FastParsers/Hmmer/Standard/Iteration.pm  view on Meta::CPAN

package Bio::FastParsers::Hmmer::Standard::Iteration;
# ABSTRACT: Front-end class for standard HMMER parser
# CONTRIBUTOR: Arnaud DI FRANCO <arnaud.difranco@gmail.com>
$Bio::FastParsers::Hmmer::Standard::Iteration::VERSION = '0.221230';
use Moose;
use namespace::autoclean;

use autodie;

use List::AllUtils qw(indexes firstidx mesh);

use Bio::FastParsers::Constants qw(:files);
use aliased 'Bio::FastParsers::Hmmer::Standard::Target';


# public attributes

lib/Bio/FastParsers/Hmmer/Standard/Target.pm  view on Meta::CPAN

package Bio::FastParsers::Hmmer::Standard::Target;
# ABSTRACT: Internal class for standard HMMER parser
# CONTRIBUTOR: Arnaud DI FRANCO <arnaud.difranco@gmail.com>
$Bio::FastParsers::Hmmer::Standard::Target::VERSION = '0.221230';
use Moose;
use namespace::autoclean;

use List::AllUtils qw(indexes);

use aliased 'Bio::FastParsers::Hmmer::Standard::Domain';


# public attributes

# TODO: check if this an empty ArrayRef would not make more sense than Maybe
# We dont want smth else than a Domain in this ArrayRef

lib/Bio/FastParsers/Hmmer/Table.pm  view on Meta::CPAN

package Bio::FastParsers::Hmmer::Table;
# ABSTRACT: Front-end class for tabular HMMER parser
# CONTRIBUTOR: Arnaud DI FRANCO <arnaud.difranco@gmail.com>
$Bio::FastParsers::Hmmer::Table::VERSION = '0.221230';
use Moose;
use namespace::autoclean;

use autodie;

use List::AllUtils qw(mesh);

extends 'Bio::FastParsers::Base';

use Bio::FastParsers::Constants qw(:files);
use aliased 'Bio::FastParsers::Hmmer::Table::Hit';

lib/Bio/FastParsers/Hmmer/Table/Hit.pm  view on Meta::CPAN

package Bio::FastParsers::Hmmer::Table::Hit;
# ABSTRACT: Internal class for tabular HMMER parser
# CONTRIBUTOR: Arnaud DI FRANCO <arnaud.difranco@gmail.com>
$Bio::FastParsers::Hmmer::Table::Hit::VERSION = '0.221230';
use Moose;
use namespace::autoclean;


# public attributes

has $_ => (
    is       => 'ro',
    isa      => 'Maybe[Str]',
    required => 1,
) for qw(target_accession query_accession);

lib/Bio/FastParsers/Uclust.pm  view on Meta::CPAN

package Bio::FastParsers::Uclust;
# ABSTRACT: Front-end class for UCLUST parser
# CONTRIBUTOR: Amandine BERTRAND <amandine.bertrand@doct.uliege.be>
$Bio::FastParsers::Uclust::VERSION = '0.221230';
use Moose;
use namespace::autoclean;

use autodie;

use Tie::IxHash;

extends 'Bio::FastParsers::Base';


# public attributes (inherited)

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