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bin/HmmCleaner.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: HmmCleaner.pl
# ABSTRACT: Removing low similarity segments from your MSA

use Modern::Perl;
use Getopt::Euclid;

## no critic (RequireLocalizedPunctuationVars)
BEGIN{
    $ENV{Smart_Comments} = $ARGV{-v}

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bin/ompa-pa.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: ompa-pa.pl
# ABSTRACT: Extract seqs from BLAST/HMMER interactively or in batch mode
# CONTRIBUTOR: Amandine BERTRAND <amandine.bertrand@doct.uliege.be>

use Modern::Perl '2011';
use autodie;

use Getopt::Euclid qw(:vars);
use Smart::Comments;

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bin/physeter.pl  view on Meta::CPAN

# ABSTRACT: Taxonomic parser for BLAST reports
# CONTRIBUTOR: Valerian LUPO <valerian.lupo@doct.uliege.be>
# CONTRIBUTOR: Mick VAN VLIERBERGHE <mvanvlierberghe@doct.uliege.be>
# CONTRIBUTOR: Luc CORNET <luc.cornet@uliege.be>

use Modern::Perl '2011';
use autodie;

use Smart::Comments '###';

use Getopt::Euclid qw(:vars);

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bin/two-scalp.pl  view on Meta::CPAN

# PODNAME: two-scalp.pl
# ABSTRACT: Align or re-align sequences using various strategies
# CONTRIBUTOR: Amandine BERTRAND <amandine.bertrand@doct.uliege.be>
# CONTRIBUTOR: Valerian LUPO <valerian.lupo@doct.uliege.be>

use Modern::Perl '2011';
use Getopt::Euclid qw(:vars);

## no critic (RequireLocalizedPunctuationVars)
BEGIN{
    $ENV{Smart_Comments} = $ARGV_verbosity

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bin/ali2fasta.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: ali2fasta.pl
# ABSTRACT: Convert ALI files to FASTA files

use Modern::Perl '2011';
use autodie;

use Getopt::Euclid qw(:vars);
use Smart::Comments;

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codegen/build_provis.pl  view on Meta::CPAN

#!/usr/bin/env perl

use Modern::Perl '2011';
use autodie;

use Template;
use Path::Class qw(file dir);

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bin/abbr-ids-fas.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: abbr-ids-fas.pl
# ABSTRACT: Abbreviate (standardize) seq ids in FASTA files

use Modern::Perl '2011';
use autodie;

use File::Basename;
use Getopt::Euclid qw(:vars);
use Smart::Comments;

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bin/tree-clan-splitter.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: tree-clan-splitter.pl
# ABSTRACT: Extract clans (FASTA files) from trees based on taxonomic filters
# CONTRIBUTOR: Mick VAN VLIERBERGHE <mvanvlierberghe@doct.uliege.be>

use Modern::Perl '2011';
use autodie;

use Smart::Comments '###';
use Getopt::Euclid qw( :vars );

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bin/draw_bgc_maps.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: draw_bgc_maps.pl
# ABSTRACT: This script draws NRPS/PKS BGC clusters maps in PNG
# CONTRIBUTOR: Denis BAURAIN <denis.baurain@uliege.be>

use Modern::Perl '2011';
use autodie;

use Carp;
use GD::Simple;
use Getopt::Euclid qw(:vars);

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

    1;

Then you can use your class easily in your application:

    #!/usr/bin/env perl
    use Modern::Perl;

    use My::Ridiculously::Specific::Protease;

    my $protease = My::Ridiculously::Specific::Protease->new;
    my @products = $protease->digest( 'AAAAMAELVIKPYYYYYYY' );

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Build.PL  view on Meta::CPAN

    "strict" => 0,
    "warnings" => 0
  },
  "test_requires" => {
    "IO::All" => 0,
    "Modern::Perl" => 0,
    "Test::More" => "0.88",
    "Test::Pod" => 0
  }
);


my %fallback_build_requires = (
  "IO::All" => 0,
  "Modern::Perl" => 0,
  "Module::Build" => "0.28",
  "Test::More" => "0.88",
  "Test::Pod" => 0
);

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lib/BioX/Map.pm  view on Meta::CPAN

package BioX::Map;
use Modern::Perl;
use IO::All;
use Moo;
use Carp qw/confess/;
use Types::Standard qw/Str Int Enum Bool/;
use File::Which;

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Build.PL  view on Meta::CPAN

    "strict" => 0,
    "warnings" => 0
  },
  "test_requires" => {
    "IO::All" => 0,
    "Modern::Perl" => 0,
    "Test::More" => "0.88",
    "Test::Pod" => 0
  }
);


my %fallback_build_requires = (
  "IO::All" => 0,
  "Modern::Perl" => 0,
  "Module::Build" => "0.28",
  "Test::More" => "0.88",
  "Test::Pod" => 0
);

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lib/Bioinfo.pm  view on Meta::CPAN

package Bioinfo;
use Moo;
use Modern::Perl;
use namespace::clean;

our $VERSION = '0.1.15'; # VERSION: 
# ABSTRACT: my perl module and CLIs for Biology

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lib/Book/Chinese/MasterPerlToday/BeACPANAuthor.pod  view on Meta::CPAN

☻ 唐鳳 ☺, 国人的骄傲（台湾）。Perl6 pugs 的开发者。L<Locale::Maketext::Lexicon>, L<Module::Install>, L<PAR> 的发起者

=item * CHROMATIC L<http://search.cpan.org/~CHROMATIC/>

chromatic, L<Modern::Perl>.

=item * DROLSKY L<http://search.cpan.org/~DROLSKY/>

Dave Rolsky, L<Moose>, L<DateTime> 和 L<HTML::Mason> 的开发者和维护者。

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t/perlcriticrc  view on Meta::CPAN

# add_themes                         =
# severity                           = 5
# maximum_violations_per_document    = 1

# The additional modules to treat as equivalent to "strict".
# Values that are always included: Any::Moose, Dancer, Dancer2, Mo, Modern::Perl, Mojo::Base, Mojolicious::Lite, Moo, Moo::Role, Moos, Moose, Moose::Exporter, Moose::Role, Moose::Util::TypeConstraints, MooseX::NonMoose, MooseX::Role::Parameterized, M...
# equivalent_modules =


# Always `use warnings'.
[TestingAndDebugging::RequireUseWarnings]

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bin/clidriver.pl  view on Meta::CPAN

=cut

###### PACKAGES ######

use Modern::Perl;
use English;
use CLI::Driver;

###### CONSTANTS ######

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lib/CLIPSeqTools.pm  view on Meta::CPAN

# Let the code begin...


package CLIPSeqTools;
$CLIPSeqTools::VERSION = '1.0.0';
use Modern::Perl;

1;

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lib/CSS/Prepare.pm  view on Meta::CPAN

package CSS::Prepare;

use Modern::Perl;

use CSS::Prepare::CSSGrammar;
use CSS::Prepare::Property::Background;
use CSS::Prepare::Property::Border;
use CSS::Prepare::Property::BorderRadius;

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lib/Cache/MemcachedBinary.pm  view on Meta::CPAN

Cache::MemcachedBinary - Perl extension for Memcached server with binary protocol.

=head1 SYNOPSIS

    use Modern::Perl;
    use Cache::MemcachedBinary;

    my $logger = sub {say @_};
    my $obj_mem = Cache::MemcachedBinary->new(
        host     => '127.0.0.1',

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inc/MyContainer.pm  view on Meta::CPAN

package MyContainer;

use Modern::Perl;

use Carp qw(confess);

sub new {
    my $class = ref $_[0] || $_[0]; shift;

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inc/MyContainer.pm  view on Meta::CPAN

package MyContainer;

use Modern::Perl;

use Carp qw(confess);

sub new {
    my $class = ref $_[0] || $_[0]; shift;

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lib/Catalyst/Plugin/BigSitemap.pm  view on Meta::CPAN

package Catalyst::Plugin::BigSitemap;
use Modern::Perl '2010';
use Catalyst::Plugin::BigSitemap::SitemapBuilder;
use WWW::SitemapIndex::XML;
use WWW::Sitemap::XML;
use Path::Class;
use Carp;

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share/starter/script/db_deploy.pl  view on Meta::CPAN

#!/usr/bin/env perl
use Modern::Perl '2012';
use FindBin qw($Bin);
use lib "$Bin/../lib";
use <% dist_module %>::Schema;
use <% dist_module %>::Util::Primer qw(prime_database);
my $schema = <% dist_module %>::Schema->connect("dbi:SQLite:dbname=$Bin/../<% dist_file %>.db")

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lib/Cfwp/fio.pm  view on Meta::CPAN

#!/usr/bin/env perl
package Cfwp::fio;
our $VERSION = 0.04;

use Modern::Perl;

sub read_file {
    $_ = shift;
    open( IN, $_ ) or die "Can't open $_";
    my @texts = <IN>;

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lib/Class/Easy.pm  view on Meta::CPAN

Class::Easy - make class routine easy

=head1 ABSTRACT

This module is a functionality compilation of some good modules from CPAN.
Ideas are taken from Class::Data::Inheritable, Class::Accessor, Modern::Perl
and Moose at least.

Instead of building monstrous alternatives to Moose or making thousand modules
for every function I need, I decide to write small and efficient libraries for
everyday use. Class::Easy::Base is a base component for classes.

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author_scripts/refcount_constructor.pl  view on Meta::CPAN

#!/usr/bin/env perl

# confirm the refcounts/flags are correct for
# objects returned by the XS constructor

use Modern::Perl;
use Devel::Peek;

use blib;

use Class::XSAccessor {

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lib/Classic/Perl.pm  view on Meta::CPAN

C<C<$[> in perlvar|perlvar/$[>

L<any::feature> is an experimental module that backports new Perl features
to older versions.

The L<Modern::Perl> module enables various pragmata which are currently
popular.