Bio-MUST-Apps-HmmCleaner

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META.yml  view on Meta::CPAN

  Bio::MUST::Core::Seq: '0'
  Bio::MUST::Core::SeqMask: '0'
  Bio::MUST::Core::Utils: '0'
  Bio::MUST::Drivers: '0.180270'
  Bio::MUST::Drivers::Hmmer::Model::Temporary: '0'
  Carp: '0'
  File::Basename: '0'
  Getopt::Euclid: '0'
  IPC::System::Simple: '0'
  List::AllUtils: '0'
  Modern::Perl: '0'
  Moose: '0'
  Path::Class: '0'
  Smart::Comments: '0'
  Template: '0'
  Test::Most: '0'
  aliased: '0'
  namespace::autoclean: '0'
  perl: '5.010'
version: '0.180750'

Makefile.PL  view on Meta::CPAN

    "Bio::MUST::Core::Seq" => 0,
    "Bio::MUST::Core::SeqMask" => 0,
    "Bio::MUST::Core::Utils" => 0,
    "Bio::MUST::Drivers" => "0.180270",
    "Bio::MUST::Drivers::Hmmer::Model::Temporary" => 0,
    "Carp" => 0,
    "File::Basename" => 0,
    "Getopt::Euclid" => 0,
    "IPC::System::Simple" => 0,
    "List::AllUtils" => 0,
    "Modern::Perl" => 0,
    "Moose" => 0,
    "Path::Class" => 0,
    "Smart::Comments" => 0,
    "Template" => 0,
    "Test::Most" => 0,
    "aliased" => 0,
    "namespace::autoclean" => 0
  },
  "TEST_REQUIRES" => {
    "Test::Files" => 0,

bin/frameshiftSimul_final.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: frameshiftSimul_final.pl
# ABSTRACT: Simulation for HmmCleaner

use Modern::Perl;
use Carp;
use Path::Class;
use File::Basename;
#~ use File::Temp qw(tempfile); my $template = 'tmpfile_XXXX';
use List::AllUtils qw(shuffle sum0 any firstidx);
use IPC::System::Simple qw(system);
use Getopt::Euclid qw(:vars);
use Template;

bin/transferCleaner.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: transferCleaner.pl
# ABSTRACT: transfer amino acid LSSs on corresponding nucleotide alignment

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

## no critic (RequireLocalizedPunctuationVars)
BEGIN{
    $ENV{Smart_Comments} = $ARGV{-v}
        ? join q{ }, map { '#' x (2 + $_) } 1..$ARGV{-v}
        : q{}
    ;
}
## use critic

docs/include.pl  view on Meta::CPAN

#!/usr/bin/env perl

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


# process first file on command line or STDIN
my $infile = shift @ARGV;
my $in = \*STDIN;
open $in, '<', $infile if $infile;

parse(q{}, $in);

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

package Bio::MUST::Apps::HmmCleaner;
# ABSTRACT: Main class for HmmCleaner
$Bio::MUST::Apps::HmmCleaner::VERSION = '0.180750';
use Moose;
use namespace::autoclean;

use Smart::Comments -ENV;
use List::AllUtils qw/uniq max/;
use Modern::Perl;

use Carp;
use Path::Class;

use Bio::MUST::Core 0.180230;
use Bio::MUST::Core::Constants qw(:gaps :files);
use Bio::MUST::Drivers 0.180270;
use Bio::MUST::Drivers::Hmmer::Model::Temporary;

use aliased 'Bio::MUST::Core::Seq';

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

package Bio::MUST::Apps::HmmCleaner::Cleaner;
# ABSTRACT: Cleaner class for HmmCleaner
$Bio::MUST::Apps::HmmCleaner::Cleaner::VERSION = '0.180750';
use Moose;
use namespace::autoclean;

use Carp;
use Smart::Comments -ENV;
use List::AllUtils qw/max pairmap indexes/;
use Modern::Perl;

use Bio::MUST::Core 0.180230;
use Bio::MUST::Core::Constants qw(:gaps :files);
use aliased 'Bio::MUST::Core::SeqMask';
use aliased 'Bio::MUST::Core::Seq';

####### [PROCESS] Value of env verbosity : scalar(split ' ', $ENV{Smart_Comments})

# ATTRIBUTES

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

package Bio::MUST::Apps::HmmCleaner::Process;
# ABSTRACT: Process class for HmmCleaner
$Bio::MUST::Apps::HmmCleaner::Process::VERSION = '0.180750';
use Moose;
use namespace::autoclean;

use Carp;
use Smart::Comments -ENV;
use Modern::Perl;

use Bio::MUST::Core 0.180230;
use Bio::MUST::Core::Constants qw(:gaps :files);
use Bio::FastParsers::Hmmer;
use aliased 'Bio::MUST::Core::Seq';

####### [PROCESS] Value of env verbosity : scalar(split ' ', $ENV{Smart_Comments})

# ATTRIBUTES
has 'ali' => (

t/cleaner.t  view on Meta::CPAN

#!/usr/bin/env perl

use Test::Most;
use Test::Files;

use autodie;
use Modern::Perl;

use Smart::Comments;

use Path::Class qw(file);

use Bio::MUST::Apps::HmmCleaner;

my $class = 'Bio::MUST::Apps::HmmCleaner::Cleaner';

# Needed elements for cleaner objetc

t/hmmcleaner.t  view on Meta::CPAN

#!/usr/bin/env perl

use Test::Most;
use Test::Files;

use autodie;
use Modern::Perl;

use Smart::Comments;

use Path::Class qw(file);

use Bio::MUST::Apps::HmmCleaner;

my $class = 'Bio::MUST::Apps::HmmCleaner';

#~ check_test('GNTPAN12210.ali', 'GNTPAN12210_hmm10_global', { 'perseq' => 0, 'X' => 0});

t/process.t  view on Meta::CPAN

#!/usr/bin/env perl

use Test::Most;
use Test::Files;

use autodie;
use Modern::Perl;

use Smart::Comments;

use Path::Class qw(file);

use Bio::MUST::Core;
use Bio::MUST::Drivers::Hmmer::Model::Temporary;

use Bio::FastParsers::Hmmer;

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