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lib/Alien/SeqAlignment/hmmer3.pm  view on Meta::CPAN

use strict;
use warnings;

package Alien::SeqAlignment::hmmer3;
$Alien::SeqAlignment::hmmer3::VERSION = '0.03';
use parent qw( Alien::Base );
use Carp;
our $AUTOLOAD;

sub AUTOLOAD {
    my ($self) = @_;
    our $AUTOLOAD;
    $AUTOLOAD =~ s/.*::(\w+)$//;
    my $method = $1;
    unless ( exists $self->runtime_prop->{command}->{$method} ) {
        croak "Method $method not found";
    }
    else {
        no strict 'refs';
        *$AUTOLOAD = sub {
            shift->runtime_prop->{command}->{$method};
        };
    }
    use strict 'refs';
    goto &$AUTOLOAD;
}

=head1 NAME

Alien::SeqAlignment::hmmer3 - find, build and install the hmmer3 tools

=head1 VERSION

version 0.03

=head1 SYNOPSIS

To execute the hmmer3 set of tools, you can use the following code:

 use Alien::SeqAlignment::hmmer3;
 use Env qw( @PATH );
 unshift @PATH, Alien::SeqAlignment::hmmer3->bin_dir;

Now you can run the hmmer3 tools as:
 
HMMER3 SUITE

  system Alien::SeqAlignment::hmmer3->alimask       (parameters & options);
  system Alien::SeqAlignment::hmmer3->hmmalign      (parameters & options);
  system Alien::SeqAlignment::hmmer3->hmmbuild      (parameters & options);
  system Alien::SeqAlignment::hmmer3->hmmconvert    (parameters & options);
  system Alien::SeqAlignment::hmmer3->hmmemit       (parameters & options);
  system Alien::SeqAlignment::hmmer3->hmmfetch      (parameters & options);
  system Alien::SeqAlignment::hmmer3->hmmlogo       (parameters & options);
  system Alien::SeqAlignment::hmmer3->hmmpgmd       (parameters & options);
  system Alien::SeqAlignment::hmmer3->hmmpgmd_shard (parameters & options);
  system Alien::SeqAlignment::hmmer3->hmmpress      (parameters & options);
  system Alien::SeqAlignment::hmmer3->hmmsearch     (parameters & options);
  system Alien::SeqAlignment::hmmer3->hmmsim        (parameters & options);
  system Alien::SeqAlignment::hmmer3->hmmstat       (parameters & options);
  system Alien::SeqAlignment::hmmer3->jackhmmer     (parameters & options);
  system Alien::SeqAlignment::hmmer3->makehmmerdb   (parameters & options);
  system Alien::SeqAlignment::hmmer3->nhmmer        (parameters & options);
  system Alien::SeqAlignment::hmmer3->nhmmscan      (parameters & options);
  system Alien::SeqAlignment::hmmer3->phmmer        (parameters & options);