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lib/Bio/RNA/RNAaliSplit/WrapRNAz.pm  view on Meta::CPAN

# -*-CPerl-*-
# Last changed Time-stamp: <2019-08-25 21:19:14 mtw>

# Bio::RNA::RNAaliSplit::WrapRNAz.pm: A versatile object-oriented
# wrapper for RNAz
#
# Requires RNAz executable available to the Perl interpreter.
# This package contains code fragments from the original RNAz Perl module

package Bio::RNA::RNAaliSplit::WrapRNAz;

use version; our $VERSION = qv('0.11');
use Carp;
use Data::Dumper;
use Moose;
use Path::Class;
use IPC::Cmd qw(can_run run);
use File::Path qw(make_path);
#use diagnostics;

my ($rnaz,$oodir);

has 'basename' => (
		   is => 'rw',
		   isa => 'Str',
		   predicate => 'has_basename',
		   documentation => q(Set this to override output basename),
		  );

has 'P' => (
	    is => 'rw',
	    isa => 'Num',
	    init_arg => undef,
	    documentation => q(SVM RNA-class probability),
	   );

has 'z' => (
	    is => 'rw',
	    isa => 'Num',
	    init_arg => undef,
	    documentation => q(Mean z-score),
	   );

has 'sci' => (
	      is => 'rw',
	      isa => 'Num',
	      init_arg => undef,
	      documentation => q(Structure conservation index),
	     );

with 'FileDirUtil';

sub BUILD {
  my $self = shift;
  my $this_function = (caller(0))[3];
  confess "ERROR [$this_function] \$self->ifile not available"
    unless ($self->has_ifile);
   $rnaz = can_run('RNAz') or
     croak "ERROR [$this_function] RNAz not found";
  unless($self->has_odir){
    my $odir_name = "as";
    $self->odir( [$self->ifile->dir,$odir_name] );
  }
  $oodir = $self->odir->subdir("rnaz");
  my @created = make_path($oodir, {error => \my $err});
  confess "ERROR [$this_function] could not create output directory $self->oodir"
    if (@$err);
  $self->set_ifilebn;