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lib/Bio/Tools/Run/Phylo/Phyml.pm  view on Meta::CPAN

        $param_string .= ' -s ' . $self->search;

        if ( $self->search eq 'SPR' ) {
            $param_string .= ' --rand_start ' if $self->rand_start;
            $param_string .= ' --n_rand_starts ' . $self->rand_starts
              if $self->rand_starts;
            $param_string .= ' --r_seed ' . $self->rand_seed;
        }

        $param_string .= ' --no_memory_check '
          if $self->no_memory_check;

    }
    else {

        # version 2
        $param_string = ' ' . $self->data_type;
        $param_string .= ' ' . $self->data_format;
        $param_string .= ' ' . $self->dataset_count;
        $param_string .= ' 0';                         # no bootstrap sets
        $param_string .= ' ' . $self->model;

        unless ( $self->data_type ) {                  # only for DNA
            $param_string .= ' ' . $self->kappa;
        }

        $param_string .= ' ' . $self->invar;
        $param_string .= ' ' . $self->category_number;
        $param_string .= ' ' . $self->alpha;
        $param_string .= ' ' . $self->tree;
        $param_string .= ' ' . $self->opt_topology;
        $param_string .= ' ' . $self->opt_lengths;

    }
    return $param_string;
}

=head2 _write_phylip_align_file

 Title   : _write_phylip_align_file
 Usage   : obj->__write_phylip_align_file($aln)
 Function: Internal (not to be used directly)

           Writes the alignment into the tmp directory
           in PHYLIP interlieved format

 Returns : filename
 Args    : Bio::Align::AlignI

=cut

sub _write_phylip_align_file {
    my ( $self, $align ) = @_;

    my $tempfile = File::Spec->catfile( $self->tempdir, "aln$$.phylip" );
    $self->data_format('i');
    my $out = Bio::AlignIO->new(
        -file        => ">$tempfile",
        -format      => 'phylip',
        -interleaved => 1,
        -longid      => 1
    );
    $out->write_aln($align);
    $out->close();
    $out = undef;
    return $tempfile;
}

1;