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Summary

Bio::Tools::Run::BlastPlus - A wrapper for NCBI's blast+ suite

Package variables

Included modules

Inherit

Bio::Root::Root Bio::Tools::Run::WrapperBase

Synopsis

Give standard usage here

Description

Blast+ is NCBI's successor to the blastall family of programs.

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::Tools::Run::BlastPlus();
 Function: Builds a new Bio::Tools::Run::BlastPlus object
 Returns : an instance of Bio::Tools::Run::BlastPlus
 Args    :

 Title   : program_version
 Usage   : $version = $bedtools_fac->program_version()
 Function: Returns the program version (if available)
 Returns : string representing location and version of the program
 Note    : this works around the WrapperBase::version() method conflicting with
           the -version parameter for SABlast (good argument for not having
           getter/setters for these)

 Title   : package_version
 Usage   : $version = $bedtools_fac->version()
 Function: Returns the BLAST+ package version (if available)
 Returns : string representing BLAST+ package version (may differ from version())

Methods code

sub new {

    my ($class,@args) = @_;
    $program_dir ||= $ENV{BLASTPLUSDIR};
    my $self = $class->SUPER::new(@args);
    return $self;

}

sub program_version {

	my ($self) = @_;
    if (!defined $self->{program_version}) {
        $self->_version;
    }
    $self->{program_version} || '';

}

sub package_version {

	my ($self) = @_;
    if (!defined $self->{package_version}) {
        $self->_version;
    }
    $self->{package_version} || '';

}

sub _version {

    my $self = shift;
    my ($in, $out, $err);

	# Get program executable
	my $exe = $self->executable;
	my @ipc_args = ( $exe, '-version');
	
	eval {
		IPC::Run::run(\@ipc_args,\$ in,\$ out,\$ err) or
			die ("There was a problem running $exe : $!");
	};
	
    if ($out =~ /blastdbcmd\:\s+(\S+)\nPackage\:\s+([^,]+)/xms) {
        @{$self}{qw(program_version package_version)} = ($1, $2);
    } else {
        $self->throw("Unknown version output: $out");
    }
}

1;

}

General documentation

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rather than to the module maintainer directly. Many experienced and
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address it. Please include a thorough description of the problem
with code and data examples if at all possible.

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of the bugs and their resolution. Bug reports can be submitted via
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Describe contact details here

Additional contributors names and emails here

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _