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

BioPerl-Run documentation Contained in the BioPerl-Run distribution.

Index

Code Index:

NAME

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

SYNOPSIS

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Give standard usage here

DESCRIPTION

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

FEEDBACK

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Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

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

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Mark A. Jensen

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Email maj -at- fortinbras -dot- us

Describe contact details here

CONTRIBUTORS

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Additional contributors names and emails here

APPENDIX

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

new

 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    :

program_version()

 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)

package_version()

 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())
BioPerl-Run documentation Contained in the BioPerl-Run distribution. 
# $Id$
#
# BioPerl module for Bio::Tools::Run::BlastPlus
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Mark A. Jensen <maj -at- fortinbras -dot- us>
#
# Copyright Mark A. Jensen
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code


# Let the code begin...


package Bio::Tools::Run::BlastPlus;
use strict;
use warnings;

use lib '../../..';
use Bio::Root::Root;
use Bio::Tools::Run::BlastPlus::Config;
use Bio::Tools::Run::WrapperBase;
use Bio::Tools::Run::WrapperBase::CommandExts;

use base qw(Bio::Tools::Run::WrapperBase Bio::Root::Root);


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;