lib/Bio/Tools/Run/BlastPlus.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Tools::Run::BlastPlus
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Mark A. Jensen <maj -at- fortinbras -dot- us>
   8 #
   9 # Copyright Mark A. Jensen
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Tools::Run::BlastPlus - A wrapper for NCBI's blast+ suite
  18
  19 =head1 SYNOPSIS
  20
  21 Give standard usage here
  22
  23 =head1 DESCRIPTION
  24
  25 Blast+ is NCBI's successor to the C<blastall> family of programs.
  26
  27 =head1 FEEDBACK
  28
  29 =head2 Mailing Lists
  30
  31 User feedback is an integral part of the evolution of this and other
  32 Bioperl modules. Send your comments and suggestions preferably to
  33 the Bioperl mailing list.  Your participation is much appreciated.
  34
  35   bioperl-l@bioperl.org                  - General discussion
  36 http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  37
  38 =head2 Support
  39
  40 Please direct usage questions or support issues to the mailing list:
  41
  42 L<bioperl-l@bioperl.org>
  43
  44 rather than to the module maintainer directly. Many experienced and
  45 reponsive experts will be able look at the problem and quickly
  46 address it. Please include a thorough description of the problem
  47 with code and data examples if at all possible.
  48
  49 =head2 Reporting Bugs
  50
  51 Report bugs to the Bioperl bug tracking system to help us keep track
  52 of the bugs and their resolution. Bug reports can be submitted via
  53 the web:
  54
  55   http://redmine.open-bio.org/projects/bioperl/
  56
  57 =head1 AUTHOR - Mark A. Jensen
  58
  59 Email maj -at- fortinbras -dot- us
  60
  61 Describe contact details here
  62
  63 =head1 CONTRIBUTORS
  64
  65 Additional contributors names and emails here
  66
  67 =head1 APPENDIX
  68
  69 The rest of the documentation details each of the object methods.
  70 Internal methods are usually preceded with a _
  71
  72 =cut
  73
  74 # Let the code begin...
  75
  76
  77 package Bio::Tools::Run::BlastPlus;
  78 use strict;
  79 use warnings;
  80
  81 use lib '../../..';
  82 use Bio::Root::Root;
  83 use Bio::Tools::Run::BlastPlus::Config;
  84 use Bio::Tools::Run::WrapperBase;
  85 use Bio::Tools::Run::WrapperBase::CommandExts;
  86
  87 use base qw(Bio::Tools::Run::WrapperBase Bio::Root::Root);
  88
  89 =head2 new
  90
  91  Title   : new
  92  Usage   : my $obj = new Bio::Tools::Run::BlastPlus();
  93  Function: Builds a new Bio::Tools::Run::BlastPlus object
  94  Returns : an instance of Bio::Tools::Run::BlastPlus
  95  Args    :
  96
  97 =cut
  98
  99 sub new {
 100     my ($class,@args) = @_;
 101     $program_dir ||= $ENV{BLASTPLUSDIR};
 102     my $self = $class->SUPER::new(@args);
 103     return $self;
 104 }
 105
 106 =head2 program_version()
 107
 108  Title   : program_version
 109  Usage   : $version = $bedtools_fac->program_version()
 110  Function: Returns the program version (if available)
 111  Returns : string representing location and version of the program
 112  Note    : this works around the WrapperBase::version() method conflicting with
 113            the -version parameter for SABlast (good argument for not having
 114            getter/setters for these)
 115
 116 =cut
 117
 118 =head2 package_version()
 119
 120  Title   : package_version
 121  Usage   : $version = $bedtools_fac->version()
 122  Function: Returns the BLAST+ package version (if available)
 123  Returns : string representing BLAST+ package version (may differ from version())
 124
 125 =cut
 126
 127 sub program_version {
 128         my ($self) = @_;
 129     if (!defined $self->{program_version}) {
 130         $self->_version;
 131     }
 132     $self->{program_version} || '';
 133 }
 134
 135 sub package_version {
 136         my ($self) = @_;
 137     if (!defined $self->{package_version}) {
 138         $self->_version;
 139     }
 140     $self->{package_version} || '';
 141 }
 142
 143 sub _version {
 144     my $self = shift;
 145     my ($in, $out, $err);
 146
 147         # Get program executable
 148         my $exe = $self->executable;
 149         my @ipc_args = ( $exe, '-version');
 150
 151         eval {
 152                 IPC::Run::run(\@ipc_args, \$in, \$out, \$err) or
 153                         die ("There was a problem running $exe : $!");
 154         };
 155
 156     if ($out =~ /blastdbcmd\:\s+(\S+)\nPackage\:\s+([^,]+)/xms) {
 157         @{$self}{qw(program_version package_version)} = ($1, $2);
 158     } else {
 159         $self->throw("Unknown version output: $out");
 160     }
 161 }
 162
 163 1;