Bio::Tools::Run Meme
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Summary
Bio::Tools::Run::Meme - Wrapper for Meme Program
Package variables
No package variables defined.
Included modules
Bio::AlignIO
Bio::Map::Position
Bio::Map::Prediction
Bio::SeqIO
Inherit
Bio::Tools::Run::WrapperBase
Synopsis
  use Bio::Tools::Run::Meme;

  my $factory = Bio::Tools::Run::Meme->new(-dna => 1, -mod => 'zoops');

  # return a Bio::AlignIO given Bio::PrimarySeqI objects
  my $alignio = $factory->run($seq1, $seq2, $seq3...);

  # add a Bio::Map::Prediction to the appropriate maps given Bio::Map::GeneMap
  # objects (predict on the full map sequences supplied) or Bio::Map::Gene
  # objects (predict on the full map sequences of the maps the supplied Genes
  # are on) or Bio::Map::PositionWithSequence objects
  my $prediction = $factory->run($biomap1, $biomap2, $biomap3...);
Description
This is a wrapper for running meme, a transcription factor binding site
prediction program. It can be found here:
http://meme.sdsc.edu/meme4/meme-download.html
You can try supplying normal meme command-line arguments to new(), eg.
new(-mod => 'oops') or calling arg-named methods (excluding the initial
hyphen(s), eg. $factory->mod('oops') to set the -mod option to 'oops').
You will need to enable this MEME wrapper to find the meme program. During
standard installation of meme you will have set up an environment variable
called MEME_BIN which is used for this purpose.
Methods
newDescriptionCode
program_nameDescriptionCode
program_dirDescriptionCode
versionDescriptionCode
runDescriptionCode
_runDescriptionCode
_setparamsDescriptionCode
_setinputDescriptionCode
Methods description
newcode    nextTop
 Title   : new
 Usage   : $rm->new($seq)
 Function: creates a new wrapper
 Returns:  Bio::Tools::Run::Meme
 Args    : Most options understood by meme can be supplied as key =>
           value pairs, with a boolean value for switches. -quiet can also be
           set to silence meme completely.

           These options can NOT be used with this wrapper (they are handled
           internally or don't make sense in this context):
           -h -text -nostatus
program_namecodeprevnextTop
 Title   : program_name
 Usage   : $factory>program_name()
 Function: holds the program name
 Returns:  string
 Args    : None
program_dircodeprevnextTop
 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtained from ENV variable.
 Returns:  string
 Args    :
versioncodeprevnextTop
 Title   : version
 Usage   : n/a
 Function: Determine the version number of the program, which is
           non-discoverable for Meme
 Returns : undef
 Args    : none
runcodeprevnextTop
 Title   : run
 Usage   : $rm->run($seq1, $seq2, $seq3...);
 Function: Run Meme on the sequences/Bio::Map::* set as the argument
 Returns : Bio::AlignIO if sequence objects supplied, OR
           Bio::Map::Prediction if Bio::Map::* objects supplied
           undef if no executable found
 Args    : list of Bio::PrimarySeqI compliant objects, OR
           list of Bio::Map::GeneMap objects, OR
           list of Bio::Map::Gene objects, OR
           list of Bio::Map::PositionWithSequence objects
_runcodeprevnextTop
 Title   : _run
 Usage   : $rm->_run ($filename,$param_string)
 Function: internal function that runs meme
 Returns : as per run(), undef if no executable found
 Args    : the filename to the input sequence file
_setparams()codeprevnextTop
 Title   : _setparams
 Usage   : Internal function, not to be called directly
 Function: Create parameter inputs for meme program
 Returns : parameter string to be passed to meme
 Args    : none
_setinput()codeprevnextTop
 Title   : _setinput
 Usage   : Internal function, not to be called directly
 Function: writes input sequence to file and return the file name
 Returns : string (file name)
 Args    : as per run()
Methods code
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    
    $self->_set_from_args(\@args, -methods => [@PARAMS, @SWITCHES, 'quiet'],
                                  -create => 1);
    
    return $self;
}
program_namedescriptionprevnextTop
sub program_name {
    return $PROGRAM_NAME;
}
program_dirdescriptionprevnextTop
sub program_dir {
    return $PROGRAM_DIR;
}
versiondescriptionprevnextTop
sub version {
    return;
}
rundescriptionprevnextTop
sub run {
    my ($self, @things) = @_;
    
    my $infile = $self->_setinput(@things);
    
    return $self->_run($infile);
}
_rundescriptionprevnextTop
sub _run {
    my ($self, $infile) = @_;
    
    my $exe = $self->executable || return;
    
    my $outfile = $infile.".out";
    
    my $command = $exe.$self->_setparams($infile, $outfile);
    $self->debug("meme command = $command\n");
    
    open(my $pipe, "$command |") || $self->throw("meme call ($command) failed to start: $? | $!");
    my $error = '';
    while (<$pipe>) {
        print unless $self->quiet;
        $error .= $_;
    }
    close($pipe) || ($error ? $self->throw("meme call ($command) failed: $error") : $self->throw("meme call ($command) crashed: $?"));
    
    #my $status = system($cmd_str);
    #$self->throw("Meme call ($cmd_str) crashed: $?\n") unless $status == 0;
    
    my $aio = Bio::AlignIO->new(-format => 'meme', -file => $outfile);
    unless ($self->{map_mode}) {
        # return directly the AlignIO
        return $aio;
    }
    else {
        # use the AlignIO meme parser to generate a Bio::Map::Prediction and
        # return that
        my $pred = Bio::Map::Prediction->new(-source => "meme");
        while (my $aln = $aio->next_aln) {
            foreach my $seq ($aln->each_seq) {
                my $id = $seq->id;
                unless ($id) {
                    $self->warn("Got a sequence in the alignment with no id, but I need one to determine the map");
                    next;
                }
                my ($uid) = $id =~ /^([^\[]+)/;
                my $map = Bio::Map::GeneMap->get(-uid => $uid);
                
                my ($start, $end) = ($seq->start, $seq->end);
                if ($seq->strand == -1) {
                    my $length;
                    my ($pos_s, $pos_e) = $id =~ /\[(\d+)\.\.(\d+)\]$/;
                    if (defined($pos_s) && defined($pos_e)) {
                        $length = $pos_e - $pos_s + 1;
                    }
                    else {
                        $length = length($map->seq);
                    }
                    my $motif_length = $end - $start + 1;
                    $end = $length - $start + 1;
                    $start = $end - $motif_length + 1;
                }
                
                Bio::Map::Position->new(-element => $pred,
                                        -start => $start,
                                        -end => $end,
                                        -map => $map);
            }
        }
        delete $self->{map_mode};
        return $pred;
    }
}
_setparamsdescriptionprevnextTop
sub _setparams {
    my ($self, $infile, $outfile) = @_;
    
    my $param_string = ' '.$infile;
    
    # -text and -nostatus must be set
    $param_string .= ' -text -nostatus';
    
    $param_string .= $self->SUPER::_setparams(-params =>\@ PARAMS,
                                              -switches =>\@ SWITCHES,
                                              -dash => 1);
    
    $param_string .= " > $outfile";
    $param_string .= ' 2> /dev/null' if $self->quiet || $self->verbose < 0;
    
    return $param_string;
}
_setinputdescriptionprevnextTop
sub _setinput {
    my ($self, @inputs) = @_;
    $self->throw("At least two sequence or map objects must be supplied") unless @inputs >= 2;
    ref($inputs[0]) || $self->throw("Inputs must be object references");
    
    my ($fh, $outfile) = $self->io->tempfile(-dir => $self->tempdir);
    my $out = Bio::SeqIO->new(-fh => $fh, '-format' => 'fasta');
    
    my %done;
    foreach my $input (@inputs) {
        if ($input->isa('Bio::Map::MappableI')) {
            # we want to work on all its maps, since mappables themselves don't
            # have sequences
            push(@inputs, $input->known_maps);
            next;
        }
        
        $input->can('seq') || $self->throw("Supplied an input [$input] with no seq() method!");
        
        if ($input->isa('Bio::Map::EntityI')) {
            $self->{map_mode} = 1;
            
            if ($input->isa('Bio::Map::MapI')) {
                # change the id of the seq so we'll know what input object it
                # came from later
                my $id = $input->unique_id;
                next if $done{$id};
                $input->id($id);
                $done{$id} = 1;
                #*** should this be automatic in GeneMap? Anyway, we don't want
                #    to alter users genemap id here permanently...
            }
            else {
                my $id = $input->id;
                unless ($id) {
                    $input->id($input->map->unique_id.'['.$input->toString.']');
                }
            }
        }
        
        $out->write_seq($input);
    }
    close($fh);
    
    return $outfile;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
Support Top
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 BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
  http://redmine.open-bio.org/projects/bioperl/
AUTHOR - Sendu BalaTop
Email bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".
Bio::Tools::Run::Wrapper methodsTop
no_param_checksTop
 Title   : no_param_checks
 Usage   : $obj->no_param_checks($newval)
 Function: Boolean flag as to whether or not we should
           trust the sanity checks for parameter values  
 Returns : value of no_param_checks
 Args    : newvalue (optional)
save_tempfilesTop
 Title   : save_tempfiles
 Usage   : $obj->save_tempfiles($newval)
 Function: 
 Returns : value of save_tempfiles
 Args    : newvalue (optional)
outfile_nameTop
 Title   : outfile_name
 Usage   : my $outfile = $codeml->outfile_name();
 Function: Get/Set the name of the output file for this run
           (if you wanted to do something special)
 Returns : string
 Args    : [optional] string to set value to
tempdirTop
 Title   : tempdir
 Usage   : my $tmpdir = $self->tempdir();
 Function: Retrieve a temporary directory name (which is created)
 Returns : string which is the name of the temporary directory
 Args    : none
cleanupTop
 Title   : cleanup
 Usage   : $codeml->cleanup();
 Function: Will cleanup the tempdir directory
 Returns : none
 Args    : none
ioTop
 Title   : io
 Usage   : $obj->io($newval)
 Function:  Gets a Bio::Root::IO object
 Returns : Bio::Root::IO
 Args    : none