Bio::Tools::Run Glimmer
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Summary
Bio::Tools::Run::Glimmer - Wrapper for local execution of Glimmer,
GlimmerM and GlimmerHMM.
Package variables
No package variables defined.
Included modules
Bio::Root::Root
Bio::SeqIO
Bio::Tools::Glimmer
Bio::Tools::Run::WrapperBase
English
IPC::Run
Inherit
Bio::Root::Root Bio::Tools::Run::WrapperBase
Synopsis
  # glimmer2
  my $factory =
      Bio::Tools::Run::Glimmer->new('-program' => 'glimmer3',
                                    '-model'   => 'model.icm');
  # glimmer3
  my $factory =
      Bio::Tools::Run::Glimmer->new('-program' => 'glimmer2',
                                    '-model'   => 'model.icm');
  # glimmerm
  my $factory =
      Bio::Tools::Run::Glimmer->new('-program' => 'glimmerm');

  # glimmerHMM
  my $factory =
      Bio::Tools::Run::Glimmer->new('-program' => 'glimmerHMM');

  # Pass the factory Bio::Seq objects
  # returns a Bio::Tools::Glimmer object
  my $glimmer = $factory->run($seq);
  or
  my $glimmer = $factor->run(@seq);
Description
Wrapper module for the Glimmer family of programs. Should work with
all currently available flavors: Glimmer, GlimmerM and GlimmerHMM.
However, only Glimmer 2.X and 3.X have been tested.
Glimmer is open source and available at
http://www.cbcb.umd.edu/software/glimmer/.
GlimmerM is open source and available at
http://www.tigr.org/software/glimmerm/.
GlimmerHMM is open source and available at
http://www.cbcb.umd.edu/software/GlimmerHMM/.
Note that Glimmer 2.X will only process the first
sequence in a fasta file (if you run() more than one
sequence at a time, only the first will be processed).
Note that Glimmer 3.X produces two output files. This
module only passes the .predict file to Bio::Tools::Glimmer.
Methods
program_nameDescriptionCode
program_dirDescriptionCode
modelDescriptionCode
newDescriptionCode
runDescriptionCode
_runDescriptionCode
_setparams
No description
Code
_write_seq_fileDescriptionCode
Methods description
program_namecode    nextTop
 Title   : program_name
 Usage   : $factory>program_name()
 Function: gets/sets the program name
 Returns:  string
 Args    : string
program_dircodeprevnextTop
 Title   : program_dir
 Usage   : $factory->program_dir()
 Function: gets/sets the program dir
 Returns:  string
 Args    : string
modelcodeprevnextTop
 Title   : model
 Usage   : $factory>model()
 Function: gets/sets the name of the model (icm) file
 Returns:  string
 Args    : string
newcodeprevnextTop
 Title   : new
 Usage   : $glimmer->new(@params)
 Function: creates a new Glimmer factory
 Returns:  Bio::Tools::Run::Glimmer
 Args    :
runcodeprevnextTop
 Title   :   run
 Usage   :   $obj->run($seq_file)
 Function:   Runs Glimmer/GlimmerM/GlimmerHMM
 Returns :   A Bio::Tools::Glimmer object
 Args    :   An array of Bio::PrimarySeqI objects
_runcodeprevnextTop
 Title   :   _run
 Usage   :   $obj->_run()
 Function:   Internal(not to be used directly)
 Returns :   An instance of Bio::Tools::Glimmer 
 Args    :   file name, sequence identifier (optional)
_write_seq_filecodeprevnextTop
 Title   :   _write_seq_file
 Usage   :   obj->_write_seq_file($seq) or obj->_write_seq_file(@seq)
 Function:   Internal(not to be used directly)
 Returns :   Name of a temp file containing program output
 Args    :   One or more Bio::PrimarySeqI objects
Methods code
program_namedescriptionprevnextTop
sub program_name {
    
    my ($self, $val) = @_;
    
    $self->program($val) if $val;
    
    return $self->program();
}
program_dirdescriptionprevnextTop
sub program_dir {
    
    my ($self, $val) = @_;
    
    $self->{'_program_dir'} = $val if $val;
    
    return $self->{'_program_dir'};
}
modeldescriptionprevnextTop
sub model {
    
    my ($self, $val) = @_;
    
    $self->{'_model'} = $val if $val;
    
    return $self->{'_model'};
}
newdescriptionprevnextTop
sub new {
    
       my ($class,@args) = @_;
       my $self = $class->SUPER::new(@args);
       
       $self->io->_initialize_io();

       $self->_set_from_args(\@
                             args,
                             -methods => [
                                          @params,
                                          @glimmer2_params,
                                          @glimmer2_switches,
                                          @glimmer3_params,
                                          @glimmer3_switches,
                                          @glimmerM_params,
                                          @glimmerM_switches,
                                          @glimmerHMM_params,
                                          @glimmerHMM_switches
                                         ],
                             -create =>  1,
                         );

       unless (defined($self->program())) {
           $self->throw('Must specify program');
       }

       unless (defined($self->model())) {
           $self->throw('Must specify model');
       }
       
       return $self;
}
rundescriptionprevnextTop
sub run {
    
    my ($self, @seq) = @_;

    unless (@seq) {
        $self->throw("Must supply at least one Bio::PrimarySeqI");
    }
    
    foreach my $seq (@seq) {
        
        unless ($seq->isa('Bio::PrimarySeqI')) {
            $self->throw("Object does not implement Bio::PrimarySeqI");
        }
        
    }

    my $program_name = $self->program_name();
    my $file_name    = $self->_write_seq_file(@seq);

    my @run_args = ( $file_name );

    # Glimmer 2.X ignores sequences after the first in a fasta file
    # Glimmer 3.X will process multiple sequences at once
    if ($program_name eq 'glimmer2') {
        if (@seq > 1) {
            $self->warn("Program $program_name processes one sequence at a time");
        }
        push @run_args, $seq[0]->display_id();
        push @run_args, $seq[0]->length();
    }
    
    return $self->_run(@run_args);
}
_rundescriptionprevnextTop
sub _run {
    
    my ($self, $seq_file_name, $seq_id, $seq_length) = @_;
    
    my @cmd = (
               $self->executable(),
               $seq_file_name,
               $self->model(),
               split(/\s+/, $self->_setparams()),
           );

    my $cmd = join(' ', @cmd);
    $self->debug("Glimmer Command = $cmd");
    
    my $program_name = $self->program_name();
    my ($output_fh, $output_file_name, $detail_file_name);
    my ($program_stdout, $program_stderr);
        
    my @ipc_args = (\@cmd,\u ndef);
    
    # No STDOUT option for glimmer3, it takes a
    # 'tag' argument, and outputs tag.predict and
    # tag.detail.  It seems that tag can be a path,
    # which is handy.  
    if ($program_name eq 'glimmer3') {
        
        my $temp_dir     = $self->tempdir();
        my $glimmer3_tag = "$temp_dir/glimmer3";

        push @cmd, $glimmer3_tag;     
        $output_file_name = "$glimmer3_tag.predict";
        $detail_file_name = "$glimmer3_tag.detail";
        push @ipc_args,\$ program_stdout,\$ program_stderr;
        
    }
    else {
        
        ($output_fh, $output_file_name) = $self->io->tempfile(-dir=>$self->tempdir());
        close($output_fh);
        push @ipc_args, '>', $output_file_name;
        push @ipc_args, '2>',\$ program_stderr;
        
    }

    # Run the program via IPC::Run so:
    # 1) The console doesn't get cluttered up with the program's STDERR/STDOUT
    # 2) We don't have to embed STDERR/STDOUT redirection in $cmd
    # 3) We don't have to deal with signal handling (IPC::Run should take care
    #    of everything automagically. 

    eval {
        IPC::Run::run(@ipc_args) || die $CHILD_ERROR;;
    };

    if ($EVAL_ERROR) {
        $self->throw("Glimmer call crashed: $EVAL_ERROR"); 
    }

    $self->debug(join("\n", 'Glimmer STDOUT:', $program_stdout)) if $program_stdout;
    $self->debug(join("\n", 'Glimmer STDERR:', $program_stderr)) if $program_stderr;
    
    my %parser_args = (-file => $output_file_name);

    # Pass along $seq_id and $seq_length if they were provided
    # (only should be for glimmer2).
    if (defined($seq_id))     { $parser_args{-seqname  } = $seq_id;     }
    if (defined($seq_length)) { $parser_args{-seqlength} = $seq_length; }

    # Pass along the name of extra output file, with handy information about
    # sequence lengths (only produced by glimmer3)
    if (defined($detail_file_name)) { $parser_args{-detail} = $detail_file_name; }
    
    return Bio::Tools::Glimmer->new(%parser_args);
}
_setparamsdescriptionprevnextTop
sub _setparams {
    my ($self) = @_;

    my $param_string = $self->SUPER::_setparams(
                                                -params   => [
                                                              @glimmer2_params,
                                                              @glimmer3_params,
                                                              @glimmerM_params,
                                                              @glimmerHMM_params,
                                                             ],
                                                -switches => [
                                                              @glimmer2_switches,
                                                              @glimmer2_switches,
                                                              @glimmerM_switches,
                                                              @glimmerHMM_switches,
                                                             ],
                                                -dash     => 1

                                            );
    
    # Kill leading and trailing whitespace
    $param_string =~ s/^\s+//g;
    $param_string =~ s/\s+$//g;

    return $param_string;
}
_write_seq_filedescriptionprevnextTop
sub _write_seq_file {
    my ($self, @seq) = @_;
    
    my ($fh, $file_name) = $self->io->tempfile(-dir=>$self->tempdir());
    my $out              = Bio::SeqIO->new(-fh => $fh , '-format' => 'Fasta');

    foreach my $seq (@seq){
	$out->write_seq($seq);
    }

    close($fh);
    $out->close();
    
    return $file_name;

}

1;
}
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 - Mark Johnson Top
 Email: johnsonm-at-gmail-dot-com
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _