tRNAscanSE documentation.

 Title   : program_name
 Usage   : $factory>program_name()
 Function: gets/sets the program name
 Returns:  string
 Args    : string

program_dir

 Title   : program_dir
 Usage   : $factory->program_dir()
 Function: gets/sets the program dir
 Returns:  string
 Args    : string

new

 Title   : new
 Usage   : $tRNAscanSE->new(@params)
 Function: creates a new tRNAscanSE factory
 Returns:  Bio::Tools::Run::tRNAscanSE
 Args    :

run

 Title   :   run
 Usage   :   $obj->run($seq_file)
 Function:   Runs tRNAscan-SE
 Returns :   A Bio::Tools::tRNAscanSE object
 Args    :   An array of Bio::PrimarySeqI objects

_run

 Title   :   _run
 Usage   :   $obj->_run()
 Function:   Internal(not to be used directly)
 Returns :   An instance of Bio::Tools::tRNAscanSE 
 Args    :   file name

_write_seq_file

 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_name

sub program_name {

    
    my ($self, $val) = @_;
    
    $self->program($val) if $val;
    
    return $self->program();

}

program_dir

sub program_dir {

    
    my ($self, $val) = @_;
    
    $self->{'_program_dir'} = $val if $val;
    
    return $self->{'_program_dir'};

}

new

sub new {

    
       my ($class,@args) = @_;
       my $self = $class->SUPER::new(@args);
       
       $self->io->_initialize_io();

       $self->_set_from_args(\@
                             args,
                             -methods => [
                                          @params,
                                          @tRNAscanSE_switches,
                                         ],
                             -create =>  1,
                         );

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

       return $self;

}

run

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);

    return $self->_run($file_name);

}

_run

sub _run {

    
    my ($self, $seq_file_name) = @_;
    
    my @cmd = (
               $self->executable(),
               split(/\s+/, $self->_setparams()),
               $seq_file_name,
           );

    my $cmd = join(' ', @cmd);
    $self->debug("tRNAscan-SE Command = $cmd");
    
    my $program_name = $self->program_name();
    my ($program_stderr);

    my ($output_fh, $output_file_name) = $self->io->tempfile(-dir=> $self->tempdir());
    
    
    my @ipc_args = (\@cmd,\u ndef, '>', $output_file_name, '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("tRNAscan-SE call crashed: $EVAL_ERROR"); 
    }

    $self->debug(join("\n", 'tRNAscanSE STDERR:', $program_stderr)) if $program_stderr;
        
    return Bio::Tools::tRNAscanSE->new(-file => $output_file_name);

}

_setparams

description

sub _setparams {

    my ($self) = @_;

    my $param_string = $self->SUPER::_setparams(
                                                -params   => [ ],
                                                -switches => [
                                                              @tRNAscanSE_switches,
                                                             ],
                                                -dash     => 1

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

    return $param_string;

}

_write_seq_file

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

FEEDBACK

Mailing Lists

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

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
the bugs and their resolution. Bug reports can be submitted via the
web:

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

AUTHOR - Mark Johnson

 Email: johnsonm-at-gmail-dot-com

APPENDIX