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lib/Bio/Tools/Run/Primer3.pm  view on Meta::CPAN

}

=head2 run()

 Title   : run()
 Usage   : $primer3->run();
 Function: Run the primer3 program with the arguments that you have supplied.
 Returns : A Bio::Tools::Primer3 object containing the results.
 Args    : None.
 Note    : See the Bio::Tools::Primer3 documentation for those functions.

=cut

sub run {
	my($self) = @_;
	my $executable = $self->executable;
	my $input = $self->{'primer3_input'};
	unless ($executable && -e $executable) {
		$self->throw("Executable was not found. Do not know where primer3 is!") if !$executable;
		$self->throw("$executable was not found. Do not know where primer3 is!");
		exit(-1);
	}

	# note that I write this to a temp file because we need both read 
	# and write access to primer3, therefore,
	# we can't use a simple pipe.

	if ($self->{'verbose'}) {print STDERR "TRYING\n", 
				 join "\n", @{$self->{'primer3_input'}}, "=\n"}

	# make a temporary file and print the instructions to it.
	my ($temphandle, $tempfile) = $self->io->tempfile;
	print $temphandle join "\n", @{$self->{'primer3_input'}}, "=\n";
	close($temphandle);

  my $executable_command = $executable;
  if ( $executable =~ m{^[^\'\"]+(.+)[^\'\"]+$} ) { 
    $executable_command = "\"$executable\" < \"$tempfile\"|";
  }

	open (RESULTS, $executable_command) || $self->throw("Can't open RESULTS");
	if ($self->{'_outfilename'}) {
		# I can't figure out how to use either of these to write the results out.
		# neither work, what am I doing wrong or missing in the docs?
		#  $self->{output}=$self->_initialize_io(-file=>$self->{'outfile'});
		#  $self->{output}=$self->io;
		# OK, for now, I will just do it myself, because I need this to 
		# check the parser :)
		open (OUT, ">".$self->{'_outfilename'}) || 
		  $self->throw("Can't open ".$self->{'_outfilename'}." for writing");
	}

	my @results;
	while (<RESULTS>) {
	    if ($self->{'_outfilename'}) {
		# this should work, but isn't
		#$self->{output}->_print($_);
		print OUT $_;
	    }
	    chomp;
	    next if( $_ eq '='); # skip over bolderio record terminator
	    my ($return, $value) = split('=',$_);
	    $self->{'results'}->{$return} = $value;
	}
	close RESULTS;

	# close the output file
	if ($self->{'_outfilename'}) { 
		close OUT;
	}

	$self->cleanup;
	# convert the results to individual results
	$self->{results_obj} = Bio::Tools::Primer3->new;
	$self->{results_obj}->_set_variable('results', $self->{results});
	$self->{results_obj}->_set_variable('seqobject', $self->{seqobject});

        # Bio::Tools::Primer3::_separate needs a hash of the primer3 arguments,
 	# with the arg as the key and the value as the value (surprise!).
 	my %input_hash = map {split '='} @{$self->{'primer3_input'}};
 	$self->{results_obj}->_set_variable('input_options', \%input_hash);
	$self->{results_separated}= $self->{results_obj}->_separate();
	return $self->{results_obj};
}

=head2 arguments()

 Title   : arguments()
 Usage   : $hashref = $primer3->arguments();
 Function: Describes the options that you can set through Bio::Tools::Run::Primer3, 
           with a brief (one line) description of what they are and their 
           default values
 Returns : A string (if an argument is supplied) or a reference to a hash.
 Args    : If supplied with an argument will return a string of its 
           description.
           If no arguments are supplied, will return all the arguments as a 
           reference to a hash
 Notes   : Much of this is taken from the primer3 README file, and you should 
           read that file for a more detailed description.

=cut

sub arguments {
	my ($self, $required) = @_;
	unless ($self->{'input_options'}) {$self->_input_args}
	if ($required) {return ${$self->{'input_options'}}{'$required'}}
	else {return $self->{'input_options'}}
}

=head2  version

 Title   : version
 Usage   : $v = $prog->version();
 Function: Determine the version number of the program
 Example :
 Returns : float or undef
 Args    : none

=cut

sub version {