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Summary

Bio::Tools::Run::EMBOSSApplication - class for EMBOSS Applications

Package variables

Included modules

Inherit

Bio::Root::Root Bio::Tools::Run::WrapperBase

Synopsis

  use Bio::Factory::EMBOSS;
  # get an EMBOSS application object from the EMBOSS factory
  $factory = Bio::Factory::EMBOSS->new();
  $application = $factory->program('embossversion');
  # run the application with an optional hash containing parameters
  $result = $application->run(); # returns a string or creates a file
  print $result . "\n";

  $water = $factory->program('water');

  # here is an example of running the application
  # water can compare 1 seq against 1->many sequences
  # in a database using Smith-Waterman
  my $seq_to_test;     # this would have a seq here
  my @seqs_to_check; # this would be a list of seqs to compare 

  my $wateroutfile = 'out.water';
  $water->run({-sequencea => $seq_to_test,
               -seqall    => \@seqs_to_check,
               -gapopen   => '10.0',
               -gapextend => '0.5',
               -outfile   => $wateroutfile});
  # now you might want to get the alignment
  use Bio::AlignIO;
  my $alnin = Bio::AlignIO->new(-format => 'emboss',
			                      -file   => $wateroutfile);

  while ( my $aln = $alnin->next_aln ) {
      # process the alignment -- these will be Bio::SimpleAlign objects
  }

Description

The EMBOSSApplication class can represent EMBOSS any program. It is
created by a Bio::Factory::EMBOSS object.
If you want to check command line options before sending them to the
program set $prog->verbose to positive integer. The ADC
description of the available command line options is then parsed in
and compared to input.
See also Bio::Factory::EMBOSS and Bio::Tools::Run::EMBOSSacd.

Methods

Methods description

 Title   : run
 Usage   : $embossapplication->run($attribute_hash)
 Function: Runs the EMBOSS program.
 Returns : string or creates files for now; will return objects!
 Args    : hash of input to the program

 Title   : acd
 Usage   : $embossprogram->acd
 Function: finds out all the possible qualifiers for this
           EMBOSS application. They can be used to debug the
           options given.
 Throws  : 
 Returns : boolean
 Args    :

 Title   : name
 Usage   : $embossprogram->name
 Function: sets/gets the name of the EMBOSS program
           Setting is done by the EMBOSSFactory object,
           you should only get it.
 Throws  : 
 Returns : name string
 Args    : None

 Title   : descr
 Usage   : $embossprogram->descr
 Function: sets/gets the descr of the EMBOSS program
           Setting is done by the EMBOSSFactory object,
           you should only get it.
 Throws  : 
 Returns : description string
 Args    : None

 Title   : group
 Usage   : $embossprogram->group
 Function: sets/gets the group of the EMBOSS program
           Setting is done by the EMBOSSFactory object,
           you should only get it.

           If the application is assigned into a subgroup
           use l to get it.
 Throws  : 
 Returns : string, group name
 Args    : group string

 Title   : subgroup
 Usage   : $embossprogram->subgroup
 Function: sets/gets the subgroup of the EMBOSS program
           Setting is done by the EMBOSSFactory object,
           you should only get it.
 Throws  : 
 Returns : string, subgroup name; undef if not defined
 Args    : None

 Title   : program_dir
 Usage   :
 Function: Required by WrapperBase
 Throws  :
 Returns : Name of directory with EMBOSS programs
 Args    :

 Title   : program_path
 Usage   :
 Function: Required by WrapperBase
 Throws  :
 Returns : Full path of program
 Args    :

 Title   : executable
 Usage   :
 Function: Required by WrapperBase
 Throws  :
 Returns : Name of program
 Args    :

Methods code

sub new {

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

  $self->name($args->{'name'});
  $self->verbose($args->{'verbose'});

  $self->acd if $self->verbose > 0;

  return $self;

}

sub run {

	my ($self, $input) = @_;
	$self->io->_io_cleanup();
	# test input
	$self->debug( Dumper($input) );

	# parse ACD information
	$self->acd if $self->verbose > 0;

	# collect the options into a string
	my $option_string = '';
	foreach my $attr (keys %{$input}) {
		my $attr_name = substr($attr, 1) if substr($attr, 0, 1) =~ /\W/;

		my $array = 0;

		if( defined $input->{$attr} && ref($input->{$attr}) ) {

			my (@pieces);

			if( $array = (ref($input->{$attr}) =~ /array/i) ) {
				foreach my $s ( @{$input->{$attr}} ) {
					@pieces = @{$input->{$attr}};
				}
			} else {
				@pieces = ($input->{$attr});
			}
			if( ! defined $pieces[0] ) {
				# we ignore for now
				$self->warn("specified a parameter $attr with no value");
				$input->{$attr} = undef;
				return;
			} elsif( $pieces[0]->isa('Bio::PrimarySeqI') ) {
				unless(  $SEQIOLOADED ) { 
					require Bio::SeqIO;
					$SEQIOLOADED = 1;
				}
				my ($tfh,$tempfile) = $self->io->tempfile(-dir => $self->tempdir);
				my $out = Bio::SeqIO->new(-format => 'fasta',
												 -fh     => $tfh);
				foreach my $seq ( @pieces ) {
					$out->write_seq($seq);
				}
				$out->close();
				$input->{$attr} = $tempfile;
				close($tfh);
				undef $tfh;
			} elsif( $pieces[0]->isa('Bio::Align::AlignI') ) {
				unless(  $ALIGNIOLOADED ) { 
					require Bio::AlignIO;
					$ALIGNIOLOADED = 1;
				}
				my ($tfh,$tempfile) = $self->io->tempfile();
				my $out = Bio::AlignIO->new(-format => 'msf',
													-fh     => $tfh);
				foreach my $p ( @pieces ) {
					$out->write_aln($p);
				}
				$input->{$attr} = $tempfile;
				close($tfh);
				undef $tfh;
			}
		}

		# check each argument against ACD
		if ($self->verbose > 0) {

			last unless defined $self->acd; # might not have the parser

			$self->throw("Attribute [$attr] not recognized!\n")
			  unless $self->acd->qualifier($attr);
		}

		# print out debugging info
		$self->debug("Input attr: ". $attr_name. " => ".
						 $input->{$attr}. "\n");
		$option_string .= " " . $attr;
		$option_string .= " ". $input->{$attr}
		  if defined $input->{$attr};
	}

	# check mandatory attributes against given ones
	if ($self->verbose > 0) {
		last unless defined $self->acd; # might not have the parser
		#	$self->acd->mandatory->print;
		#	if ($self->name eq 'water') {
		#	    print Dumper($self->acd->mandatory);
		#	}
		foreach my $attr (keys %{$self->acd->mandatory} ) {
			last unless defined $self->acd; # might not have the parser
			unless (defined $input->{$attr}) {
				print "-" x 38, "\n", "MISSING MANDATORY ATTRIBUTE: $attr\n", 
				  "-" x 38, "\n";
				$self->acd->print($attr) and
				  $self->throw("Program ". $self->name.
									" needs attribute [$attr]!\n")
			  }
		}
	}
	my $runstring = join (' ', $self->name, $option_string, '-auto');
	$self->debug( "Command line: ", $runstring, "\n"); 
	return `$runstring`;

}

sub acd {

    my ($self) = @_;
    unless ( $self->{'_acd'} ) {
	$self->{'_acd'} =
	    Bio::Tools::Run::EMBOSSacd->new($self->name);
    }
    return $self->{'_acd'};

}

sub name {

    my ($self,$value) = @_;
    if (defined $value) {
	$self->{'_name'} = $value;
    }
    return $self->{'_name'};

}

sub descr {

    my ($self,$value) = @_;
    if (defined $value) {
	$self->{'_descr'} = $value;
    }
    return $self->{'_descr'};

}

sub group {

    my ($self,$value) = @_;
    if (defined $value) {
	my ($group, $subgroup) = split ':', $value;
	$self->{'_group'} = $group;
	$self->{'_subgroup'} = $subgroup;
    }
    return $self->{'_group'};

}

sub subgroup {

    my ($self) = @_;
    return $self->{'_subgroup'};

}

sub program_dir {

	return Bio::Root::IO->catfile($ENV{EMBOSS_ACDROOT});

}

sub program_path {

	my $self = shift;
	my $name = $self->{_name};
	my $dir = Bio::Root::IO->catfile($ENV{EMBOSS_ACDROOT});
	return "$dir/$name";

}

sub executable {

	my $self = shift;
	$self->{_name};
}

1;

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
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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.

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/

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The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _