Summary

Bio::SearchIO - Driver for parsing Sequence Database Searches (Blast,FASTA,...)

Package variables

Included modules

Inherit

Bio::AnalysisParserI Bio::Event::EventGeneratorI Bio::Root::IO

Synopsis

    use Bio::SearchIO;
    # format can be 'fasta', 'blast'
    my $searchio = new Bio::SearchIO( -format => 'blastxml',
                                      -file   => 'blastout.xml' );
    while ( my $result = $searchio->next_result() ) {
       while( my $hit = $result->next_hit ) {
	# process the Bio::Search::Hit::HitI object
           while( my $hsp = $hit->next_hsp ) { 
	    # process the Bio::Search::HSP::HSPI object
	}
    }

Description

This is a driver for instantiating a parser for report files from
sequence database searches. This object serves as a wrapper for the
format parsers in Bio::SearchIO::* - you should not need to ever
use those format parsers directly. (For people used to the SeqIO
system it, we are deliberately using the same pattern).
Once you get a SearchIO object, calling next_result() gives you back
a Bio::Search::Result::ResultI compliant object, which is an object that
represents one Blast/Fasta/HMMER whatever report.

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::SearchIO();
 Function: Builds a new Bio::SearchIO object 
 Returns : Bio::SearchIO initialized with the correct format
 Args    : Args    : -file => $filename
           -format => format
           -fh => filehandle to attach to
           -result_factory => Object implementing Bio::Factory::ResultFactoryI
           -hit_factory    => Object implementing Bio::Factory::HitFactoryI
           -writer         => Object implementing Bio::SearchIO::SearchWriterI
           -output_format  => output format, which will dynamically load writer

 Title   : newFh
 Usage   : $fh = Bio::SearchIO->newFh(-file=>$filename,
                                      -format=>'Format')
 Function: does a new() followed by an fh()
 Example : $fh = Bio::SearchIO->newFh(-file=>$filename,
                                      -format=>'Format')
           $result = <$fh>;   # read a ResultI object
           print $fh $result; # write a ResultI object
 Returns : filehandle tied to the Bio::SearchIO::Fh class
 Args    :

 Title   : fh
 Usage   : $obj->fh
 Function:
 Example : $fh = $obj->fh;      # make a tied filehandle
           $result = <$fh>;     # read a ResultI object
           print $fh $result;   # write a ResultI object
 Returns : filehandle tied to the Bio::SearchIO::Fh class
 Args    :

 Title   : attach_EventHandler
 Usage   : $parser->attatch_EventHandler($handler)
 Function: Adds an event handler to listen for events
 Returns : none
 Args    : Bio::SearchIO::EventHandlerI

 Title   : _eventHandler
 Usage   : private
 Function: Get the EventHandler
 Returns : Bio::SearchIO::EventHandlerI
 Args    : none

 Title   : next_result
 Usage   : $result = stream->next_result
 Function: Reads the next ResultI object from the stream and returns it.

           Certain driver modules may encounter entries in the stream that
           are either misformatted or that use syntax not yet understood
           by the driver. If such an incident is recoverable, e.g., by
           dismissing a feature of a feature table or some other non-mandatory
           part of an entry, the driver will issue a warning. In the case
           of a non-recoverable situation an exception will be thrown.
           Do not assume that you can resume parsing the same stream after
           catching the exception. Note that you can always turn recoverable
           errors into exceptions by calling $stream->verbose(2) (see
           Bio::Root::RootI POD page).
 Returns : A Bio::Search::Result::ResultI object
 Args    : n/a

 Title   : write_result
 Usage   : $stream->write_result($result_result, @other_args)
 Function: Writes data from the $result_result object into the stream.
         : Delegates to the to_string() method of the associated 
         : WriterI object.
 Returns : 1 for success and 0 for error
 Args    : Bio::Search:Result::ResultI object,
         : plus any other arguments for the Writer
 Throws  : Bio::Root::Exception if a Writer has not been set.

 Title   : writer
 Usage   : $writer = $stream->writer;
 Function: Sets/Gets a SearchWriterI object to be used for this searchIO.
 Returns : 1 for success and 0 for error
 Args    : Bio::SearchIO::SearchWriterI object (when setting)
 Throws  : Bio::Root::Exception if a non-Bio::SearchIO::SearchWriterI object
           is passed in.

 Title   : hit_factory
 Usage   : $hit_factory = $stream->hit_factory;  (get)
         : $stream->hit_factory( $factory );     (set)
 Function: Sets/Gets a factory object to create hit objects for this SearchIO
 Returns : Bio::Factory::HitFactoryI object 
 Args    : Bio::Factory::HitFactoryI object (when setting)
 Throws  : Bio::Root::Exception if a non-Bio::Factory::HitFactoryI object  
           is passed in.
 Comments: A SearchIO implementation should provide a default hit factory.

 Title   : result_factory
 Usage   : $result_factory = $stream->result_factory;  (get)
         : $stream->result_factory( $factory );        (set)
 Function: Sets/Gets a factory object to create result objects for this
           SearchIO.
 Returns : Bio::Factory::ResultFactoryI object 
 Args    : Bio::Factory::ResultFactoryI object (when setting)
 Throws  : Bio::Root::Exception if a non-Bio::Factory::ResultFactoryI object
           is passed in.
 Comments: A SearchIO implementation should provide a default result factory.

 Title   : result_count
 Usage   : $num = $stream->result_count;
 Function: Gets the number of Blast results that have been parsed.
 Returns : integer
 Args    : none
 Throws  : none

 Title   : default_hit_factory_class
 Usage   : $res_factory = $obj->default_hit_factory_class()->new( @args )
 Function: Returns the name of the default class to be used for creating
           Bio::Search::Hit::HitI objects.
 Example :
 Returns : A string containing the name of a class that implements 
           the Bio::Search::Hit::HitI interface.
 Args    : none
 Comments: Bio::SearchIO does not implement this method. It throws a
           NotImplemented exception

 Title   : _load_format_module
 Usage   : *INTERNAL SearchIO stuff*
 Function: Loads up (like use) a module at run time on demand
 Example : 
 Returns : 
 Args    :

 Title   : _guess_format
 Usage   : $obj->_guess_format($filename)
 Function:
 Example :
 Returns : guessed format of filename (lower case)
 Args    :

Methods code

sub new {

  my($caller,@args) = @_;
  my $class = ref($caller) || $caller;
    
  # or do we want to call SUPER on an object if $caller is an
  # object?
  if( $class =~ /Bio::SearchIO::(\S+)/ ) {
    my ($self) = $class->SUPER::new(@args);	
    $self->_initialize(@args);
    return $self;
  } else { 
    my %param = @args;
    @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
    my $format = $param{'-format'} ||
      $class->_guess_format( $param{'-file'} || $ARGV[0] ) || 'blast';

    my $output_format = $param{'-output_format'};
    my $writer = undef;

    if( defined $output_format ) {
	if( defined $param{'-writer'} ) {
	    my $dummy = Bio::Root::Root->new();
	    $dummy->throw("Both writer and output format specified - not good");
	}

	if( $output_format =~ /^blast$/i ) {
	    $output_format = 'TextResultWriter';
	}
	my $output_module = "Bio::SearchIO::Writer::".$output_format;
	$class->_load_module($output_module);
	$writer = $output_module->new();
	push(@args,"-writer",$writer);
    }


    # normalize capitalization to lower case
    $format = "\L$format";
    
    return undef unless( $class->_load_format_module($format) );
    return "Bio::SearchIO::${format}"->new(@args);
  }

}

sub newFh {

  my $class = shift;
  return unless my $self = $class->new(@_);
  return $self->fh;

}

sub fh {

  my $self = shift;
  my $class = ref($self) || $self;
  my $s = Symbol::gensym;
  tie $$s,$class,$self;
  return $s;

}

sub attach_EventHandler {

    my ($self,$handler) = @_;
    return if( ! $handler );
    if( ! $handler->isa('Bio::SearchIO::EventHandlerI') ) {
	$self->warn("Ignoring request to attatch handler ".ref($handler). ' because it is not a Bio::SearchIO::EventHandlerI');
    }
    $self->{'_handler'} = $handler;
    return;

}

sub _eventHandler {

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

}

sub _initialize {

    my($self, @args) = @_;
    $self->{'_handler'} = undef;
    # not really necessary unless we put more in RootI
    #$self->SUPER::_initialize(@args);
    
    # initialize the IO part
    $self->_initialize_io(@args);
    $self->attach_EventHandler(new Bio::SearchIO::SearchResultEventBuilder());
    $self->{'_reporttype'} = '';

    my ( $writer, $rfactory, $hfactory, $use_factories ) =
      $self->_rearrange([qw(WRITER 
			    RESULT_FACTORY 
			    HIT_FACTORY
			    USE_FACTORIES)], @args);

    $self->writer( $writer ) if $writer;

    # TODO: Resolve this issue:
    # The $use_factories flag is a temporary hack to allow factory-based and 
    # non-factory based SearchIO objects to co-exist. 
    # steve --- Sat Dec 22 04:41:20 2001
    if( $use_factories) {
      if( not defined $self->{'_result_factory'}) {
	$self->result_factory( $rfactory || $self->default_result_factory_class->new );
      }
      if( not defined $self->{'_hit_factory'}) {
	$self->hit_factory( $hfactory || $self->default_hit_factory_class->new );
      }
    }

}

sub next_result {

   my ($self) = @_;
   $self->throw_not_implemented;

}

sub write_result {

   my ($self, $result, @args) = @_;

   if( not ref($self->{'_result_writer'}) ) {
       $self->throw("ResultWriter not defined.");
   }
   my $str = $self->writer->to_string( $result, @args );
   #print "Got string: \n$str\n";
   $self->_print( "$str" );
   
   return 1;

}

sub writer {

    my ($self, $writer) = @_;
    if( ref($writer) and $writer->isa( 'Bio::SearchIO::SearchWriterI' )) {
        $self->{'_result_writer'} = $writer;
    }
    elsif( defined $writer ) {
        $self->throw("Can't set ResultWriter. Not a Bio::SearchIO::SearchWriterI: $writer");
    }
    return $self->{'_result_writer'};

}

sub hit_factory {

    my ($self, $fact) = @_;
    if( ref $fact and $fact->isa( 'Bio::Factory::HitFactoryI' )) {
    	   $self->{'_hit_factory'} = $fact;
    }
    elsif( defined $fact ) {
        $self->throw("Can't set HitFactory. Not a Bio::Factory::HitFactoryI: $fact");
    }
    return $self->{'_hit_factory'};

}

sub result_factory {

    my ($self, $fact) = @_;
    if( ref $fact and $fact->isa( 'Bio::Factory::ResultFactoryI' )) {
    	   $self->{'_result_factory'} = $fact;
    }
    elsif( defined $fact ) {
        $self->throw("Can't set ResultFactory. Not a Bio::Factory::ResultFactoryI: $fact");
    }
    return $self->{'_result_factory'};

}

sub result_count {

    my $self = shift;
    $self->throw_not_implemented;

}

sub default_hit_factory_class {

    my $self = shift;
# TODO: Uncomment this when Jason's SearchIO code conforms
#    $self->throw_not_implemented;

}

sub _load_format_module {

  my ($self,$format) = @_;
  my $module = "Bio::SearchIO::" . $format;
  my $ok;
  
  eval {
      $ok = $self->_load_module($module);
  };
  if ( $@ ) {
      print STDERR <<END
$self: $format cannot be found
Exception $@
For more information about the SearchIO system please see the SearchIO docs.
This includes ways of checking for formats at compile time, not run time
END
  ;
  }
  return $ok;

}

sub _guess_format {

   my $class = shift;
   return unless $_ = shift;
   return 'blast'   if (/blast/i or /\.bl\w$/i);
   return 'fasta' if (/fasta/i or /\.fas$/i);
   return 'blastxml' if (/blast/i and /\.xml$/i);
   return 'exonerate' if ( /\.exonerate/i or /\.exon/i );

}

sub close {

     my $self = shift;
    if( $self->writer ) {
	$self->_print($self->writer->end_report());
    }
    $self->SUPER::close(@_);

}

sub DESTROY {

    my $self = shift;
    $self->close();

}

sub TIEHANDLE {

  my $class = shift;
  return bless {processor => shift}, $class;

}

sub READLINE {

  my $self = shift;
  return $self->{'processor'}->next_result() unless wantarray;
  my (@list, $obj);
  push @list, $obj while $obj = $self->{'processor'}->next_result();
  return @list;

}

sub PRINT {

  my $self = shift;
  $self->{'processor'}->write_result(@_);

}

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 Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:

  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/

Email jason@bioperl.org
Email sac@bioperl.org

Additional contributors names and emails here

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