Bio::SearchIO wise
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::SearchIO::wise - Parsing of wise output as alignments
Package variables
No package variables defined.
Included modules
Bio::SearchIO
Bio::Tools::Genewise
Bio::Tools::Genomewise
Inherit
Bio::SearchIO
Synopsis
  use Bio::SearchIO;
  my $parser = new Bio::SearchIO(-file    => 'file.genewise', 
                                 -format  => 'wise',
                                 -wisetype=> 'genewise');

  while( my $result = $parser->next_result ) {}
Description
This object parsers Wise output using Bio::Tools::Genewise or
Bio::Tools::Genomewise as a helper.
Methods
_initialize
No description
Code
next_resultDescriptionCode
start_elementDescriptionCode
end_elementDescriptionCode
elementDescriptionCode
charactersDescriptionCode
within_elementDescriptionCode
in_elementDescriptionCode
start_documentDescriptionCode
end_documentDescriptionCode
write_result
No description
Code
result_count
No description
Code
report_count
No description
Code
wiseDescriptionCode
wisetypeDescriptionCode
Methods description
next_resultcode    nextTop
 Title   : next_result
 Usage   : my $hit = $searchio->next_result;
 Function: Returns the next Result from a search
 Returns : Bio::Search::Result::ResultI object
 Args    : none
start_elementcodeprevnextTop
 Title   : start_element
 Usage   : $eventgenerator->start_element
 Function: Handles a start element event
 Returns : none
 Args    : hashref with at least 2 keys 'Data' and 'Name'
end_elementcodeprevnextTop
 Title   : start_element
 Usage   : $eventgenerator->end_element
 Function: Handles an end element event
 Returns : none
 Args    : hashref with at least 2 keys 'Data' and 'Name'
elementcodeprevnextTop
 Title   : element
 Usage   : $eventhandler->element({'Name' => $name, 'Data' => $str});
 Function: Convience method that calls start_element, characters, end_element
 Returns : none
 Args    : Hash ref with the keys 'Name' and 'Data'
characterscodeprevnextTop
 Title   : characters
 Usage   : $eventgenerator->characters($str)
 Function: Send a character events
 Returns : none
 Args    : string
within_elementcodeprevnextTop
 Title   : within_element
 Usage   : if( $eventgenerator->within_element($element) ) {}
 Function: Test if we are within a particular element
           This is different than 'in' because within can be tested
           for a whole block.
 Returns : boolean
 Args    : string element name
in_elementcodeprevnextTop
 Title   : in_element
 Usage   : if( $eventgenerator->in_element($element) ) {}
 Function: Test if we are in a particular element
           This is different than 'in' because within can be tested
           for a whole block.
 Returns : boolean
 Args    : string element name
start_documentcodeprevnextTop
 Title   : start_document
 Usage   : $eventgenerator->start_document
 Function: Handle a start document event
 Returns : none
 Args    : none
end_documentcodeprevnextTop
 Title   : end_document
 Usage   : $eventgenerator->end_document
 Function: Handles an end document event
 Returns : Bio::Search::Result::ResultI object
 Args    : none
wisecodeprevnextTop
 Title   : wise
 Usage   : $obj->wise($newval)
 Function: Get/Set the Wise object parser
 Returns : value of wise (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
wisetypecodeprevnextTop
 Title   : wisetype
 Usage   : $obj->wisetype($newval)
 Function: Wise program type
 Returns : value of wisetype (a scalar)
 Args    : on set, new value (a scalar or undef, optional)
Methods code
_initializedescriptionprevnextTop
sub _initialize {
    my ($self,@args) = @_;
    my ( $wisetype, $file,$fh ) =
	$self->_rearrange([qw(WISETYPE FILE FH)], @args);
    my @newargs;
    while( @args ) {
	my $a = shift @args;
	if( $a =~ /FILE|FH/i ) {
	    shift @args;
	    next;
	}
	push @newargs, $a, shift @args;
    }
    $self->SUPER::_initialize(@newargs);

    # Optimization: caching the EventHandler 
    # since it's use a lot during the parse.
    $self->{'_handler_cache'} = $self->_eventHandler;

    $self->wisetype($wisetype);
    my @ioargs;
    if( $fh ) { 
	push @ioargs, ('-fh' => $fh);
    } elsif( $file ) {
	push @ioargs, ('-file' => $file);
    }

    if( $wisetype =~ /genewise/i ) {
	$self->wise(new Bio::Tools::Genewise(@ioargs));
    } elsif( $wisetype =~ /genomewise/i ) {
	$self->wise(new Bio::Tools::Genomewise(@ioargs));
    } else { 
	$self->throw("Must supply a -wisetype to ".ref($self)." which is one of 'genomewise' 'genewise'\n");
    }
    return $self;
}
next_resultdescriptionprevnextTop
sub next_result {
   my ($self) = @_;

   return undef unless $self->wise;
   my $prediction = $self->wise->next_prediction;
   return undef unless $prediction;
   $self->{'_reporttype'} = uc $self->wisetype;
   $self->start_element({'Name' => 'WiseOutput'});
   $self->element({'Name' => 'WiseOutput_program',
		   'Data' => $self->wisetype});
   $self->element({'Name' => 'WiseOutput_query-def',
		   'Data' => $self->wise->_target_id});
   my @transcripts = $prediction->transcripts;

   foreach my $transcript ( @transcripts ) {
       my @exons =  $transcript->exons;
       my $protid;
       $self->start_element({'Name' => 'Hit'});
       
       if( $exons[0]->has_tag('supporting_feature') ) {
	   my ($supporting_feature) = $exons[0]->get_tag_values('supporting_feature');
	   $protid = $supporting_feature->feature2->seq_id;
	   $self->element({'Name' => 'Hit_id',
			   'Data' => $protid});       
       } 
       $self->element({'Name' => 'Hit_score',
		       'Data' => $exons[0]->score});
       foreach my $exon ( @exons ) {
	   $self->start_element({'Name' => 'Hsp'});
	   if( $exon->strand < 0 ) { 
	       $self->element({'Name' => 'Hsp_query-from',
			       'Data' => $exon->end});
	       $self->element({'Name' => 'Hsp_query-to',
			       'Data' => $exon->start});
	   } else { 
	       $self->element({'Name' => 'Hsp_query-from',
			       'Data' => $exon->start});
	       $self->element({'Name' => 'Hsp_query-to',
			       'Data' => $exon->end});
	   }
	   $self->element({'Name' => 'Hsp_score',
			   'Data' => $exon->score});
	   if( $exon->has_tag('supporting_feature') ) {
	       my ($sf) = $exon->get_tag_values('supporting_feature');
	       my $protein = $sf->feature2;
	       if( $protein->strand < 0 ) {
		   $self->element({'Name' => 'Hsp_hit-from',
				   'Data' => $protein->end});
		   $self->element({'Name' => 'Hsp_hit-to',
				   'Data' => $protein->start});
	       } else { 
		   $self->element({'Name' => 'Hsp_hit-from',
				   'Data' => $protein->start});
		   $self->element({'Name' => 'Hsp_hit-to',
				   'Data' => $protein->end});
	       }
	   }
	   $self->element({'Name' => 'Hsp_identity',
			   'Data' => 0});
	   $self->element({'Name' => 'Hsp_positive',
			   'Data' => 0});
	   $self->end_element({'Name' => 'Hsp'});
       }
       $self->end_element({'Name' => 'Hit'});
   }
   $self->end_element({'Name' => 'WiseOutput'});
   return $self->end_document();
}
start_elementdescriptionprevnextTop
sub start_element {
   my ($self,$data) = @_;
   # we currently don't care about attributes
   my $nm = $data->{'Name'};
   my $type = $MODEMAP{$nm};

   if( $type ) {
       if( $self->_eventHandler->will_handle($type) ) {
	   my $func = sprintf("start_%s",lc $type);
	   $self->_eventHandler->$func($data->{'Attributes'});
       }
       unshift @{$self->{'_elements'}}, $type;

       if($type eq 'result') {
	   $self->{'_values'} = {};
	   $self->{'_result'}= undef;
       }
   }
}
end_elementdescriptionprevnextTop
sub end_element {
    my ($self,$data) = @_;
    my $nm = $data->{'Name'};
    my $type = $MODEMAP{$nm};
    my $rc;

    if( $type = $MODEMAP{$nm} ) {
	if( $self->_eventHandler->will_handle($type) ) {
	    my $func = sprintf("end_%s",lc $type);
	    $rc = $self->_eventHandler->$func($self->{'_reporttype'},
					      $self->{'_values'});
	}
	shift @{$self->{'_elements'}};

    } elsif( $MAPPING{$nm} ) {

	if ( ref($MAPPING{$nm}) =~ /hash/i ) {
	    my $key = (keys %{$MAPPING{$nm}})[0];
	    $self->{'_values'}->{$key}->{$MAPPING{$nm}->{$key}} = $self->{'_last_data'};
	} else {
	    $self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'};
	}
    } else {
	$self->debug( "unknown nm $nm, ignoring\n");
    }
    $self->{'_last_data'} = ''; # remove read data if we are at
				# end of an element
    $self->{'_result'} = $rc if( defined $type && $type eq 'result' );
    return $rc;
}
elementdescriptionprevnextTop
sub element {
   my ($self,$data) = @_;
   $self->start_element($data);
   $self->characters($data);
   $self->end_element($data);
}
charactersdescriptionprevnextTop
sub characters {
   my ($self,$data) = @_;

   return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/ );

   $self->{'_last_data'} = $data->{'Data'};
}
within_elementdescriptionprevnextTop
sub within_element {
   my ($self,$name) = @_;
   return 0 if ( ! defined $name &&
		 ! defined  $self->{'_elements'} ||
		 scalar @{$self->{'_elements'}} == 0) ;
   foreach (  @{$self->{'_elements'}} ) {
       if( $_ eq $name  ) {
	   return 1;
       }
   }
   return 0;
}
in_elementdescriptionprevnextTop
sub in_element {
   my ($self,$name) = @_;
   return 0 if ! defined $self->{'_elements'}->[0];
   return ( $self->{'_elements'}->[0] eq $name)
}
start_documentdescriptionprevnextTop
sub start_document {
    my ($self) = @_;
    $self->{'_lasttype'} = '';
    $self->{'_values'} = {};
    $self->{'_result'}= undef;
    $self->{'_elements'} = [];
    $self->{'_reporttype'} = 'exonerate';
}
end_documentdescriptionprevnextTop
sub end_document {
   my ($self,@args) = @_;
   return $self->{'_result'};
}
write_resultdescriptionprevnextTop
sub write_result {
   my ($self, $blast, @args) = @_;

   if( not defined($self->writer) ) {
       $self->warn("Writer not defined. Using a $DEFAULT_WRITER_CLASS");
       $self->writer( $DEFAULT_WRITER_CLASS->new() );
   }
   $self->SUPER::write_result( $blast, @args );
}
result_countdescriptionprevnextTop
sub result_count {
    my $self = shift;
    return $self->{'_result_count'};
}
report_countdescriptionprevnextTop
sub report_count {
 shift->result_count
}
wisedescriptionprevnextTop
sub wise {
    my $self = shift;
    return $self->{'wise'} = shift if @_;
    return $self->{'wise'};
}
wisetypedescriptionprevnextTop
sub wisetype {
    my $self = shift;

    return $self->{'wisetype'} = shift if @_;
    return $self->{'wisetype'};
}
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
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists
Reporting BugsTop
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
the web:
  http://bugzilla.bioperl.org/
AUTHOR - Jason StajichTop
Email jason-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 Title   : new
 Usage   : my $obj = new Bio::SearchIO::wise();
 Function: Builds a new Bio::SearchIO::wise object 
 Returns : an instance of Bio::SearchIO::wise
 Args    : -wise => a Bio::Tools::Genewise or Bio::Tools::Genomewise object