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Summary

Bio::SearchIO::exonerate - parser for Exonerate

Package variables

Included modules

Inherit

Bio::SearchIO

Synopsis

  # do not use this module directly, it is a driver for SearchIO

  use Bio::SearchIO;
  my $searchio = new Bio::SearchIO(-file => 'file.exonerate',
                                   -format => 'exonerate');

  while( my $r = $searchio->next_result ) {
    print $r->query_name, "\n";
  }

Description

This is a driver for the SearchIO system for parsing Exonerate (Guy
Slater) output. You can get Exonerate at
http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/exonerate/?cvsroot=Ensembl [until Guy puts up a Web reference,publication for it.]).
An optional parameter -min_intron is supported by the new
initialization method. This is if you run Exonerate with a different
minimum intron length (default is 30) the parser will be able to
detect the difference between standard deletions and an intron. Still
some room to play with there that might cause this to get
misinterpreted that has not been fully tested or explored.

Methods

Methods description

 Title   : characters
 Usage   : $eventgenerator->characters($str)
 Function: Send a character events
 Returns : none
 Args    : string

 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'

 Title   : end_document
 Usage   : $eventgenerator->end_document
 Function: Handles an end document event
 Returns : Bio::Search::Result::ResultI object
 Args    : none

 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'

 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

 Title   : new
 Usage   : my $obj = new Bio::SearchIO::exonerate();
 Function: Builds a new Bio::SearchIO::exonerate object
 Returns : an instance of Bio::SearchIO::exonerate
 Args    :

 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

 Title   : start_document
 Usage   : $eventgenerator->start_document
 Function: Handle a start document event
 Returns : none
 Args    : none

 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'

 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

Methods code

sub characters {

   my ($self,$data) = @_;

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

   $self->{'_last_data'} = $data->{'Data'};

}

sub element {

   my ($self,$data) = @_;
   $self->start_element($data);
   $self->characters($data);
   $self->end_element($data);

}

sub end_document {

   my ($self,@args) = @_;
   return $self->{'_result'};

}

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;

}

sub in_element {

   my ($self,$name) = @_;
   return 0 if ! defined $self->{'_elements'}->[0];
   return ( $self->{'_elements'}->[0] eq $name)

}

sub new {

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

    my ($min_intron) = $self->_rearrange([qw(MIN_INTRON)], @_);
    if( $min_intron ) {
	$MIN_INTRON = $min_intron;
    }
    $self;

}

sub next_result {

   my ($self) = @_;
   $self->{'_last_data'} = '';
   my ($reporttype,$seenquery,$reportline);
   $self->start_document();
   my @hit_signifs;
   my $seentop;
   my (@q_ex, @m_ex, @h_ex); ## gc addition
   while( defined($_ = $self->_readline) ) {
       if( /^Query:\s+(\S+)(\s+(.+))?/ ) {
	   if( $seentop ) {
	       $self->end_element({'Name' => 'ExonerateOutput'});
	       $self->_pushback($_);
	       return $self->end_document();
	   }
	   $seentop = 1;
	   my ($nm,$desc) = ($1,$2);
	   chomp($desc) if defined $desc;
	   $self->{'_result_count'}++;
	   $self->start_element({'Name' => 'ExonerateOutput'});
	   $self->element({'Name' => 'ExonerateOutput_query-def',
			   'Data' => $nm });
	   $self->element({'Name' => 'ExonerateOutput_query-desc',
			   'Data' => $desc });
	   $self->element({'Name' => 'ExonerateOutput_program',
			    'Data' => 'Exonerate' });

       } elsif ( /^Target:\s+(\S+)(\s+(.+))?/ ) {
	    my ($nm,$desc) = ($1,$2);
	   chomp($desc) if defined $desc;
	   $self->start_element({'Name' => 'Hit'});
	   $self->element({'Name' => 'Hit_id',
			   'Data' => $nm});
	   $self->element({'Name' => 'Hit_desc',
			   'Data' => $desc});
       } elsif(  s/^cigar:\s+(\S+)\s+          # query sequence id
		 (\d+)\s+(\d+)\s+([\-\+])\s+   # query start-end-strand
		 (\S+)\s+                      # target sequence id
		 (\d+)\s+(\d+)\s+([\-\+])\s+   # target start-end-strand
		 (\d+)\s+                      # score
		 //ox ) {
	
	   ## gc note:
	   ## $qe and $he are no longer used for calculating the ends,
	   ## just the $qs and $hs values and the alignment and insert lenghts
	   my ($qs,$qe,$qstrand) = ($2,$3,$4);
	   my ($hs,$he,$hstrand) = ($6,$7,$8);
	   my $score = $9;
#	   $self->element({'Name' => 'ExonerateOutput_query-len',
#			   'Data' => $qe});
#	   $self->element({'Name' => 'Hit_len',
#			   'Data' => $he});
	
	   my @rest = split;
	   if( $qstrand eq '-' ) {
	       $qstrand = -1;
	       ($qs,$qe) = ($qe,$qs); # flip-flop if we're on opp strand
	   		$qs--; $qe++;
	   } else { $qstrand = 1; }
	   if( $hstrand eq '-' ) {
	       $hstrand = -1;
	       ($hs,$he) = ($he,$hs); # flip-flop if we're on opp strand
	       $hs--; $he++;
	   } else { $hstrand = 1; }
	   # okay let's do this right and generate a set of HSPs
	   # from the cigar line

		## gc note:
		## add one because these values are zero-based
		## this calculation was originally done lower in the code,
		## but it's clearer to do it just once at the start
	   $qs++;
	   $hs++;

	   my ($aln_len,$inserts,$deletes) = (0,0,0);
	   while( @rest >= 2 ) {
	       my ($state,$len) = (shift @rest, shift @rest);
	       if( $state eq 'I' ) {
		   $inserts+=$len;
	       } elsif( $state eq 'D' ) {
		   if( $len >= $MIN_INTRON ) {
		       $self->start_element({'Name' => 'Hsp'});

		       $self->element({'Name' => 'Hsp_score',
				       'Data' => $score});
		       $self->element({'Name' => 'Hsp_align-len',
				       'Data' => $aln_len});
		       $self->element({'Name' => 'Hsp_identity',
				       'Data' => $aln_len -
					   ($inserts + $deletes)});
		
		       # HSP ends where the other begins
		       $self->element({'Name' => 'Hsp_query-from',
				       'Data' => $qs});
		       ## gc note:
		       ## $qs is now the start of the next hsp
		       ## the end of this hsp is 1 before this position
		       ## (or 1 after in case of reverse strand)
		       $qs += $aln_len*$qstrand;
		       $self->element({'Name' => 'Hsp_query-to',
				       'Data' => $qs - ($qstrand*1)});
		
		       $hs += $deletes*$hstrand;
		       $self->element({'Name' => 'Hsp_hit-from',
				       'Data' => $hs});
		       $hs += $aln_len*$hstrand;
		       $self->element({'Name' => 'Hsp_hit-to',
				       'Data' => $hs-($hstrand*1)});
		
		       $self->element({'Name' => 'Hsp_align-len',
				       'Data' => $aln_len + $inserts
					   + $deletes});
		       $self->element({'Name' => 'Hsp_identity',
				       'Data' => $aln_len });

		       $self->element({'Name' => 'Hsp_gaps',
				       'Data' => $inserts + $deletes});
		       $self->element({'Name' => 'Hsp_querygaps',
				       'Data' => $inserts});
		       $self->element({'Name' => 'Hsp_hitgaps',
				       'Data' => $deletes});
		
## gc addition start
		
		       $self->element({'Name' => 'Hsp_qseq',
				       'Data' => shift @q_ex,
				   });
		       $self->element({'Name' => 'Hsp_hseq',
				       'Data' => shift @h_ex,
				   });
		       $self->element({'Name' => 'Hsp_midline',
				       'Data' => shift @m_ex,
				   });
## gc addition end
		       $self->end_element({'Name' => 'Hsp'});
		       		
		       $aln_len = $inserts = $deletes = 0;
		   }
		   $deletes+=$len;		
	       } else {
		   $aln_len += $len;
	       }
	   }
	   $self->start_element({'Name' => 'Hsp'});
	
## gc addition start
		
		       $self->element({'Name' => 'Hsp_qseq',
				       'Data' => shift @q_ex,
				   });
		       $self->element({'Name' => 'Hsp_hseq',
				       'Data' => shift @h_ex,
				   });
		       $self->element({'Name' => 'Hsp_midline',
				       'Data' => shift @m_ex,
				   });
## gc addition end

	   $self->element({'Name' => 'Hsp_score',
			   'Data' => $score});
	
	   $self->element({'Name' => 'Hsp_query-from',
			   'Data' => $qs});

	   $qs += $aln_len*$qstrand;
	   $self->element({'Name' => 'Hsp_query-to',
				       'Data' => $qs - ($qstrand*1)});

	   $hs += $deletes*$hstrand;
	   $self->element({'Name' => 'Hsp_hit-from',
			   'Data' => $hs});
	   $hs += $aln_len*$hstrand;
	   $self->element({'Name' => 'Hsp_hit-to',
			   'Data' => $hs -($hstrand*1)});	

	   $self->element({'Name' => 'Hsp_align-len',
			   'Data' => $aln_len});
	
	   $self->element({'Name' => 'Hsp_identity',
			   'Data' => $aln_len - ($inserts + $deletes)});

	   $self->element({'Name' => 'Hsp_gaps',
			   'Data' => $inserts + $deletes});
	
	   $self->element({'Name' => 'Hsp_querygaps',
			   'Data' => $inserts});
	   $self->element({'Name' => 'Hsp_hitgaps',
			   'Data' => $deletes});	   	
	   $self->end_element({'Name' => 'Hsp'});
	   $self->element({'Name' => 'Hit_score',
			   'Data' => $score});
	   $self->end_element({'Name' => 'Hit'});
	   $self->end_element({'Name' => 'ExonerateOutput'});

	   return $self->end_document();	
       } else {
       }
   }
   return $self->end_document() if( $seentop );

}

sub result_count {

    my $self = shift;
    return $self->{'_result_count'};

}

sub start_document {

    my ($self) = @_;
    $self->{'_lasttype'} = '';
    $self->{'_values'} = {};
    $self->{'_result'}= undef;
    $self->{'_elements'} = [];
    $self->{'_reporttype'} = 'exonerate';

}

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;
       }
   }

}

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;

}

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 );

}

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://bioperl.org/bioperl-bugs/

Email jason@bioperl.org
Describe contact details here

Additional contributors names and emails here

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