Bio::SearchIO waba
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Summary
Bio::SearchIO::waba - SearchIO parser for Jim Kent WABA program
alignment output
Package variables
No package variables defined.
Included modules
Bio::Search::HSP::HSPFactory
Bio::Search::Result::ResultFactory
POSIX
Inherit
Bio::SearchIO
Synopsis
    # do not use this object directly, rather through Bio::SearchIO

    use Bio::SearchIO;
    my $in = Bio::SearchIO->new(-format => 'waba',
			       -file   => 'output.wab');
    while( my $result = $in->next_result ) {
	while( my $hit = $result->next_hit ) {
	    while( my $hsp = $result->next_hsp ) {

	    }
	}
    }
Description
This parser will process the waba output (NOT the human readable format).
Methods
BEGIN Code
_initialize
No description
Code
next_resultDescriptionCode
start_elementDescriptionCode
end_elementDescriptionCode
elementDescriptionCode
charactersDescriptionCode
_modeDescriptionCode
within_elementDescriptionCode
in_elementDescriptionCode
start_documentDescriptionCode
end_documentDescriptionCode
result_countDescriptionCode
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
_modecodeprevnextTop
 Title   : _mode
 Usage   : $obj->_mode($newval)
 Function: 
 Example : 
 Returns : value of _mode
 Args    : newvalue (optional)
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: Handles 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
result_countcodeprevnextTop
 Title   : result_count
 Usage   : my $count = $searchio->result_count
 Function: Returns the number of results we have processed
 Returns : integer
 Args    : none
Methods code
BEGINTop
BEGIN {
     # mapping of NCBI Blast terms to Bioperl hash keys
    %MODEMAP = ('WABAOutput' => 'result',
		'Hit'         => 'hit',
		'Hsp'         => 'hsp'
		);
    @STATES = qw(Hsp_qseq Hsp_hseq Hsp_stateseq);
    %MAPPING = 
	( 
	  'Hsp_query-from'=>  'HSP-query_start',
	  'Hsp_query-to'  =>  'HSP-query_end',
	  'Hsp_hit-from'  =>  'HSP-hit_start',
	  'Hsp_hit-to'    =>  'HSP-hit_end',
	  'Hsp_qseq'      =>  'HSP-query_seq',
	  'Hsp_hseq'      =>  'HSP-hit_seq',
	  'Hsp_midline'   =>  'HSP-homology_seq',
	  'Hsp_stateseq'  =>  'HSP-hmmstate_seq',
	  'Hsp_align-len' =>  'HSP-hsp_length',
	  
	  'Hit_id'        => 'HIT-name',
	  'Hit_accession' => 'HIT-accession',

	  'WABAOutput_program'  => 'RESULT-algorithm_name',
	  'WABAOutput_version'  => 'RESULT-algorithm_version',
	  'WABAOutput_query-def'=> 'RESULT-query_name',
	  'WABAOutput_query-db' => 'RESULT-query_database',
 	  'WABAOutput_db'       => 'RESULT-database_name',
	  );
}
_initializedescriptionprevnextTop
sub _initialize {
    my ($self,@args) = @_;
    $self->SUPER::_initialize(@args);
    $self->_eventHandler->register_factory('result', Bio::Search::Result::ResultFactory->new(-type => 'Bio::Search::Result::WABAResult'));

    $self->_eventHandler->register_factory('hsp', Bio::Search::HSP::HSPFactory->new(-type => 'Bio::Search::HSP::WABAHSP'));
}
next_resultdescriptionprevnextTop
sub next_result {
    my ($self) = @_;
    local $/ = "\n";
    local $_;
    
    my ($curquery,$curhit);
    my $state = -1;
    $self->start_document();
    my @hit_signifs;
    while( defined ($_ = $self->_readline )) { 
	
	if( $state == -1 ) {
	    my ($qid, $qhspid,$qpercent, $junk,
		$alnlen,$qdb,$qacc,$qstart,$qend,$qstrand,
		$hitdb,$hacc,$hstart,$hend,
		$hstrand) =
		    ( /^(\S+)\.(\S+)\s+align\s+ # get the queryid
		      (\d+(\.\d+)?)\%\s+     # get the percentage
		      of\s+(\d+)\s+  # get the length of the alignment
		      (\S+)\s+           # this is the query database
		      (\S+):(\-?\d+)\-(\-?\d+) # The accession:start-end for query
		      \s+([\-\+])        # query strand
		      \s+(\S+)\.         # hit db
		      (\S+):(\-?\d+)\-(\-?\d+) # The accession:start-end for hit
		      \s+([\-\+])\s*$    # hit strand
		      /ox );
	    
	    # Curses.  Jim's code is 0 based, the following is to readjust
	    if( $hstart < 0 ) { $hstart *= -1}
	    if( $hend   < 0 ) { $hend   *= -1}
	    if( $qstart < 0 ) { $qstart *= -1}
	    if( $qend   < 0 ) { $qend   *= -1}
	    $hstart++; $hend++; $qstart++; $qend++;
	    if( ! defined $alnlen ) {
		$self->warn("Unable to parse the rest of the WABA alignment info for: '$_'");
		last;
	    }
	    $self->{'_reporttype'} = 'WABA'; # hardcoded - only 
	                                     # one type of WABA AFAIK	    
	    if( defined $curquery && 
		$curquery ne $qid ) { 
		$self->end_element({'Name' => 'Hit'});
		$self->_pushback($_);
		$self->end_element({'Name' => 'WABAOutput'});
		return $self->end_document();
	    } 
	    
	    if( defined $curhit &&
		$curhit ne $hacc) {
		# slight duplication here -- keep these in SYNC
		$self->end_element({'Name' => 'Hit'});
		$self->start_element({'Name' => 'Hit'});
		$self->element({'Name' => 'Hit_id',
				'Data' => $hacc});
		$self->element({'Name' => 'Hit_accession',
				'Data' => $hacc});

	    } elsif ( ! defined $curquery ) {
		$self->start_element({'Name' => 'WABAOutput'});
		$self->{'_result_count'}++;
		$self->element({'Name' => 'WABAOutput_query-def',
				'Data' => $qid });
		$self->element({'Name' => 'WABAOutput_program',
				'Data' => 'WABA'});
		$self->element({'Name' => 'WABAOutput_query-db',
				'Data' => $qdb});
		$self->element({'Name' => 'WABAOutput_db',
				'Data' => $hitdb});
		
		# slight duplication here -- keep these N'SYNC ;-)
		$self->start_element({'Name' => 'Hit'});
		$self->element({'Name' => 'Hit_id',
				'Data' => $hacc});
		$self->element({'Name' => 'Hit_accession',
				'Data' => $hacc});
	    }

	    
	    # strand is inferred by start,end values
	    # in the Result Builder
	    if( $qstrand eq '-' ) {
		($qstart,$qend) = ($qend,$qstart);
	    }
	    if( $hstrand eq '-' ) {
		($hstart,$hend) = ($hend,$hstart);
	    }

	    $self->start_element({'Name' => 'Hsp'});
	    $self->element({'Name' => 'Hsp_query-from',
			    'Data' => $qstart});
	    $self->element({'Name' => 'Hsp_query-to',
			    'Data' => $qend});
	    $self->element({'Name' => 'Hsp_hit-from',
			    'Data' => $hstart});
	    $self->element({'Name' => 'Hsp_hit-to',
			    'Data' => $hend});
	    $self->element({'Name' => 'Hsp_align-len',
			    'Data' => $alnlen});
	    
	    $curquery = $qid;
	    $curhit   = $hacc;
	    $state = 0;
	} elsif( ! defined $curquery ) {
	    $self->warn("skipping because no Hit begin line was recognized\n$_") if( $_ !~ /^\s+$/ );
	    next;
	} else { 
	    chomp;
	    $self->element({'Name' => $STATES[$state++],
			    'Data' => $_});
	    if( $state >= scalar @STATES ) {
		$state = -1;
		$self->end_element({'Name' => 'Hsp'});
	    }
	}
    }
    if( defined $curquery  ) {
	$self->end_element({'Name' => 'Hit'});
	$self->end_element({'Name' => 'WABAOutput'});
	return $self->end_document();
    }
    return;
}
start_elementdescriptionprevnextTop
sub start_element {
   my ($self,$data) = @_;
    # we currently don't care about attributes
    my $nm = $data->{'Name'};    
   if( my $type = $MODEMAP{$nm} ) {
	$self->_mode($type);
	if( $self->_eventHandler->will_handle($type) ) {
	    my $func = sprintf("start_%s",lc $type);
	    $self->_eventHandler->$func($data->{'Attributes'});
	}						 
	unshift @{$self->{'_elements'}}, $type;
    }
    if($nm eq 'WABAOutput') {
	$self->{'_values'} = {};
	$self->{'_result'}= undef;
	$self->{'_mode'} = '';
    }
}
end_elementdescriptionprevnextTop
sub end_element {
    my ($self,$data) = @_;
    my $nm = $data->{'Name'};
    my $rc;
    # Hsp are sort of weird, in that they end when another
    # object begins so have to detect this in end_element for now
    if( $nm eq 'Hsp' ) {
	foreach ( qw(Hsp_qseq Hsp_midline Hsp_hseq) ) {
	    $self->element({'Name' => $_,
			    'Data' => $self->{'_last_hspdata'}->{$_}});
	}
	$self->{'_last_hspdata'} = {}
    }

    if( my $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->warn( "unknown nm $nm ignoring\n");
    }
    $self->{'_last_data'} = ''; # remove read data if we are at 
				# end of an element
    $self->{'_result'} = $rc if( $nm eq 'WABAOutput' );
    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'} );
   if( $data->{'Data'} =~ /^\s+$/ ) {
       return unless $data->{'Name'} =~ /Hsp\_(midline|qseq|hseq)/;
   }

   if( $self->in_element('hsp') && 
       $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/ ) {
       
       $self->{'_last_hspdata'}->{$data->{'Name'}} .= $data->{'Data'};
   }  
   
   $self->{'_last_data'} = $data->{'Data'};
}
_modedescriptionprevnextTop
sub _mode {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'_mode'} = $value;
    }
    return $self->{'_mode'};
}
within_elementdescriptionprevnextTop
sub within_element {
   my ($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->{'_mode'} = '';
    $self->{'_elements'} = [];
}
end_documentdescriptionprevnextTop
sub end_document {
   my ($self,@args) = @_;
   return $self->{'_result'};
}
result_countdescriptionprevnextTop
sub result_count {
    my $self = shift;
    return $self->{'_result_count'};
}
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/wiki/Mailing_lists  - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
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.
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:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason-at-bioperl.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 = Bio::SearchIO::waba->new();
 Function: Builds a new Bio::SearchIO::waba object 
 Returns : Bio::SearchIO::waba
 Args    : see Bio::SearchIO