Summary

Bio::SearchIO::axt - a parser for axt format reports

Package variables

Included modules

Synopsis

  use Bio::SearchIO;
  my $parser = new Bio::SearchIO(-format => 'axt',
                                 -file   => 't/data/report.blastz');
  while( my $result = $parser->next_result ) {
    while( my $hit = $result->next_hit ) {
      while( my $hsp = $hit->next_hsp ) {
      }
    }
  }

Description

This is a parser and event-generator for AXT format reports. BLASTZ
reports (Schwartz et al,(2003) Genome Research, 13:103-107) are normally
in LAV format but are commonly post-processed to AXT format; many precomputed
BLASTZ reports, such as those found in the UCSC Genome
Browser, are in AXT format. This parser will also parse any
AXT format produced from any lav report and directly out of BLAT.

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::SearchIO::axt();
 Function: Builds a new Bio::SearchIO::axt object 
 Returns : an instance of Bio::SearchIO::axt
 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_element
 Usage   : $eventgenerator->start_element
 Function: Handles a start element event
 Returns : none
 Args    : hashref with at least 2 keys 'Data' and 'Name'

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

 Title   : _mode
 Usage   : $obj->_mode($newval)
 Function: 
 Example : 
 Returns : value of _mode
 Args    : newvalue (optional)

 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

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

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

 Title   : result_count
 Usage   : my $count = $searchio->result_count
 Function: Returns the number of results we have processed
 Returns : integer
 Args    : none

Methods code

BEGIN {

     # mapping of NCBI Blast terms to Bioperl hash keys
    %MODEMAP = ('AXTOutput'   => 'result',
		'Hit'         => 'hit',
		'Hsp'         => 'hsp'
		);
    $GAPCHAR = '-';
    %MAPPING = 
	( 
	  'Hsp_score'      => 'HSP-score',
          '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_positive'   => 'HSP-conserved',
          'Hsp_identity'   => 'HSP-identical',
          'Hsp_gaps'       => 'HSP-hsp_gaps',
          'Hsp_hitgaps'    => 'HSP-hit_gaps',
          'Hsp_querygaps'  => 'HSP-query_gaps',
          'Hsp_qseq'       => 'HSP-query_seq',
          'Hsp_hseq'       => 'HSP-hit_seq',
          'Hsp_midline'    => 'HSP-homology_seq', # ignoring this for now
          'Hsp_align-len'  => 'HSP-hsp_length',
	  
	  'Hit_id'        => 'HIT-name',	  
	  'AXTOutput_query-def'=> 'RESULT-query_name',	  
	  );

}

sub new {

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

}

sub next_result {

    my ($self) = @_;
    local $/ = "\n";
    local $_;

    my ($curquery,$curhit);
    $self->start_document();
    my @hit_signifs;
    while( defined ($_ = $self->_readline )) { 
	next if (/^\s+$/);
	if( m/^(\d+)\s+      # alignment number - we'll throw this away anyways
	    (\S+)\s+         # Query name      
	    (\d+)\s+(\d+)\s+ # Query start Query end (always + strand, 0 based)
	    (\S+)\s+         # Hit name
	    (\d+)\s+(\d+)\s+ # Hit start Hit end (0 based)
	    ([\-\+])\s+      # Hit strand
	    ([\d\.\-]+)\s+   # Score
	    /ox ) {
	    my ($alnnum, $qname,$qstart,$qend, $hname,
		$hstart,$hend,$hstrand, $score) = ($1,$2,$3,$4,$5,
						   $6,$7,$8,$9);
	    $self->{'_reporttype'} = 'AXT';
	    # Jim's code is 0 based
	    $qstart++;  $qend++; $hstart++; $hend++;
	    if( defined $curquery && 
		$curquery ne $qname ) { 
		$self->end_element({'Name' => 'Hit'});
		$self->_pushback($_);
		$self->end_element({'Name' => 'AXTOutput'});
		return $self->end_document();
	    }
	    
	    if( defined $curhit &&
		$curhit ne $hname) {
		# slight duplication here -- keep these in SYNC
		$self->end_element({'Name' => 'Hit'});
		$self->start_element({'Name' => 'Hit'});
		$self->element({'Name' => 'Hit_id',
				'Data' => $hname});
	    } elsif ( ! defined $curquery ) { 
		$self->start_element({'Name' => 'AXTOutput'});
		$self->{'_result_count'}++;
		$self->element({'Name' => 'AXTOutput_query-def',
				'Data' => $qname });
		
		$self->start_element({'Name' => 'Hit'});
		$self->element({'Name' => 'Hit_id',
				'Data' => $hname});
	    }
	    $self->start_element({'Name' => 'Hsp'});
	    my $queryalign = $self->_readline;
	    my $hitalign   = $self->_readline;
	    chomp($queryalign);
	    chomp($hitalign);
	    my $alnlen = length($queryalign);
	    my $qgapnum = ( $queryalign =~ s/\Q$GAPCHAR/$GAPCHAR/g); 
	    my $hgapnum = ( $hitalign =~ s/\Q$GAPCHAR/$GAPCHAR/g); 
	    my $totalgaps = ($qgapnum + $hgapnum);
	    
	    if( $hstrand eq '-' ) { # strand gets inferred by start/end
		($hstart,$hend) = ($hend,$hstart);
	    }
	    $self->element({'Name' => 'Hsp_score',
			    'Data' => $score});
	    $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_gaps',
			    'Data' => $qgapnum + $hgapnum});
	    $self->element({'Name' => 'Hsp_querygaps',
			    'Data' => $qgapnum});
	    $self->element({'Name' => 'Hsp_hitgaps',
			    'Data' => $hgapnum});
	    
	    $self->element({'Name' => 'Hsp_identity',
			    'Data' => $alnlen - $totalgaps});
	    $self->element({'Name' => 'Hsp_positive',
			    'Data' => $alnlen - $totalgaps});
	    $self->element({'Name' => 'Hsp_qseq',
			    'Data' => $queryalign});
	    $self->element({'Name' => 'Hsp_hseq',
			    'Data' => $hitalign});
	    
	    $self->end_element({'Name' => 'Hsp'});	    
	    $curquery = $qname;
	    $curhit   = $hname;	   
	}

}

sub _initialize {

    my ($self,@args) = @_;
    $self->SUPER::_initialize(@args);
    $self->_eventHandler->register_factory('result', Bio::Search::Result::ResultFactory->new(-type => 'Bio::Search::Result::GenericResult'));

    $self->_eventHandler->register_factory('hsp', Bio::Search::HSP::HSPFactory->new(-type => 'Bio::Search::HSP::GenericHSP'));

}

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 'AXTOutput') {
	$self->{'_values'} = {};
	$self->{'_result'}= undef;
	$self->{'_mode'} = '';
    }

}

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( 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 'AXTOutput' );
    return $rc;

}

sub element {

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

}

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'};

}

sub _mode {

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

}

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 in_element {

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

}

sub start_document {

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

}

sub end_document {

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

}

sub result_count {

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

}

sub report_count {

 shift->result_count

}

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/wiki/Mailing_lists  - 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 the
web:

  http://bugzilla.open-bio.org/

Email jason-at-bioperl.org

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