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Summary

Bio::Search::Hit::BlastPullHit - A parser and hit object for BLASTN hits

Package variables

Included modules

Inherit

Bio::Root::Root Bio::Search::Hit::PullHitI

Synopsis

    # generally we use Bio::SearchIO to build these objects
    use Bio::SearchIO;
    my $in = Bio::SearchIO->new(-format => 'blast_pull',
							   -file   => 'result.blast');

    while (my $result = $in->next_result) {
		while (my $hit = $result->next_hit) {
			print $hit->name, "\n";
			print $hit->score, "\n";
			print $hit->significance, "\n";

			while (my $hsp = $hit->next_hsp) {
				# process HSPI objects
			}
		}
    }

Description

This object implements a parser for BLASTN hit output.

Methods

Methods description

 Title   : new
 Usage   : my $obj = Bio::Search::Hit::BlastNHit->new();
 Function: Builds a new Bio::Search::Hit::BlastNHit object.
 Returns : Bio::Search::Hit::BlastNHit
 Args    : -chunk    => [Bio::Root::IO, $start, $end] (required if no -parent)
           -parent   => Bio::PullParserI object (required if no -chunk)
           -hit_data => array ref with [name description score significance]

           where the array ref provided to -chunk contains an IO object
           for a filehandle to something representing the raw data of the
           hit, and $start and $end define the tell() position within the
           filehandle that the hit data starts and ends (optional; defaults
           to start and end of the entire thing described by the filehandle)

 Title    : next_hsp
 Usage    : while( $hsp = $obj->next_hsp()) { ... }
 Function : Returns the next available High Scoring Pair
 Example  : 
 Returns  : Bio::Search::HSP::HSPI object or null if finished
 Args     : none

 Usage     : $hit_object->hsps();
 Purpose   : Get a list containing all HSP objects.
 Example   : @hsps = $hit_object->hsps();
 Returns   : list of Bio::Search::HSP::BlastHSP objects.
 Argument  : none

 Usage     : $hit_object->hsp( [string] );
 Purpose   : Get a single HSPI object for the present HitI object.
 Example   : $hspObj  = $hit_object->hsp;  # same as 'best'
           : $hspObj  = $hit_object->hsp('best');
           : $hspObj  = $hit_object->hsp('worst');
 Returns   : Object reference for a Bio::Search::HSP::HSPI object.
 Argument  : String (or no argument).
           :   No argument (default) = highest scoring HSP (same as 'best').
           :   'best'  = highest scoring HSP.
           :   'worst' = lowest scoring HSP.
 Throws    : Exception if an unrecognized argument is used.

 Title   : rewind
 Usage   : $result->rewind;
 Function: Allow one to reset the HSP iterator to the beginning, so that
           next_hsp() will subsequently return the first hsp and so on.
 Returns : n/a
 Args    : none

Methods code

sub new {

    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
	
	$self->_setup(@args);
	
	my $fields = $self->_fields;
	foreach my $field (qw( header start_end )) {
		$fields->{$field} = undef;
	}
	
    my $hit_data = $self->_raw_hit_data;
	if ($hit_data && ref($hit_data) eq 'ARRAY') {
		foreach my $field (qw(name description score significance)) {
			$fields->{$field} = shift(@{$hit_data});
		}
	}
    
	$self->_dependencies( { ( name => 'header',
							  length => 'header',
							  description => 'header',
							  accession => 'header',
                              next_hsp => 'header',
                              query_start => 'start_end',
                              query_end => 'start_end',
                              hit_start => 'start_end',
                              hit_end => 'start_end' ) } );
    
    return $self;
}

#
# PullParserI discovery methods so we can answer all HitI questions
#

}

sub _discover_header {

	my $self = shift;
	$self->_chunk_seek(0);
	my $header = $self->_get_chunk_by_end("\n Score = ");
    
    unless ($header) {
        # no alignment or other data; all information was in the hit table of
        # the result
        $self->_calculate_accession_from_name;
        
        $self->_fields->{header} = 1;
        return;
    }
    
	$self->{_after_header} = $self->_chunk_tell;
	
    ($self->_fields->{name}, $self->_fields->{description}, $self->_fields->{length}) = $header =~ /^(\S+)\s+(\S.+?)?\s+Length\s*=\s*(\d+)/sm;
    if ($self->_fields->{description}) {
        $self->_fields->{description} =~ s/\n//g;
    }
    else {
        $self->_fields->{description} = '';
    }
	
    $self->_calculate_accession_from_name;
	
	$self->_fields->{header} = 1;

}

sub _calculate_accession_from_name {

    my $self = shift;
    my $name = $self->get_field('name');
    if ($name =~ /.+?\|.+?\|.+?\|(\w+)/) {
        $self->_fields->{accession} = $1;
    }
    elsif ($self->_fields->{name} =~ /.+?\|(\w+)?\./) {
        # old form?
        $self->_fields->{accession} = $1;
    }
    else {
        $self->_fields->{accession} = $name;
    }

}

sub _discover_start_end {

    my $self = shift;
    
    my ($q_start, $q_end, $h_start, $h_end);
    foreach my $hsp ($self->hsps) {
        my ($this_q_start, $this_h_start) = $hsp->start;
        my ($this_q_end, $this_h_end) = $hsp->end;
        
        if (! defined $q_start || $this_q_start < $q_start) {
            $q_start = $this_q_start;
        }
        if (! defined $h_start || $this_h_start < $h_start) {
            $h_start = $this_h_start;
        }
        
        if (! defined $q_end || $this_q_end > $q_end) {
            $q_end = $this_q_end;
        }
        if (! defined $h_end || $this_h_end > $h_end) {
            $h_end = $this_h_end;
        }
    }
    
    $self->_fields->{query_start} = $q_start;
    $self->_fields->{query_end} = $q_end;
    $self->_fields->{hit_start} = $h_start;
    $self->_fields->{hit_end} = $h_end;

}

sub _discover_next_hsp {

	my $self = shift;
    my $pos = $self->{_end_of_previous_hsp} || $self->{_after_header};
    return unless $pos;
    $self->_chunk_seek($pos);
    
    my ($start, $end) = $self->_find_chunk_by_end("\n Score = ");
    if ((defined $end && ($end + $self->_chunk_true_start) > $self->_chunk_true_end) || ! $end) {
		$start = $self->{_end_of_previous_hsp} || $self->{_after_header};
		$end = $self->_chunk_true_end;
	}
	else {
		$end += $self->_chunk_true_start;
	}
	$start += $self->_chunk_true_start;
    
    return if $start >= $self->_chunk_true_end;
    
    $self->{_end_of_previous_hsp} = $end - $self->_chunk_true_start;
    
    #*** needs to inherit piped_behaviour, and we need to deal with _sequential
	#    ourselves
	$self->_fields->{next_hsp} = Bio::Search::HSP::BlastPullHSP->new(-parent => $self,
                                                                    -chunk => [$self->chunk, $start, $end]);

}

sub _discover_num_hsps {

    my $self = shift;
    $self->_fields->{num_hsps} = $self->hsps;

}

sub next_hsp {

    my $self = shift;
    my $hsp = $self->get_field('next_hsp');
	undef $self->_fields->{next_hsp};
	return $hsp;

}

sub hsps {

    my $self = shift;
	my $old = $self->{_end_of_previous_hsp};
	$self->rewind;
	my @hsps;
	while (defined(my $hsp = $self->next_hsp)) {
		push(@hsps, $hsp);
	}
	$self->{_end_of_previous_hsp} = $old;
	return @hsps;

}

sub hsp {

    my ($self, $type) = @_;
	$type ||= 'best';
	$self->throw_not_implemented;

}

sub rewind {

	my $self = shift;
	delete $self->{_end_of_previous_hsp};
}

# have p() a synonym of significance()

}

sub p {

	return shift->significance;
}

1;

}

General documentation

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with code and data examples if at all possible.

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