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Summary

Bio::Search::HSP::BlastPullHSP - A parser and HSP object for BlastN hsps

Package variables

Inherit

Bio::Search::HSP::PullHSPI

Synopsis

    # generally we use Bio::SearchIO to build these objects
    use Bio::SearchIO;
    my $in = Bio::SearchIO->new(-format => 'hmmer_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 hsp output.

Methods

Methods description

 Title   : new
 Usage   : my $obj = Bio::Search::HSP::BlastNHSP->new();
 Function: Builds a new Bio::Search::HSP::BlastNHSP object.
 Returns : Bio::Search::HSP::BlastNHSP
 Args    : -chunk  => [Bio::Root::IO, $start, $end] (required if no -parent)
           -parent => Bio::PullParserI object (required if no -chunk)

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

 Title   : query
 Usage   : my $query = $hsp->query
 Function: Returns a SeqFeature representing the query in the HSP
 Returns : Bio::SeqFeature::Similarity
 Args    : none

 Title   : hit
 Usage   : my $hit = $hsp->hit
 Function: Returns a SeqFeature representing the hit in the HSP
 Returns : Bio::SeqFeature::Similarity
 Args    : [optional] new value to set

 Title    : gaps
 Usage    : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
 Function : Get the number of gap characters in the query, hit, or total alignment.
 Returns  : Integer, number of gap characters or 0 if none
 Args     : 'query' = num conserved / length of query seq (without gaps)
            'hit'   = num conserved / length of hit seq (without gaps)
            'total' = num conserved / length of alignment (with gaps)
            default = 'total'

 Title   : strand
 Usage   : $hsp->strand('query')
 Function: Retrieves the strand for the HSP component requested
 Returns : +1 or -1 (0 if unknown)
 Args    : 'hit' or 'subject' or 'sbjct' to retrieve the strand of the subject
           'query' to retrieve the query strand (default)
           'list' or 'array' to retreive both query and hit together

 Title   : start
 Usage   : $hsp->start('query')
 Function: Retrieves the start for the HSP component requested
 Returns : integer, or list of two integers (query start and subject start) in
           list context
 Args    : 'hit' or 'subject' or 'sbjct' to retrieve the start of the subject
           'query' to retrieve the query start (default)

 Title   : end
 Usage   : $hsp->end('query')
 Function: Retrieves the end for the HSP component requested
 Returns : integer, or list of two integers (query end and subject end) in
           list context
 Args    : 'hit' or 'subject' or 'sbjct' to retrieve the end of the subject
           'query' to retrieve the query end (default)

 Title   : pvalue
 Usage   : my $pvalue = $hsp->pvalue();
 Function: Returns the P-value for this HSP
 Returns : undef (Hmmpfam reports do not have p-values)
 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 alignment query_strand hit_strand )) {
		$fields->{$field} = undef;
	}
	
	$self->_dependencies( { ( score => 'header',
                              bits => 'header',
                              evalue => 'header',
                              total_gaps => 'header',
                              query_strand => 'header',
                              hit_strand => 'header',
                              alignment => 'header',
                              query_string => 'alignment',
                              hit_string => 'alignment',
                              homology_string => 'alignment',
                              query_start => 'alignment',
                              query_end => 'alignment',
                              hit_start => 'alignment',
                              hit_end => 'alignment',
                              hit_identical_inds => 'seq_inds',
							  hit_conserved_inds => 'seq_inds',
							  hit_nomatch_inds => 'seq_inds',
                              hit_gap_inds => 'seq_inds',
                              query_identical_inds => 'seq_inds',
							  query_conserved_inds => 'seq_inds',
							  query_nomatch_inds => 'seq_inds',
							  query_gap_inds => 'seq_inds' ) } );
	
    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("\nQuery");
	$self->{_after_header} = $self->_chunk_tell;
	
	($self->_fields->{bits}, $self->_fields->{score}, $self->_fields->{evalue},
     $self->_fields->{total_gaps}, $self->_fields->{query_strand}, $self->_fields->{hit_strand})
     = $header =~ /^\s*(\S+) bits \((\d+)\),\s+Expect = (\S+)(?:\s+.+Gaps = (\d+))?(?:.+Strand\s*=\s*(\w+)\s*\/\s*(\w+))?/sm;
    
    if ($self->_fields->{query_strand}) {
        # protein blasts don't have strand
        for my $strand_type ('query_strand', 'hit_strand') {
            $self->_fields->{$strand_type} = $self->_fields->{$strand_type} eq 'Plus' ? 1 : -1;
        }
    }
    else {
        $self->_fields->{query_strand} = 0;
        $self->_fields->{hit_strand} = 0;
    }
	
	if ($self->_fields->{evalue} =~ /^e/) {
		$self->_fields->{evalue} = '1'.$self->_fields->{evalue};
	}
    
    # query_gaps isn't always given
    $self->_fields->{total_gaps} = '[unset]' unless $self->_fields->{total_gaps};
    
	$self->_fields->{header} = 1;

}

sub _discover_alignment {

    my $self = shift;
    $self->_chunk_seek($self->{_after_header});
    
    # work out various basic fields for the hsp
    # (quicker to do this all at once instead of each method working on
    # alignment itself)
    my ($query_string, $hit_string, $homology_string, $q_start, $h_start, $q_end, $h_end);
    while (my $strip = $self->_get_chunk_by_end("\nQuery") || $self->_get_chunk_by_nol(4)) {
        $strip =~ /\s+(\d+)\s+(\S+)\s+(\d+)\s+(\S.+)\nSbjct:?\s+(\d+)\s+(\S+)\s+(\d+)/gm || last;
        my $q1 = $1;
        $query_string .= $2;
        my $q2 = $3;
        my $hom = $4;
        my $h1 = $5;
        $hit_string .= $6;
        my $h2 = $7;
        
        $hom = ' 'x(length($6) - length($hom)).$hom;
        $homology_string .= $hom;
        
        for my $q ($q1, $q2) {
            if (! defined $q_start || $q < $q_start) {
                $q_start = $q;
            }
            if (! defined $q_end || $q > $q_end) {
                $q_end = $q;
            }
        }
        for my $h ($h1, $h2) {
            if (! defined $h_start || $h < $h_start) {
                $h_start = $h;
            }
            if (! defined $h_end || $h > $h_end) {
                $h_end = $h;
            }
        }
    }
    
    $self->_fields->{query_string} = $query_string;
    $self->_fields->{hit_string} = $hit_string;
    $self->_fields->{homology_string} = $homology_string;
    
    $self->_fields->{query_start} = $q_start;
    $self->_fields->{query_end} = $q_end;
    $self->_fields->{hit_start} = $h_start;
    $self->_fields->{hit_end} = $h_end;
    
    ($self->{_query_gaps}) = $query_string =~ tr/-//;
    ($self->{_hit_gaps}) = $hit_string =~ tr/-//;
    ($self->{_total_gaps}) = $self->{_query_gaps} + $self->{_hit_gaps};
    
    $self->_fields->{alignment} = 1; # stop this method being called again
}

# seq_inds related methods, all just need seq_inds field to have been gotten

}

sub _discover_seq_inds {

    my $self = shift;
    my ($seqString, $qseq, $sseq) = ( $self->get_field('homology_string'),
                                      $self->get_field('query_string'),
                                      $self->get_field('hit_string') );
    
    # (code largely lifted from GenericHSP)
    
    # Using hashes to avoid saving duplicate residue numbers.
    my %identicalList_query = ();
    my %identicalList_sbjct = ();
    my %conservedList_query = ();
    my %conservedList_sbjct = ();
    my @gapList_query = ();
    my @gapList_sbjct = ();
    my %nomatchList_query = ();
    my %nomatchList_sbjct = ();
    
    my $resCount_query = $self->get_field('query_end');
    my $resCount_sbjct = $self->get_field('hit_end');
    
    my ($mchar, $schar, $qchar);
    while ($mchar = chop($seqString) ) {
        ($qchar, $schar) = (chop($qseq), chop($sseq));
        
        if ($mchar eq '+' || $mchar eq '.' || $mchar eq ':') { 
            $conservedList_query{ $resCount_query } = 1; 
            $conservedList_sbjct{ $resCount_sbjct } = 1;
        }
        elsif ($mchar eq ' ') { 
            $nomatchList_query{ $resCount_query } = 1;
            $nomatchList_sbjct{ $resCount_sbjct } = 1;
        }
        else { 
            $identicalList_query{ $resCount_query } = 1; 
            $identicalList_sbjct{ $resCount_sbjct } = 1;
        }
        
        if ($qchar eq '-') {
            push(@gapList_query, $resCount_query);
        }
        else { 	    
            $resCount_query -= 1;
        }
        if ($schar eq '-') {
            push(@gapList_sbjct, $resCount_sbjct);
        }
        else { 	    
            $resCount_sbjct -= 1;
        }
    }
    
    my $fields = $self->_fields;
    $fields->{hit_identical_inds} = [ sort { $a <=> $b } keys %identicalList_sbjct ];
    $fields->{hit_conserved_inds} = [ sort { $a <=> $b } keys %conservedList_sbjct ];
    $fields->{hit_nomatch_inds} = [ sort { $a <=> $b } keys %nomatchList_sbjct ];
    $fields->{hit_gap_inds} = [ reverse @gapList_sbjct ];
    $fields->{query_identical_inds} = [ sort { $a <=> $b } keys %identicalList_query ];
    $fields->{query_conserved_inds} = [ sort { $a <=> $b } keys %conservedList_query ];
    $fields->{query_nomatch_inds} = [ sort { $a <=> $b } keys %nomatchList_query ];
    $fields->{query_gap_inds} = [ reverse @gapList_query ];
    
    $fields->{seq_inds} = 1;

}

sub query {

    my $self = shift;
    unless ($self->{_created_query}) {
        $self->SUPER::query( new  Bio::SeqFeature::Similarity
                  ('-primary'  => $self->primary_tag,
                   '-start'    => $self->get_field('query_start'),
                   '-end'      => $self->get_field('query_end'),
                   '-expect'   => $self->get_field('evalue'),
                   '-score'    => $self->get_field('score'),
                   '-strand'   => $self->get_field('query_strand'),
                   '-seq_id'   => $self->get_field('query_name'),
                   '-seqlength'=> $self->get_field('query_length'),
                   '-source'   => $self->get_field('algorithm'),
                   '-seqdesc'  => $self->get_field('query_description'),
                   '-frame'    => 0 # not known?
                   ) );
		$self->{_created_query} = 1;
    }
    return $self->SUPER::query(@_);

}

sub hit {

    my $self = shift;
    unless ($self->{_created_hit}) {
        $self->SUPER::hit( new  Bio::SeqFeature::Similarity
                  ('-primary'  => $self->primary_tag,
                   '-start'    => $self->get_field('hit_start'),
                   '-end'      => $self->get_field('hit_end'),
                   '-expect'   => $self->get_field('evalue'),
                   '-score'    => $self->get_field('score'),
                   '-strand'   => $self->get_field('hit_strand'),
                   '-seq_id'   => $self->get_field('name'),
                   '-seqlength'=> $self->get_field('length'),
                   '-source'   => $self->get_field('algorithm'),
                   '-seqdesc'  => $self->get_field('description'),
                   '-frame'    => 0 # not known?
                   ) );
		$self->{_created_hit} = 1;
    }
    return $self->SUPER::hit(@_);

}

sub gaps {

    my ($self, $type) = @_;
    
    $type = lc $type if defined $type;
    $type = 'total' if (! defined $type || $type eq 'hsp' || $type !~ /query|hit|subject|sbjct|total/); 
    $type = 'hit' if $type =~ /sbjct|subject/;
    
    if ($type eq 'total') {
        my $answer = $self->get_field('total_gaps');
        return $answer unless $answer eq '[unset]';
    }
    
    $self->get_field('alignment'); # make sure gaps have been calculated
    
    return $self->{'_'.$type.'_gaps'};

}

sub strand {

    my $self = shift;
    my $val = shift;
    $val = 'query' unless defined $val;
    $val =~ s/^\s+//;

    if ($val =~ /^q/i) {
        return $self->get_field('query_strand');
    }
    elsif ($val =~ /^hi|^s/i) {
        return $self->get_field('hit_strand');
    }
    elsif ($val =~ /^list|array/i) {
        return ($self->get_field('query_strand'), $self->get_field('hit_strand'));
    }
    else { 
        $self->warn("unrecognized component '$val' requested\n");
    }
    return 0;

}

sub start {

    my $self = shift;
    my $val = shift;
    $val = (wantarray ? 'list' : 'query') unless defined $val;
    $val =~ s/^\s+//;
    
    if ($val =~ /^q/i) { 
        return $self->get_field('query_start');
    }
    elsif ($val =~ /^(hi|s)/i) {
        return $self->get_field('hit_start');
    }
    elsif ($val =~ /^list|array/i) {
        return ($self->get_field('query_start'), $self->get_field('hit_start') );
    }
    else { 
        $self->warn("unrecognized component '$val' requested\n");
    }
    return 0;

}

sub end {

    my $self = shift;
    my $val = shift;
    $val = (wantarray ? 'list' : 'query') unless defined $val;
    $val =~ s/^\s+//;
    
    if ($val =~ /^q/i) { 
        return $self->get_field('query_end');
    }
    elsif ($val =~ /^(hi|s)/i) {
        return $self->get_field('hit_end');
    }
    elsif ($val =~ /^list|array/i) {
        return ($self->get_field('query_end'), $self->get_field('hit_end'));
    }
    else {
        $self->warn("unrecognized end component '$val' requested\n");
    }
    return 0;

}

sub pvalue {

}

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 _