Summary

Bio::Search::HSP::HmmpfamHSP - A parser and HSP object for hmmpfam hsps

Package variables

Inherit

Bio::Search::HSP::PullHSPI

Synopsis

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

    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 hmmpfam hsp output, a program in the HMMER
package.

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::Search::HSP::HmmpfamHSP();
 Function: Builds a new Bio::Search::HSP::HmmpfamHSP object.
 Returns : Bio::Search::HSP::HmmpfamHSP
 Args    : -chunk  => [Bio::Root::IO, $start, $end] (required if no -parent)
           -parent => Bio::PullParserI object (required if no -chunk)
           -hsp_data => array ref with [rank query_start query_end hit_start
										hit_end score evalue]

           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 gaps in the query, hit, or total alignment.
 Returns  : Integer, number of gaps 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   : 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( alignment )) {
		$fields->{$field} = undef;
	}
	
	my $hsp_data = $self->_raw_hsp_data;
	if ($hsp_data && ref($hsp_data) eq 'ARRAY') {
		my @hsp_data = @{$hsp_data}; # don't alter the reference
		foreach my $field (qw(rank query_start query_end hit_start hit_end score evalue)) {
			$fields->{$field} = shift(@hsp_data);
		}
	}
	
	$self->_dependencies( { ( query_string => 'alignment',
                              hit_string => 'alignment',
                              homology_string => '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;

}

sub _discover_alignment {

    my $self = shift;
    my $alignments_hash = $self->get_field('alignments');
	
    my $identifier = $self->get_field('name').'~~~~'.$self->get_field('rank');
    while (! defined $alignments_hash->{$identifier}) {
        last unless $self->parent->parent->_next_alignment;
    }
    my $alignment = $alignments_hash->{$identifier};
    
    if ($alignment) {
        # work out query, hit and homology strings, and some stats
        # (quicker to do this all at once instead of each method working on
        # $alignment string itself)
        
        my ($query_string, $hit_string, $homology_string);
        while ($alignment =~ /\s+(\S+)\n\s+(\S.+)\n\s+\S+\s+\d+\s+(\S+)\s+\d/gm) {
            my $hi = $1;
            my $ho = $2;
            $query_string .= $3;
            
            $hi =~ s/\*\-\>//;
            $ho = ' 'x(length($hi) - length($ho)).$ho;
			$hi =~ s/\<\-\*//;
            
            $hit_string .= $hi;
            $homology_string .= $ho;
        }
        
        $self->_fields->{query_string} = $query_string;
        $self->_fields->{hit_string} = $hit_string;
        $homology_string =~ s/   $//;
        $self->_fields->{homology_string} = $homology_string;
        
        ($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

}

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'   => 1,
                   '-seq_id'   => $self->get_field('query_name'),
                   #'-seqlength'=> $self->get_field('query_length'),  (not known)
                   '-source'   => $self->get_field('algorithm'),
                   '-seqdesc'  => $self->get_field('query_description')
                   ) );
		$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'   => 1,
                   '-seq_id'   => $self->get_field('name'),
                   '-seqlength'=> $self->get_field('length'),
                   '-source'   => $self->get_field('algorithm'),
                   '-seqdesc'  => $self->get_field('description')
                   ) );
		$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/;
    
    $self->get_field('alignment'); # make sure gaps have been calculated
    
    return $self->{'_'.$type.'_gaps'};

}

sub pvalue {

	return undef;

}

General documentation

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