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Summary

Bio::Search::Result::BlastPullResult - A parser and result object for BLASTN
results

Package variables

Included modules

Inherit

Bio::Root::Root Bio::Search::Result::PullResultI

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) {
		print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n";
    }

Description

This object implements a parser for NCBI BLASTN result output.

Methods

Methods description

 Title   : new
 Usage   : my $obj = Bio::SearchIO::Result::hmmpfam->new();
 Function: Builds a new Bio::SearchIO::Result::hmmpfam object 
 Returns : Bio::SearchIO::Result::hmmpfam
 Args    : -chunk  => [Bio::Root::IO, $start, $end] (required if no -parent)
           -parent => Bio::PullParserI object (required if no -chunk)
           -parameters => hash ref of search parameters (key => value), optional
           -statistics => hash ref of search statistics (key => value), optional

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

 Title   : next_hit
 Usage   : while( $hit = $result->next_hit()) { ... }
 Function: Returns the next available Hit object, representing potential
           matches between the query and various entities from the database.
 Returns : a Bio::Search::Hit::HitI object or undef if there are no more.
 Args    : none

 Title   : hits
 Usage   : my @hits = $result->hits
 Function: Returns the HitI objects contained within this Result
 Returns : Array of Bio::Search::Hit::HitI objects
 Args    : none

 Title		: sort_hits
 Usage		: $result->sort_hits('<score')
 Function	: Sorts the hits so that they come out in the desired order when
              hits() or next_hit() is called.
 Returns	: n/a
 Args		: A coderef for the sort function. See the documentation on the Perl
              sort() function for guidelines on writing sort functions.
			  By default the sort order is ascending significance value (ie.
			  most significant hits first).
			  *** example

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

 Title   : get_statistic
 Usage   : my $gap_ext = $result->get_statistic('kappa')
 Function: Returns the value for a specific statistic available 
           from this result
 Returns : string
 Args    : name of statistic (string)

 Title   : get_parameter
 Usage   : my $gap_ext = $result->get_parameter('gapext')
 Function: Returns the value for a specific parameter used
           when running this result
 Returns : string
 Args    : name of parameter (string)

Methods code

sub new {

    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
	
	$self->_setup(@args);
	
	foreach my $field (qw( header hit_table hsp_table alignments next_model
	models query_length stats_and_params)) {
		$self->_fields->{$field} = undef;
	}
	
	$self->_dependencies( { ( query_name => 'header',
                              query_accession => 'header',
                              query_description => 'header',
			    query_length => 'header',
                              hit_table => 'header',
			    num_hits => 'hit_table',
			    no_hits_found => 'hit_table' ) } );
    
    return $self;
}

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

}

sub _discover_header {

	my $self = shift;
	$self->_chunk_seek(0);
	my $header = $self->_get_chunk_by_end("Value\n");
	if (!$header) {
	    $header = $self->_get_chunk_by_end("***** No hits found ******\n");
	    $self->{_no_hits_found} = 1;
	}
	$self->throw("Invalid header returned") unless $header;
	$self->{_after_header} = $self->_chunk_tell;
	
	($self->_fields->{query_name}) = $header =~ /^\s*(\S+)/;
	$self->_fields->{query_accession} = '';
	$self->_fields->{query_description} = '';
	
	if ($header =~ /^Length=(\d+)/m) {
		$self->_fields->{query_length} = $1;
	}
	elsif ($header =~ /\((\d+) letters\)/) {
		# older form?
		$self->_fields->{query_length} = $1;
		
		if ($header =~ /^\s*\(\d+ letters/) {
			# there wasn't a query sequence name
			$self->_fields->{query_name} = '';
		}
	}
	
	$self->_fields->{header} = 1;

}

sub _discover_hit_table {

	my $self = shift;
	$self->_chunk_seek($self->{_after_header});
	
	my $table = $self->_get_chunk_by_end("\n>");
	
	if (!$table && !$self->{_no_hits_found}) {
		# no alignments, presumably; hit table comprises the remainder of this
		# result
		while (my $line = $self->_get_chunk_by_nol(1)) {
			$table .= $line;
		}
	}
    
	$table ||= '';
	
	$self->{_after_hit_table} = $self->_chunk_tell;
	
	my $evalue_cutoff = $self->get_field('evalue_cutoff');
	undef $evalue_cutoff if $evalue_cutoff eq '[unset]';
	my $score_cutoff = $self->get_field('score_cutoff');
	undef $score_cutoff if $score_cutoff eq '[unset]';
	
	my @table;
	my $no_hit = 1;
	while ($table =~ /^(\S+)\s+(\S.*?)?\s+(\S+)\s+([\de]\S*)\s*\n/gm) {
		$no_hit = 0;
		my ($name, $desc, $score, $evalue) = ($1, $2, $3, $4);
		$desc ||= '';
        if ($evalue =~ /^e/) {
            $evalue = '1'.$evalue;
        }
		next if ($evalue_cutoff && $evalue > $evalue_cutoff);
		next if ($score_cutoff && $score < $score_cutoff);
		push(@table, [$name, $desc, $score, $evalue]);
	}
	$self->_fields->{hit_table} =\@ table;
	$self->{_next_hit_index} = @table > 0 ? 0 : -1;
	
	$self->_fields->{no_hits_found} = $no_hit;
	$self->_fields->{num_hits} = @table;

}

sub _discover_next_hit {

	my $self = shift;
	my $hit_table = $self->get_field('hit_table');
	return if $self->{_next_hit_index} == -1;
	my $hit_row = ${$hit_table}[$self->{_next_hit_index}];
	
	$self->_chunk_seek($self->{_end_of_previous_hit} || $self->{_after_hit_table});
	
	my ($start, $end) = $self->_find_chunk_by_end("\n>");
	unless ($end) {
		$start = $self->{_end_of_previous_hit} || $self->{_after_hit_table};
		$end = $self->_chunk_true_end;
	}
	else {
		$end += $self->_chunk_true_start;
	}
	$start += $self->_chunk_true_start;
	
	$self->{_end_of_previous_hit} = $end - $self->_chunk_true_start;
	
	#*** needs to inherit piped_behaviour, and we need to deal with _sequential
	#    ourselves
	$self->_fields->{next_hit} = Bio::Search::Hit::BlastPullHit->new(-parent => $self,
								-chunk => [$self->chunk, $start, $end],
								-hit_data => $hit_row);
	
	$self->{_next_hit_index}++;
	
	if ($self->{_next_hit_index} > $#{$hit_table}) {
		$self->{_next_hit_index} = -1;
	}

}

sub _discover_stats_and_params {

	my $self = shift;
	$self->_chunk_seek(0);
	my ($start, $end) = $self->_find_chunk_by_end("\n  Database: ");
	$self->_chunk_seek($end);
	
	my $gapped = 0;
	while ($self->_get_chunk_by_nol(1)) {
		if (/Number of letters in database:\s+(\S+)/) {
			my $stat = $1;
			$stat =~ s/,//g;
			$self->add_statistic('dbletters', $stat);
		}
		elsif (/Number of sequences in database:\s+(\S+)/) {
			my $stat = $1;
			$stat =~ s/,//g;
			$self->add_statistic('dbentries', $stat);
		}
		elsif (/^Lambda/) {
			my $line = $self->_get_chunk_by_nol(1);
			$line =~ /\s+(\S+)\s+(\S+)\s+(\S+)/;
			$self->add_statistic($gapped ? 'lambda_gapped' : 'lambda', $1);
			$self->add_statistic($gapped ? 'kappa_gapped' : 'kappa', $2);
			$self->add_statistic($gapped ? 'entropy_gapped' : 'entropy', $3);
			$gapped = 1;
		}
		elsif (/^Matrix: (.+)\n/) {
			$self->add_parameter('matrix', $1);
		}
		elsif (/^Gap Penalties: Existence: (\d+), Extension: (\d+)/) {
			$self->add_parameter('gapopen', $1);
			$self->add_parameter('gapext', $2);
		}
		elsif (/^Number of Hits to DB: (\d+)/) {
			$self->add_statistic('Hits_to_DB', $1);
		}
		elsif (/^Number of extensions: (\d+)/) {
			$self->add_statistic('num_extensions', $1);
		}
		elsif (/^Number of successful extensions: (\d+)/) {
			$self->add_statistic('num_successful_extensions', $1);
		}
		elsif (/^Number of sequences better than (\S+):/) {
			$self->add_parameter('expect', $1);
		}
		elsif (/^[Ll]ength of query: (\d+)/) {
			$self->add_statistic('querylength', $1);
		}
        elsif (/^[Ee]ffective HSP length: (\d+)/) {
			$self->add_statistic('effective_hsplength', $1);
		}
		elsif (/^[Ee]ffective length of database: (\d+)/) {
			$self->add_statistic('effectivedblength', $1);
		}
		elsif (/^[Ee]ffective search space: (\d+)/) {
			$self->add_statistic('effectivespace', $1);
		}
		elsif (/^[Ee]ffective search space used: (\d+)/) {
			$self->add_statistic('effectivespaceused', $1);
		}
		elsif (/^([TAXS]\d?): (\d+)(?: \((\S+))?/) {
			$self->add_statistic($1, $2);
			$self->add_statistic($1.'_bits', $3) if $3;
		}
	}
	
	$self->_fields->{stats_and_params} = 1;

}

sub next_hit {

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

}

sub hits {

	my $self = shift;
	my $old = $self->{_next_hit_index} || 0;
	$self->rewind;
	my @hits;
	while (defined(my $hit = $self->next_hit)) {
		push(@hits, $hit);
	}
	$self->{_next_hit_index} = @hits > 0 ? $old : -1;
	return @hits;

}

sub sort_hits {

    my ($self, $code_ref) = @_;
	$self->throw("Not implemented yet");

}

sub rewind {

	my $self = shift;
	unless ($self->_fields->{hit_table}) {
		$self->get_field('hit_table');
	}
	$self->{_next_hit_index} = @{$self->_fields->{hit_table}} > 0 ? 0 : -1;

}

sub get_statistic {

	my $self = shift;
	$self->get_field('stats_and_params');
	return $self->SUPER::get_statistic(@_);

}

sub get_parameter {

	my $self = shift;
	$self->get_field('stats_and_params');
	return $self->SUPER::get_parameter(@_);
}

1;

}

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
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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.

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/

Email bix@sendu.me.uk

Additional contributors names and emails here

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