Bio::Search::Result BlastPullResult
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Summary
Bio::Search::Result::BlastPullResult - A parser and result object for BLASTN
results
Package variables
No package variables defined.
Included modules
Bio::Search::Hit::BlastPullHit
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
newDescriptionCode
_discover_header
No description
Code
_discover_hit_table
No description
Code
_discover_next_hit
No description
Code
_discover_stats_and_params
No description
Code
next_hitDescriptionCode
hitsDescriptionCode
sort_hitsDescriptionCode
rewindDescriptionCode
get_statisticDescriptionCode
get_parameterDescriptionCode
Methods description
newcode    nextTop
 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)
next_hitcodeprevnextTop
 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
hitscodeprevnextTop
 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
See Also: Bio::Search::Hit::HitI
sort_hitscodeprevnextTop
 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
rewindcodeprevnextTop
 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
get_statisticcodeprevnextTop
 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)
get_parametercodeprevnextTop
 Title   : get_parameter
Usage : my $gap_ext = $result->get_parameter('gapext')
Function: Returns the value for a specific parameter used
when running this result
Returns : string
Args : name of parameter (string)
Methods code
newdescriptionprevnextTop
sub new {
    my ($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
#
}
_discover_headerdescriptionprevnextTop
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;
}
_discover_hit_tabledescriptionprevnextTop
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;
}
_discover_next_hitdescriptionprevnextTop
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; }
}
_discover_stats_and_paramsdescriptionprevnextTop
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;
}
next_hitdescriptionprevnextTop
sub next_hit {
	my $self = shift;
    my $hit = $self->get_field('next_hit');
	undef $self->_fields->{next_hit};
	return $hit;
}
hitsdescriptionprevnextTop
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 ? $old : -1;
	return @hits;
}
sort_hitsdescriptionprevnextTop
sub sort_hits {
    my ($self, $code_ref) = @_;
	$self->throw("Not implemented yet");
}
rewinddescriptionprevnextTop
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;
}
get_statisticdescriptionprevnextTop
sub get_statistic {
	my $self = shift;
	$self->get_field('stats_and_params');
	return $self->SUPER::get_statistic(@_);
}
get_parameterdescriptionprevnextTop
sub get_parameter {
	my $self = shift;
	$self->get_field('stats_and_params');
	return $self->SUPER::get_parameter(@_);
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
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.
Reporting BugsTop
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/
AUTHOR - Sendu BalaTop
Email bix@sendu.me.uk
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _