Summary

Bio::SearchIO::Writer::BSMLResultWriter - BSML output writer

Package variables

Included modules

Inherit

Bio::Root::Root Bio::SearchIO::SearchWriterI

Synopsis

  use Bio::SearchIO;
  my $in = Bio::SearchIO->new(-file   => 'result.blast',
                             -format => 'blast');
  my $out = Bio::SearchIO->new(-output_format  => 'BSMLResultWriter',
                              -file           => ">result.bsml");
  while( my $r = $in->next_result ) {
    $out->write_result($r);
  }

Description

This is a writer to produce BSML for a search result.

Methods

Methods description

 Title   : new
 Usage   : my $obj = Bio::SearchIO::Writer::BSMLResultWriter->new();
 Function: Builds a new Bio::SearchIO::Writer::BSMLResultWriter object 
 Returns : an instance of Bio::SearchIO::Writer::BSMLResultWriter
 Args    :

 Purpose   : Produces data for each Search::Result::ResultI in a string.
           : This is an abstract method. For some useful implementations,
           : see ResultTableWriter.pm, HitTableWriter.pm, 
           : and HSPTableWriter.pm.
 Usage     : print $writer->to_string( $result_obj, @args );
 Argument  : $result_obj = A Bio::Search::Result::ResultI object
           : @args = any additional arguments used by your implementation.
 Returns   : String containing data for each search Result or any of its
           : sub-objects (Hits and HSPs).
 Throws    : n/a

Methods code

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  return $self;

}

sub to_string {

    my ($self,$result,$num) = @_;
    my $str = new IO::String();
    my $writer = new XML::Writer(OUTPUT     => $str,
				 DATA_INDENT => 1,
				 DATA_MODE   => 1);
    $writer->xmlDecl('UTF-8');
    $writer->doctype('Bsml','-//EBI//Labbook, Inc. BSML DTD//EN',
		     'http://www.labbook.com/dtd/bsml3_1.dtd');
    $writer->startTag('Bsml');
    $writer->startTag('Definitions');
    $writer->startTag('Sequences');
    my $reporttype = $result->algorithm;
    my ($qmoltype,$hmoltype);
    my $hit = $result->next_hit;
    my $hsp = $hit->next_hsp;
    if( $hsp->query->strand == 0 ) { $qmoltype = 'aa' }
    else { $qmoltype = 'nt' }
    
    if( $hsp->hit->strand == 0 ) { $hmoltype = 'aa' }
    else { $hmoltype = 'nt' }
	
    $writer->startTag('Sequence',
		      'length' => $result->query_length,
		      'title'  => $result->query_name . " ". $result->query_description,
		      'molecule' => $qmoltype,
		      'representation' => 'virtual',
		      'id'     => $result->query_name
		      );
    # Here we're annotating the Query sequence with hits
    # hence the Feature-table
    $writer->startTag('Feature-tables');
    $writer->startTag('Feature-table',
		      'title' => "$reporttype Result", 
		      'class' => $reporttype);
    my ($hitnum,$hspnum) = (1,1);
    foreach my $hit ( $result->hits ) {	
	$hspnum = 1;
	foreach my $hsp ( $hit->hsps ) {
	    $writer->startTag('Feature',
			      'class'  => $reporttype,
			      'value-type' => 'alignment',
			      'title'  => $hit->name. " ". $hit->description,
			      );

	    $writer->emptyTag('Interval-loc',
			      'startpos' => $hsp->query->start,
			      'endpos'   => $hsp->query->end);
	    $writer->emptyTag('Qualifier',
			      'value-type' => 'score',
			      'value'      => $hsp->score,
			      );
	    
	    $writer->emptyTag('Qualifier',
			      'value-type' => 'target-start',
			      'value'      => $hsp->hit->start,
			      );
	    $writer->emptyTag('Qualifier',
			      'value-type' => 'target-end',
			      'value'      => $hsp->hit->end,
			      );
	    $writer->emptyTag('Link',
			      'title' => 'alignment',
			      'href'  => sprintf("#SPA%d.%d",$hitnum,$hspnum)
			      );
	    
	    if( $hsp->hit->strand < 0 ) {
		$writer->emptyTag('Qualifier',
				  'value-type' => 'target-on-complement',
				  'value'      => 1,
				  );
	    }
	    $hspnum++;
	    $writer->endTag('Feature');
	}
	$hitnum++;
    }
    $writer->endTag('Feature-table');
    $writer->endTag('Feature-tables');
    $writer->endTag('Sequence');
    $writer->endTag('Sequences');

    $writer->startTag('Tables');
    $writer->startTag('Sequence-search-table',
		      'search-type' => $reporttype,
		      'query-length' => $result->query_length);
    $hitnum = $hspnum = 1;
    foreach my $hit ( $result->hits ) {
	$hspnum = 1;
	foreach my $hsp ( $hit->hsps ) {
	    $writer->startTag('Seq-pair-alignment',
			      'id' => sprintf("SPA%d.%d",$hitnum,$hspnum),
			      'method'       => join(' ',$result->algorithm), 
			      'compxref'     => sprintf("%s:%s",
						'',$result->query_name),
			      'refxref'      => sprintf("%s:%s",
							$result->database_name,
							$hit->name),
			      'refseq'       => $hit->name,
			      'title'        => $result->query_name,
			      'compseq'      => $result->query_name,
			      'compcaption'  => $result->query_name . ' ' .
			                         $result->query_description,
			      'refcaption'   => $hit->name . " ". 
                                                 $hit->description,
			      'totalscore'   => $hsp->score,
			      'refstart'     => $hsp->query->start,
			      'refend'       => $hsp->query->end,
			      'compstart'    => $hsp->hit->start,
			      'compend'      => $hsp->hit->end,
			      'complength'   => $hit->length,
			      'reflength'    => $result->query_length);

	    $writer->emptyTag('Attribute',
			      'name'    => 'hit-num',
			      'content' => $hitnum);
	    $writer->emptyTag('Attribute',
			      'name'    => 'hit-id',
			      'content' => $hit->name);
	    $writer->emptyTag('Attribute',
			      'name'    => 'hsp-num',
			      'content' => $hspnum);
	    $writer->emptyTag('Attribute',
			      'name'    => 'hsp-bit-score',
			      'content' => $hsp->bits);
	    $writer->emptyTag('Attribute',
			      'name'    => 'hsp-evalue',
			      'content' => $hsp->evalue);
	    $writer->emptyTag('Attribute',
			      'name'    => 'pattern-from',
			      'content' => 0);
	    $writer->emptyTag('Attribute',
			      'name'    => 'pattern-to',
			      'content' => 0);
	    $writer->emptyTag('Attribute',
			      'name'    => 'query-frame',
			      'content' => $hsp->query->frame);
	    $writer->emptyTag('Attribute',
			      'name'    => 'hit-frame',
			      'content' => $hsp->hit->frame * $hsp->hit->strand);
	    $writer->emptyTag('Attribute',
			      'name'    => 'percent_identity',
			      'content' => sprintf("%.2f",$hsp->percent_identity));
	    $writer->emptyTag('Attribute',
			      'name'    => 'percent_similarity',
			      'content' => sprintf("%.2f",$hsp->frac_conserved('total') * 100));	    
	    my $cons = $hsp->frac_conserved('total') * $hsp->length('total');
	    my $ident = $hsp->frac_identical('total') * $hsp->length('total');
	    
	    $writer->emptyTag('Attribute',
			      'name'    => 'identity',
			      'content' => $ident);
	    $writer->emptyTag('Attribute',
			      'name'    => 'positive',
			      'content' => $cons);
	    $writer->emptyTag('Attribute',
			      'name'    => 'gaps',
			      'content' => $hsp->gaps('total'));
	    $writer->emptyTag('Attribute',
			      'name'    => 'align-len',
			      'content' => $hsp->length('total'));
	    $writer->emptyTag('Attribute',
			      'name'    => 'density',
			      'content' => 0);
	    $writer->emptyTag('Attribute',
			      'name'    => 'hit-len',
			      'content' => $hit->length);
	    my @extrafields;

	    $writer->emptyTag('Seq-pair-run',
			      'runlength'     => $hsp->hit->length,
			      'comprunlength' => $hsp->hsp_length,
			      'complength'    => $hsp->hit->length,
			      'compcomplement'=> $hsp->hit->strand < 0 ? 1 :0,
			      'refcomplement' => $hsp->query->strand < 0 ? 1 :0,
			      'refdata'       => $hsp->query_string,
			      'compdata'      => $hsp->hit_string,
			      'alignment'     => $hsp->homology_string,
			      );
	    $hspnum++;
	    $writer->endTag('Seq-pair-alignment');
	}
	$hitnum++;
    }
    $writer->endTag('Sequence-search-table');
    $writer->endTag('Tables');
    
    $writer->startTag('Research');
    $writer->startTag('Analyses');
    $writer->startTag('Analysis');
    $writer->emptyTag('Attribute',
		      'name'    => 'program',
		      'content' => $reporttype);
    $writer->emptyTag('Attribute',
		      'name'    => 'version',
		      'content' => join(' ',$reporttype, 
					$result->algorithm_version));
    $writer->emptyTag('Attribute',
		      'name'     => 'reference',
		      'content'  => $result->algorithm_reference);
    $writer->emptyTag('Attribute',
		      'name'     => 'db',
		      'content'  => $result->database_name);
    $writer->emptyTag('Attribute',
		      'name'     => 'db-size',
		      'content'  => $result->database_entries);
    $writer->emptyTag('Attribute',
		      'name'     => 'db-length',
		      'content'  => $result->database_letters);
    # $writer->emptyTag('Attribute',
    # 'name'     => 'iter-num',
    # 'content'  => $result->iteration_num);
    foreach my $attr ( $result->available_parameters ) {
	$writer->emptyTag('Attribute',
			  'name'     => $attr,
			  'content'  => $result->get_parameter($attr));
    }
    foreach my $attr ( $result->available_statistics ) {
	$writer->emptyTag('Attribute',
			  'name'     => $attr,
			  'content'  => $result->get_statistic($attr));
    }
    $writer->endTag('Analysis');    
    $writer->endTag('Analyses');    
    $writer->endTag('Research');
    
    $writer->endTag('Definitions');   
    $writer->endTag('Bsml');   
    $writer->end();
    return ${$str->string_ref};
}
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
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of the bugs and their resolution. Bug reports can be submitted via
the web:

  http://bugzilla.open-bio.org/

Email jason-at-bioperl-dot-org

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