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

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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

SYNOPSIS

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  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

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

FEEDBACK

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Mailing Lists

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

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 Bugs

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 - Jason Stajich

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Email jason-at-bioperl-dot-org

APPENDIX

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

new

 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    :

to_string

 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
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::SearchIO::Writer::BSMLResultWriter
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Jason Stajich <jason-at-bioperl-dot-org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...


package Bio::SearchIO::Writer::BSMLResultWriter;
use strict;

use XML::Writer;
use IO::String;

use base qw(Bio::Root::Root Bio::SearchIO::SearchWriterI);



sub new {
  my($class,@args) = @_;

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


# this implementation is largely adapted from the Incogen XSLT stylesheet
# to convert NCBI BLAST XML to BSML

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;