Bio::SearchIO::Writer BSMLResultWriter
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Summary
Bio::SearchIO::Writer::BSMLResultWriter - BSML output writer
Package variables
No package variables defined.
Included modules
IO::String
XML::Writer
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
newDescriptionCode
to_stringDescriptionCode
Methods description
newcode    nextTop
 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_stringcodeprevnextTop
 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 : $result_obj = A Bio::Search::Result::ResultI object
: @args = any additional arguments used by your implementation.
Returns : String containing data for each search Result or any of its
: sub-objects (Hits and HSPs).
Throws : n/a
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  return $self;
}
to_stringdescriptionprevnextTop
sub to_string {
    my ($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
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 - Jason StajichTop
Email jason-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _