HTMLResultWriter documentation.

use Bio::SearchIO; use Bio::SearchIO::Writer::HTMLResultWriter; my $in = new Bio::SearchIO(-format => 'blast', -file => shift @ARGV); my $writer = new Bio::SearchIO::Writer::HTMLResultWriter(); my $out = new Bio::SearchIO(-writer => $writer); $out->write_result($in->next_result);

Title : new Usage : my $obj = new Bio::SearchIO::Writer::HTMLResultWriter(); Function: Builds a new Bio::SearchIO::Writer::HTMLResultWriter object Returns : Bio::SearchIO::Writer::HTMLResultWriter Args :

Title : remote_database_url Usage : $obj->remote_database_url($type,$newval) Function: This should return or set a string that contains a %s which can be filled in with sprintf. Returns : value of remote_database_url Args : $type - 'PROTEIN' or 'P' for protein URLS 'NUCLEOTIDE' or 'N' for nucleotide URLS $value - new value to set [optional]

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

Title : id_parser Usage : $index->id_parser( CODE ) Function: Stores or returns the code used by record_id to parse the ID for record from a string. Useful for (for instance) specifying a different parser for different flavours of FASTA file. Returns \&default_id_parser (see below) if not set. If you supply your own id_parser subroutine, then it should expect a fasta description line. An entry will be added to the index for each string in the list returned. Example : $index->id_parser( \&my_id_parser ) Returns : ref to CODE if called without arguments Args : CODE

Title : default_id_parser Usage : $id = default_id_parser( $header ) Function: The default Fasta ID parser for Fasta.pm Returns $1 from applying the regexp /^>\s*(\S+)/ to $header. Returns : ID string Args : a fasta header line string

%RemoteURLDefault = ( 'PROTEIN' => 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=protein&cmd=search&term=%s', 'NUCLEOTIDE' => 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=%s' ); $MaxDescLen = 60; $AlignmentLineWidth = 60;

my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($p,$n) = $self->_rearrange([qw(PROTEIN_URL NUCLEOTIDE_URL)],@args); $self->remote_database_url('p',$p || $RemoteURLDefault{'PROTEIN'}); $self->remote_database_url('n',$n || $RemoteURLDefault{'NUCLEOTIDE'}); return $self;

my ($self,$type,$value) = @_; if( ! defined $type || $type !~ /^(P|N)/i ) { $self->warn("Must provide a type (PROTEIN or NUCLEOTIDE)"); return ''; } $type = uc $1; if( defined $value) { $self->{'remote_database_url'}->{$type} = $value; } return $self->{'remote_database_url'}->{$type};

sub to_string {

    my ($self,$result) = @_; 
    return unless defined $result;
    my $type = ( $result->algorithm =~ /(P|X|Y)$/i ) ? 'PROTEIN' : 'NUCLEOTIDE';
    my $str = sprintf(
qq{<HTML>
    <HEAD><CENTER><TITLE>Bioperl Reformatted HTML of %s Search output with Bio::Search</TITLE></CENTER></HEAD>
    <BODY BGCOLOR="WHITE">
    <CENTER><H1>Bioperl Reformatted HTML of %s Search Report<br> for %s</H1></CENTER>
    <hr>
    <b>Query=</b>%s %s<br><dd>(%d letters)</dd>
    <p>
    <b>Database:</b> %s<br><dd>%d sequences; %d total letters<p></dd>
    <p>
    <table border=0>
    <tr><th>Sequences producing significant alignments:</th>
	<th>Score<br>(bits)</th><th>E<br>value</th></tr>
  }, 
		      $result->algorithm, $result->algorithm,
		      $result->query_name(), $result->query_name, 
		      $result->query_description, $result->query_length, 
		      $result->database_name(),
		      $result->database_entries(),$result->database_letters(),
		      );
    my $hspstr = '<p><p>';
    while( my $hit = $result->next_hit ) {
	my $nm = $hit->name();
	my $id_parser = $self->id_parser;
	print STDERR "no $nm for name (",$hit->description(), "\n" unless $nm;
	my ($gi,$acc) = &$id_parser($nm);
	my $descsub = substr($hit->description,0,$MaxDescLen);
	$descsub .= " ..." if length($descsub) < length($hit->description);
	
	$str .= sprintf('<tr><td><a href="%s">%s</a> %s </td><td>%s</td><td><a href="#%s">%s</a></td></tr>'."\n",
			sprintf($self->remote_database_url($type), 
				$gi || $acc),
			$hit->name, $descsub,
			defined $hit->raw_score ? $hit->raw_score : '?',
			$acc,
			defined $hit->significance ? $hit->significance : '?');

	$hspstr .= "<a name=\"$acc\"><pre>\n".
	    sprintf(">%s %s\n<dd>Length = %d</dd><p>\n\n", $hit->name, 
			defined $hit->description ? $hit->description : '', 
		    $hit->length);
	
	while( my $hsp = $hit->next_hsp ) {
	    if( defined $hsp->bits() ) {
		$hspstr .= sprintf(" Score = %s", $hsp->bits());
	    }
	    if( defined $hsp->bits() ) {
		$hspstr .= sprintf(" bits (%s)", $hsp->score());
	    }
	    if( defined $hsp->evalue ) {
		$hspstr.= sprintf(", Expect = %s", $hsp->evalue);
	    }
	    if( $hsp->pvalue ) {
		$hspstr .= ", P = ".$hsp->pvalue;
	    }
	    $hspstr .= "<br>\n";
	    $hspstr .= sprintf(" Identities = %d / %d (%d%%)",
			         ( $hsp->frac_identical('total') * 
				   $hsp->length('total')),
			       $hsp->length('total'),
			       $hsp->frac_identical('total') * 100);

	    if( $hit->algorithm =~ /(T)?BLAST(X|P)/ ||
		$hit->algorithm =~ /(T)?FAST(X|Y|P)/ ||
		$hit->algorithm eq 'TBLASTN' ||
		$hit->algorithm eq 'TFASTN' 
		) {
		$hspstr .= sprintf(", Positives = %d / %d (%d%%)",
				   ( $hsp->frac_conserved('total') * 
				     $hsp->length('total')),
				   $hsp->length('total'),
				   $hsp->frac_conserved('total') * 100);
		
	    }
	    if( $hsp->gaps ) {
		$hspstr .= sprintf(", Gaps = %d / %d (%d%%)",
				   $hsp->gaps('total'),
				   $hsp->length('total'),
				   (100 * $hsp->gaps('total') / 
				    $hsp->length('total')));
	    }
	    
	    my ($h,$q) = ( $hsp->hit->frame ,$hsp->query->frame);
		
	    if( $h || $q ) {
		$hspstr .= " Frame = ";
		
		if( $h && ! $q) {  $hspstr .= $h }
		elsif( $q && ! $h) {  $hspstr .= $q }
		else { 
		    $hspstr .= " $h / $q ";
		}
	    }
	    $hspstr .= "</pre></a><p>\n<pre>";
	    
	    my @hspvals = ( {'name' => 'Query:',
			     'seq'  => $hsp->query_string,
			     'start' => $hsp->query->strand > 0 ? $hsp->query->start : $hsp->query->end,
			     'end'   => $hsp->query->strand > 0 ? $hsp->query->end : $hsp->query->start,
			     'index' => 0,
			     'direction' => $hsp->query->strand
			     },
			    { 'name' => ' 'x6,
			      'seq'  => $hsp->homology_string,
			      'start' => undef,
			      'end'   => undef,
			      'index' => 0,
			      'direction' => 1
			      },
			    { 'name'  => 'Sbjct:',
			      'seq'   => $hsp->hit_string,
			      'start' => $hsp->hit->strand > 0 ? $hsp->hit->start : $hsp->hit->end,
			      'end'   => $hsp->hit->strand > 0 ? $hsp->hit->end : $hsp->hit->start,
			      'index' => 0,
			      'direction' => $hsp->query->strand
			      }
			    );	    
	    
	    
	    # let's set the expected length (in chars) of the starting number
	    # in an alignment block so we can have things line up
	    # Just going to try and set to the largest
	    
	    my ($numwidth) = sort { $b <=> $a }(length($hspvals[0]->{'start'}),
						length($hspvals[0]->{'end'}),
						length($hspvals[2]->{'start'}),
						length($hspvals[2]->{'end'}));
	    my $count = 0;
	    while ( $count <= $hsp->length('total') ) {
		foreach my $v ( @hspvals ) {
		    my $piece = substr($v->{'seq'}, $v->{'index'},
				       $AlignmentLineWidth);
		    my $cp = $piece;
		    my $plen = scalar ( $cp =~ tr/\-//);
		    my ($start,$end) = ('','');
		    if( defined $v->{'start'} ) { 
			$start = $v->{'start'};
			# since strand can be + or - use the direction
			# to signify which whether to add or substract from end
			$end   = $v->{'start'} + ( ( $v->{'direction'} ) * 
					   ( $AlignmentLineWidth - $plen ));
			$v->{'start'} += $AlignmentLineWidth;
		    }
		    $hspstr .= sprintf("%s %-".$numwidth."s %s %s\n",
				       $v->{'name'},
				       $start,
				       $piece,
				       $end
				       );
		}
		$count += $AlignmentLineWidth;
		$hspstr .= '<p>';
	    }
	}
	$hspstr .= "</pre>\n";
    }
    $str .= "</table><p>\n".$hspstr;

    foreach my $param ( $result->available_parameters ) {
	$str .= "$param=". $result->get_parameter($param) ."<br>\n";
	
    }
    $str .= "<p>";
   foreach my $stat ( sort $result->available_statistics ) {
	$str .= "$stat=". $result->get_statistic($stat). "<br>\n";
    }
    $str .=  $self->footer() . "</BODY>\n</HTML>\n";
    
    return $str;

}

my ($string) = @_; my ($gi,$acc); if( $string =~ s/gi\|(\d+)\|?// ) { $gi = $1; $acc = $1;} if( $string =~ /(\w+)\|([A-Z\d\.\_]+)(\|[A-Z\d\_]+)?/ ) { $acc = defined $2 ? $2 : $1; } else { $acc = $string; $acc =~ s/^\s+(\S+)/$1/; $acc =~ s/(\S+)\s+$/$1/; } return ($gi,$acc);

BEGIN		Code
new	Description	Code
remote_database_url	Description	Code
to_string	Description	Code
id_parser	Description	Code
default_id_parser	Description	Code
MIN	No description	Code
MAX	No description	Code
footer	No description	Code