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Bio/Search/SearchUtils.pm  view on Meta::CPAN

    # Removing all "<>" tags. 
    $str =~ s/<[^>]+>|&nbsp//sgi and $stripped = 1;

    # Re-uniting any lone '>' characters.
    $str =~ s/(\A|\n)>\s+/\n\n>/sgi and $stripped = 1;

    $$string_ref = $str;
    $stripped;
}

=head2 result2hash

 Title    : result2hash
 Usage    : my %data = &Bio::Search::SearchUtils($result)
 Function : converts ResultI data to simple hash
 Returns  : hash
 Args     : ResultI
 Note     : used mainly as a utility for running SearchIO tests

=cut

sub result2hash {
    my ($result) = @_;
    my %hash;
    $hash{'query_name'} = $result->query_name;
    my $hitcount = 1;
    my $hspcount = 1;
    foreach my $hit ( $result->hits ) {
	$hash{"hit$hitcount\_name"}   =  $hit->name;
	# only going to test order of magnitude
	# too hard as these don't always match
#	$hash{"hit$hitcount\_signif"} =  
#	    ( sprintf("%.0e",$hit->significance) =~ /e\-?(\d+)/ );
	$hash{"hit$hitcount\_bits"}   =  sprintf("%d",$hit->bits);

	foreach my $hsp ( $hit->hsps ) {
	    $hash{"hsp$hspcount\_bits"}   = sprintf("%d",$hsp->bits);
	    # only going to test order of magnitude
 	    # too hard as these don't always match
#	    $hash{"hsp$hspcount\_evalue"} =  
#		( sprintf("%.0e",$hsp->evalue) =~ /e\-?(\d+)/ );
	    $hash{"hsp$hspcount\_qs"}     = $hsp->query->start;
	    $hash{"hsp$hspcount\_qe"}     = $hsp->query->end;
	    $hash{"hsp$hspcount\_qstr"}   = $hsp->query->strand;
	    $hash{"hsp$hspcount\_hs"}     = $hsp->hit->start;
	    $hash{"hsp$hspcount\_he"}     = $hsp->hit->end;
	    $hash{"hsp$hspcount\_hstr"}   = $hsp->hit->strand;

	    #$hash{"hsp$hspcount\_pid"}     = sprintf("%d",$hsp->percent_identity);
	    #$hash{"hsp$hspcount\_fid"}     = sprintf("%.2f",$hsp->frac_identical);
	    $hash{"hsp$hspcount\_gaps"}    = $hsp->gaps('total');
	    $hspcount++;
	}
	$hitcount++;
    }
    return %hash;
}

sub _warn_about_no_hsps {
    my $hit = shift;
    my $prev_func=(caller(1))[3];
    $hit->warn("There is no HSP data for hit '".$hit->name."'.\n".
               "You have called a method ($prev_func)\n".
               "that requires HSP data and there was no HSP data for this hit,\n".
               "most likely because it was absent from the BLAST report.\n".
               "Note that by default, BLAST lists alignments for the first 250 hits,\n".
               "but it lists descriptions for 500 hits. If this is the case,\n".
               "and you care about these hits, you should re-run BLAST using the\n".
               "-b option (or equivalent if not using blastall) to increase the number\n".
               "of alignments.\n"
              );
}

1;