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lib/FAST/Bio/SearchIO/exonerate.pm  view on Meta::CPAN

	   my ($nm,$desc) = ($1,$2);
	   chomp($desc) if defined $desc;
	   $self->start_element({'Name' => 'Hit'});
	   $self->element({'Name' => 'Hit_id',
			   'Data' => $nm});
	   $self->element({'Name' => 'Hit_desc',
			   'Data' => $desc});
	   $self->{'_seencigar'} = 0;
	   $self->{'_vulgar'}    = 0;
       } elsif(  s/^vulgar:\s+(\S+)\s+         # query sequence id
		 (\d+)\s+(\d+)\s+([\-\+\.])\s+ # query start-end-strand
		 (\S+)\s+                      # target sequence id
		 (\d+)\s+(\d+)\s+([\-\+])\s+   # target start-end-strand
		 (\d+)\s+                      # score
		 //ox ) {
	   next if( $self->cigar || $self->{'_seencigar'});
	   $self->{'_vulgar'}++;
	   #
	   # Note from Ewan. This is ugly - copy and paste from
	   # cigar line parsing. Should unify somehow...
	   #
	   if( ! $self->within_element('result') ) {
	       $self->start_element({'Name' => 'ExonerateOutput'});