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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'});

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

	   # end of hit
	   $self->element({'Name' => 'Hit_score',
			   'Data' => $score});
	   # issued end...
	   $self->end_element({'Name' => 'Hit'});
	   $self->end_element({'Name' => 'ExonerateOutput'});

	   return $self->end_document();

       } elsif(  s/^cigar:\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->vulgar || $self->{'_seenvulgar'});
	   $self->{'_cigar'}++;

	   if( ! $self->within_element('result') ) {
	       $self->start_element({'Name' => 'ExonerateOutput'});
	       $self->element({'Name' => 'ExonerateOutput_query-def',
			       'Data' => $1 });
	   }

lib/FAST/Bio/SimpleAlign.pm  view on Meta::CPAN

	for ($i=0; $i < @{$self->{'_start_end_lists'}->{$id}}; $i++) {
	    if (${$self->{'_start_end_lists'}->{$id}}[$i] eq $seq) {
		$found = 1;
		last;
	    }
	}
	if ($found) {
	    splice @{$self->{'_start_end_lists'}->{$id}}, $i, 1;
	}
	else {
	    $self->throw("Could not find the sequence to remoce from the start-end list");
	}
    }
    else {
	$self->throw("There is no seq list for the name $id");
    }
    # we need to shift order hash
    my %rev_order = reverse %{$self->{'_order'}};
    my $no = $rev_order{$name};
    my $num_sequences = $self->num_sequences;
    for (; $no < $num_sequences; $no++) {