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Bio/Tools/EPCR.pm  view on Meta::CPAN

sub next_feature {
    my ($self) = @_;
    my $line = $self->_readline;
    return unless defined($line);
    chomp($line);
    my($seqname,$location,$mkrname, $rest) = split(/\s+/,$line,4);
    
    my ($start,$end) = ($location =~ /(\S+)\.\.(\S+)/);

    # `e-PCR -direct` results code match strand in $rest as (+) and (-).  Decode it if present.
    my $strandsign;
    if ($rest =~ m/^\(([+-])\)(.*)$/) {
      ($strandsign,$rest) = ($1, $2);
    } else {
      $strandsign = "?";
    }
    my $strand = $strandsign eq "+" ? 1 :  $strandsign eq "-" ? -1 : 0;

    my $markerfeature = Bio::SeqFeature::Generic->new 
	( '-start'   => $start,
	  '-end'     => $end,
	  '-strand'  => $strand,
	  '-source'  => $self->source,
	  '-primary' => $self->primary,
	  '-seq_id'  => $seqname,
	  '-tag'     => {
	      $self->groupclass => $mkrname,

t/data/tol-2010-02-18.nhx  view on Meta::CPAN

(((aquifex[&&NHX:TOL=59615],calderobacterium[&&NHX:TOL=59616],hydrogenobacter[&&NHX:TOL=59617],thermocrinis[&&NHX:TOL=59618],hydrogenothermus[&&NHX:TOL=59619],persephonella[&&NHX:TOL=59620],sulfurihydrogenibium[&&NHX:TOL=59621],balnearium[&&NHX:TOL=5...