Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Tools::EMBOSS::Palindrome - parse EMBOSS palindrome output


         # a simple script to turn palindrome output into GFF3
         use Bio::Tools::EMBOSS::Palindrome;
         use Bio::Tools::GFF;

         my $parser = Bio::Tools::EMBOSS::Palindrome->new(-file => $filename);
         my $out    = Bio::Tools::GFF->new(-gff_version => 3,
                                          -file => ">$filename.gff");
         while( my $seq = $parser->next_seq ) {
            for my $feat ( $seq->get_SeqFeatures ) {


       This is a parser for the EMBOSS tool 'palindrome'.  It will produce a Bio::Seq object for
       each sequence analyzed.  The sequence will be empty (but will be of the correct length)
       and will have attached to it Bio::SeqFeature::FeaturePair objects which wil

       It may be consolidated into another framework at a later time, but for the time being it
       will stay a separate modules.


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AUTHOR - Jason Stajich

       Email jason-at-bioperl-dot-org


       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

        Title   : new
        Usage   : my $obj = Bio::Tools::EMBOSS::Palindrome->new();
        Function: Builds a new Bio::Tools::EMBOSS::Palindrome object
        Returns : an instance of Bio::Tools::EMBOSS::Palindrome
        Args    : -file/-fh  => a filename or filehandle for
                                initializing the parser

        Title   : next_seq
        Usage   : my $seq = $parser->next_seq;
        Function: Get the next feature set from the
        Returns : L<Bio::SeqI> object
        Args    : none

        Title   : source_tag
        Usage   : $obj->source_tag($newval)
        Function: Get/Set Source Tag ('palindrome') by default
        Returns : value of source_tag (a scalar)
        Args    : on set, new value (a scalar or undef, optional)