Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

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

SYNOPSIS

         # 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 ) {
               $out->write_feature($feat);
            }
         }

DESCRIPTION

       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

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

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via email or the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

       Email jason-at-bioperl-dot-org

APPENDIX

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

   new
        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

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

   source_tag
        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)