Christopher Fields > BioPerl > Bio::Tools::EMBOSS::Palindrome



Annotate this POD


New  12
Open  4
View/Report Bugs
Module Version: 1.006924   Source  


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.


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.                  - General discussion  - About the mailing lists


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

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:

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)
syntax highlighting: