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)