debian man page for bio::tools::emboss::palindrome

Bio::Tools::EMBOSS::Palindrome(3pm)			User Contributed Perl Documentation		       Bio::Tools::EMBOSS::Palindrome(3pm)

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://redmine.open-bio.org/projects/bioperl/

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)

perl v5.14.2							    2012-03-02				       Bio::Tools::EMBOSS::Palindrome(3pm)