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 = new Bio::Tools::EMBOSS::Palindrome(-file => $filename);
my $out    = new Bio::Tools::GFF(-gff_version => 3,
                                 -file => ">$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

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:

http://bugzilla.open-bio.org/

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 = new Bio::Tools::EMBOSS::Palindrome();
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)