Bio::SeqIO::game.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::SeqIO::game -- a class for parsing and writing game-XML

SYNOPSIS

This module is not used directly, use SeqIO.
  use Bio::SeqIO;
 
  my $in = Bio::SeqIO->new ( -file    => 'file.xml', 
                             -format  =>  'game',
                             -verbose => 1 );
 
  my $seq = $in->next_seq;
 
 

DESCRIPTION

Bio::SeqIO::game will parse game XML (version 1.2) or write game XML from a Bio::SeqI implementing object. The XML is readable by the genome annotation editor 'Apollo' (www.gmod.org). It is not backwards compatible with the previous version of game XML. The XML format currently used by Apollo contains a single 'main' annotated sequence, so we will only get a single annotated sequence in the stream when parsing a game-XML record.

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 one of the Bioperl mailing lists.

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 the web:

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

AUTHOR - Sheldon McKay

Email mckays@cshl.edu

APPENDIX

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

next_seq

  Title   : next_seq
  Usage   : my $seq = $seqio->next_seq;
  Function: get the main sequence object
  Returns : a Bio::Seq::RichSeq object
  Args    : none
 
 

write_seq

  Title   : write_seq
  Usage   : $seqio->write_seq($seq)
  Function: writes a sequence object as game XML
  Returns : nothing
  Args    : a Bio::SeqI compliant object
 
 

_getseqs

  Title   : _getseqs
  Usage   : $self->_getseqs
  Function: An internal method to invoke the PerlSAX XML handler and get
            the sequence objects
  Returns : an reference to an array with sequence object and annotations
  Args    : none
 
 

_hide_dna

  Title   : _hide_dna
  Usage   : $seqio->_hide_dna
  Function: Hide the DNA for really huge sequences
  Returns : nothing 
  Args    : none