| Bio::SeqIO::game(3pm) | User Contributed Perl Documentation | Bio::SeqIO::game(3pm) |
Bio::SeqIO::game -- a class for parsing and writing game-XML
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;
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.
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
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.
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:
https://github.com/bioperl/bioperl-live/issues
Email mckays@cshl.edu
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : next_seq Usage : my $seq = $seqio->next_seq; Function: get the main sequence object Returns : a Bio::Seq::RichSeq object Args : none
Title : write_seq Usage : $seqio->write_seq($seq) Function: writes a sequence object as game XML Returns : nothing Args : a Bio::SeqI compliant object
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
Title : _hide_dna Usage : $seqio->_hide_dna Function: Hide the DNA for really huge sequences Returns : nothing Args : none
| 2021-08-15 | perl v5.32.1 |