Bio::SeqIO::chaosxml(3pm) User Contributed Perl Documentation Bio::SeqIO::chaosxml(3pm)
NAME
Bio::SeqIO::chaosxml - chaosxml sequence input/output stream
SYNOPSIS
#In general you will not want to use this module directly;
#use the chaosxml format via SeqIO
$outstream = Bio::SeqIO->new(-file => $filename, -format => 'chaosxml');
while ( my $seq = $instream->next_seq() ) {
$outstream->write_seq($seq);
}
DESCRIPTION
This object can transform Bio::Seq objects to and from chaos files.
CURRENTLY WRITE ONLY
ChaosXML is an XML mapping of the chado relational database; for more information, see http://www.fruitfly.org/chaos-xml
Chaos can have other syntaxes than XML (eg S-Expressions, Indented text)
See Bio::SeqIO::chaos for a full description
VERY VERY IMPORTANT
!!!!!!!!!!!CHADO AND CHAOS USE INTERBASE COORDINATES!!!!!!!!!!!!!!!!
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 the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chris Mungall
Email cjm@fruitfly.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
perl v5.14.2 2012-03-02 Bio::SeqIO::chaosxml(3pm)