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://github.com/bioperl/bioperl-live/issues
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 _