Christopher Fields > BioPerl-1.6.922 > Bio::SeqIO::chaosxml

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Module Version: 1.006922   Source   Latest Release: BioPerl-1.6.924

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 _

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