Bio/SeqIO/chaosxml.pm

   1 #
   2 # BioPerl module for Bio::SeqIO::chaosxml
   3 #
   4 # Chris Mungall <cjm@fruitfly.org>
   5 #
   6 # You may distribute this module under the same terms as perl itself
   7
   8 # POD documentation - main docs before the code
   9
  10 =head1 NAME
  11
  12 Bio::SeqIO::chaosxml - chaosxml sequence input/output stream
  13
  14 =head1 SYNOPSIS
  15
  16     #In general you will not want to use this module directly;
  17     #use the chaosxml format via SeqIO
  18
  19     $outstream = Bio::SeqIO->new(-file => $filename, -format => 'chaosxml');
  20
  21     while ( my $seq = $instream->next_seq() ) {
  22        $outstream->write_seq($seq);
  23     }
  24
  25 =head1 DESCRIPTION
  26
  27 This object can transform Bio::Seq objects to and from chaos files.
  28
  29 B<CURRENTLY WRITE ONLY>
  30
  31 ChaosXML is an XML mapping of the chado relational database; for more
  32 information, see http://www.fruitfly.org/chaos-xml
  33
  34 Chaos can have other syntaxes than XML (eg S-Expressions, Indented text)
  35
  36 See L<Bio::SeqIO::chaos> for a full description
  37
  38
  39 =head1 VERY VERY IMPORTANT
  40
  41 !!!!!!!!!!!CHADO AND CHAOS USE INTERBASE COORDINATES!!!!!!!!!!!!!!!!
  42
  43 =head1 FEEDBACK
  44
  45 =head2 Mailing Lists
  46
  47 User feedback is an integral part of the evolution of this and other
  48 Bioperl modules. Send your comments and suggestions preferably to one
  49 of the Bioperl mailing lists.  Your participation is much appreciated.
  50
  51   bioperl-l@bioperl.org                  - General discussion
  52   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  53
  54 =head2 Support
  55
  56 Please direct usage questions or support issues to the mailing list:
  57
  58 I<bioperl-l@bioperl.org>
  59
  60 rather than to the module maintainer directly. Many experienced and
  61 reponsive experts will be able look at the problem and quickly
  62 address it. Please include a thorough description of the problem
  63 with code and data examples if at all possible.
  64
  65 =head2 Reporting Bugs
  66
  67 Report bugs to the Bioperl bug tracking system to help us keep track
  68 the bugs and their resolution.  Bug reports can be submitted via the web:
  69
  70   https://github.com/bioperl/bioperl-live/issues
  71
  72 =head1 AUTHOR - Chris Mungall
  73
  74 Email cjm@fruitfly.org
  75
  76 =head1 APPENDIX
  77
  78 The rest of the documentation details each of the object
  79 methods. Internal methods are usually preceded with a _
  80
  81 =cut
  82
  83 # Let the code begin...
  84
  85 package Bio::SeqIO::chaosxml;
  86 use strict;
  87
  88 use Data::Stag::XMLWriter;
  89
  90 use base qw(Bio::SeqIO::chaos);
  91
  92 sub default_handler_class {
  93     return Data::Stag->getformathandler('xml');
  94 }
  95
  96 1;