Bio/SeqIO/flybase_chadoxml.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::SeqIO::flybase_chadoxml
   4 #
   5 # Peili Zhang   <peili@morgan.harvard.edu>
   6 #
   7 # You may distribute this module under the same terms as perl itself
   8
   9 # POD documentation - main docs before the code
  10
  11 =head1 NAME
  12
  13 Bio::SeqIO::flybase_chadoxml - FlyBase variant of chadoxml with sequence output stream
  14
  15 =head1 SYNOPSIS
  16
  17 It is probably best not to use this object directly, but
  18 rather go through the SeqIO handler system:
  19
  20     $writer = Bio::SeqIO->new(-file => ">chado.xml",
  21                               -format => 'flybase_chadoxml');
  22
  23     # assume you already have Sequence or SeqFeature objects
  24     $writer->write_seq($seq_obj);
  25
  26     #after writing all seqs
  27     $writer->close_chadoxml();
  28
  29
  30 =head1 DESCRIPTION
  31
  32 This is a simple subclass of L<Bio::SeqIO::chadoxml>; please see
  33 its documentation for details.
  34
  35 =head1 FEEDBACK
  36
  37 =head2 Mailing Lists
  38
  39 User feedback is an integral part of the evolution of this and other
  40 Bioperl modules. Send your comments and suggestions preferably to one
  41 of the Bioperl mailing lists.  Your participation is much appreciated.
  42
  43   bioperl-l@bioperl.org                  - General discussion
  44   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  45
  46 =head2 Support
  47
  48 Please direct usage questions or support issues to the mailing list:
  49
  50 I<bioperl-l@bioperl.org>
  51
  52 rather than to the module maintainer directly. Many experienced and
  53 reponsive experts will be able look at the problem and quickly
  54 address it. Please include a thorough description of the problem
  55 with code and data examples if at all possible.
  56
  57 =head2 Reporting Bugs
  58
  59 Report bugs to the Bioperl bug tracking system to help us keep track
  60 the bugs and their resolution.
  61 Bug reports can be submitted via the web:
  62
  63   http://bugzilla.bioperl.org
  64
  65 =head1 AUTHOR - Peili Zhang
  66
  67 Email peili@morgan.harvard.edu
  68
  69 =head1 APPENDIX
  70
  71 The rest of the documentation details each of the object
  72 methods. Internal methods are usually preceded with a _
  73
  74 =cut
  75
  76 package Bio::SeqIO::flybase_chadoxml;
  77 use strict;
  78
  79 use base 'Bio::SeqIO::chadoxml';
  80
  81 sub _initialize {
  82     my($self,%args) = @_;
  83     $self->SUPER::_initialize(%args);
  84
  85     #default for standard chado is polypeptide
  86     $Bio::SeqIO::chadoxml::feattype_args2so{'CDS'} = 'protein';
  87     $Bio::SeqIO::chadoxml::cv_name{'sequence'} = 'SO';
  88     $Bio::SeqIO::chadoxml::cv_name{'relationship'} = 'relationship type';
  89     $Bio::SeqIO::chadoxml::cv_name{'feature_property'} = 'property type';
  90
  91     return;
  92 }
  93
  94
  95 =head2 return_ftype_hash
  96
  97 =over
  98
  99 =item Usage
 100
 101   $obj->return_ftype_hash()
 102
 103 =item Function
 104
 105 A simple hash where returning it has be factored out of the main
 106 code to allow subclasses to override it.
 107
 108 =item Returns
 109
 110 A hash that indicates what the name of the SO term is and what
 111 the name of the Sequence Ontology is in the cv table.
 112
 113 =item Arguments
 114
 115 The string that represents the SO term.
 116
 117 =back
 118
 119 =cut
 120
 121 sub return_ftype_hash {
 122     my $self  = shift;
 123     my $ftype = shift;
 124     my %ftype_hash = ( "name" => $ftype,
 125                        "cv_id" => {"name" => $Bio::SeqIO::chadoxml::cv_name{'sequence'} });
 126     return %ftype_hash;
 127 }
 128
 129 =head2 return_reltypename
 130
 131 =over
 132
 133 =item Usage
 134
 135   $obj->return_reltypename()
 136
 137 =item Function
 138
 139 Return the appropriate relationship type name depending on the
 140 feature type (typically partof, but producedby for proteins).
 141
 142 =item Returns
 143
 144 A relationship type name.
 145
 146 =item Arguments
 147
 148 A SO type name.
 149
 150 =back
 151
 152 =cut
 153
 154 sub return_reltypename {
 155     my $self   = shift;
 156     my $sftype = shift;
 157
 158     my $reltypename;
 159     if ($sftype eq 'protein' || $sftype eq 'polypeptide') {
 160         $reltypename = 'producedby';
 161     } else {
 162         $reltypename = 'partof';
 163     }
 164
 165     return $reltypename;
 166 }
 167
 168 =head2 write_seq
 169
 170 =over
 171
 172 =item Usage
 173
 174   $obj->write_seq()
 175
 176 =item Function
 177
 178 Overrides Bio::SeqIO::chadoxml's write_seq method just
 179 to add an internal close_chadoxml (mimics original use
 180 by FlyBase).
 181
 182 =item Returns
 183
 184 =item Arguments
 185
 186 =back
 187
 188 =cut
 189
 190 sub write_seq {
 191     my ($self, @argv) = @_;
 192
 193     $self->SUPER::write_seq(@argv);
 194
 195     $self->close_chadoxml;
 196     return 1;
 197 }
 198
 199
 200 1;