Bio/SeqIO/flybase_chadoxml.pm

   1 #
   2 # BioPerl module for Bio::SeqIO::flybase_chadoxml
   3 #
   4 # Peili Zhang   <peili@morgan.harvard.edu>
   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::flybase_chadoxml - FlyBase variant of chadoxml with sequence output stream
  13
  14 =head1 SYNOPSIS
  15
  16 It is probably best not to use this object directly, but
  17 rather go through the SeqIO handler system:
  18
  19     $writer = Bio::SeqIO->new(-file => ">chado.xml",
  20                               -format => 'flybase_chadoxml');
  21
  22     # assume you already have Sequence or SeqFeature objects
  23     $writer->write_seq($seq_obj);
  24
  25     #after writing all seqs
  26     $writer->close_chadoxml();
  27
  28
  29 =head1 DESCRIPTION
  30
  31 This is a simple subclass of L<Bio::SeqIO::chadoxml>; please see
  32 its documentation for details.
  33
  34 =head1 FEEDBACK
  35
  36 =head2 Mailing Lists
  37
  38 User feedback is an integral part of the evolution of this and other
  39 Bioperl modules. Send your comments and suggestions preferably to one
  40 of the Bioperl mailing lists.  Your participation is much appreciated.
  41
  42   bioperl-l@bioperl.org                  - General discussion
  43   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  44
  45 =head2 Support
  46
  47 Please direct usage questions or support issues to the mailing list:
  48
  49 I<bioperl-l@bioperl.org>
  50
  51 rather than to the module maintainer directly. Many experienced and
  52 reponsive experts will be able look at the problem and quickly
  53 address it. Please include a thorough description of the problem
  54 with code and data examples if at all possible.
  55
  56 =head2 Reporting Bugs
  57
  58 Report bugs to the Bioperl bug tracking system to help us keep track
  59 the bugs and their resolution.
  60 Bug reports can be submitted via the web:
  61
  62   https://github.com/bioperl/bioperl-live/issues
  63
  64 =head1 AUTHOR - Peili Zhang
  65
  66 Email peili@morgan.harvard.edu
  67
  68 =head1 APPENDIX
  69
  70 The rest of the documentation details each of the object
  71 methods. Internal methods are usually preceded with a _
  72
  73 =cut
  74
  75 package Bio::SeqIO::flybase_chadoxml;
  76 use strict;
  77
  78 use base 'Bio::SeqIO::chadoxml';
  79
  80 sub _initialize {
  81     my($self,%args) = @_;
  82     $self->SUPER::_initialize(%args);
  83
  84     #default for standard chado is polypeptide
  85     $Bio::SeqIO::chadoxml::feattype_args2so{'CDS'} = 'protein';
  86     $Bio::SeqIO::chadoxml::cv_name{'sequence'} = 'SO';
  87     $Bio::SeqIO::chadoxml::cv_name{'relationship'} = 'relationship type';
  88     $Bio::SeqIO::chadoxml::cv_name{'feature_property'} = 'property type';
  89
  90     return;
  91 }
  92
  93 =head2 return_ftype_hash
  94
  95  Title    : return_ftype_hash
  96  Usage    : $obj->return_ftype_hash()
  97  Function : A simple hash where returning it has be factored out of the main
  98             code to allow subclasses to override it.
  99  Returns  : A hash that indicates what the name of the SO term is and what
 100             the name of the Sequence Ontology is in the cv table.
 101  Args     : The string that represents the SO term.
 102  Status   :
 103
 104 =cut
 105
 106 sub return_ftype_hash {
 107     my $self  = shift;
 108     my $ftype = shift;
 109     my %ftype_hash = ( "name" => $ftype,
 110                        "cv_id" => {"name" => $Bio::SeqIO::chadoxml::cv_name{'sequence'} });
 111     return %ftype_hash;
 112 }
 113
 114 =head2 return_reltypename
 115
 116  Title    : return_reltypename
 117  Usage    : $obj->return_reltypename
 118  Function : Return the appropriate relationship type name depending on the
 119             feature type (typically part_of, but derives_from for polypeptide).
 120  Returns  : A relationship type name.
 121  Args     : A SO type name.
 122  Status   :
 123
 124 =cut
 125
 126 sub return_reltypename {
 127     my $self   = shift;
 128     my $sftype = shift;
 129
 130     my $reltypename;
 131     if ($sftype eq 'protein' || $sftype eq 'polypeptide') {
 132         $reltypename = 'producedby';
 133     } else {
 134         $reltypename = 'partof';
 135     }
 136
 137     return $reltypename;
 138 }
 139
 140 =head2 write_seq
 141
 142  Title   : write_seq
 143  Usage   : $stream->write_seq(-seq=>$seq, -seq_so_type=>$seqSOtype,
 144                   -src_feature=>$srcfeature,
 145                   -src_feat_type=>$srcfeattype,
 146                   -nounflatten=>0 or 1,
 147                   -is_analysis=>'true' or 'false',
 148                   -data_source=>$datasource)
 149  Function: writes the $seq object (must be seq) into chadoxml.
 150  Returns : 1 for success and 0 for error
 151  Args     : A Bio::Seq object $seq, optional $seqSOtype, $srcfeature,
 152             $srcfeattype, $nounflatten, $is_analysis and $data_source.
 153
 154 Overrides Bio::SeqIO::chadoxml's write_seq method just to add an internal
 155 close_chadoxml (mimics original use by FlyBase).
 156
 157 =cut
 158
 159 sub write_seq {
 160     my ($self, @argv) = @_;
 161
 162     $self->SUPER::write_seq(@argv);
 163
 164     $self->close_chadoxml;
 165     return 1;
 166 }
 167
 168
 169 1;