Bio/DB/Expression.pm

   1 #
   2 # BioPerl module for Bio::DB::Expression
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Allen Day <allenday@ucla.edu>
   7 #
   8 # Copyright Allen Day
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::DB::Expression - DESCRIPTION of Object
  17
  18 =head1 SYNOPSIS
  19
  20   use Bio::DB::Expression;
  21   my $db = Bio::DB::Expression->new( -source => 'geo' );
  22   my @platforms = $db->get_platforms();
  23   foreach my $platform ( @platforms ) {
  24     my @datasets = $platform->get_datasets();
  25     foreach my $dataset ( @datasets ) {
  26       my @samples = $dataset->get_samples();
  27       foreach my $sample ( @samples ) {
  28         #...
  29       }
  30     }
  31   }
  32
  33 =head1 DESCRIPTION
  34
  35 Describe the object here
  36
  37 =head1 FEEDBACK
  38
  39 =head2 Mailing Lists
  40
  41 User feedback is an integral part of the evolution of this and other
  42 Bioperl modules. Send your comments and suggestions preferably to
  43 the Bioperl mailing list.  Your participation is much appreciated.
  44
  45   bioperl-l@bioperl.org                  - General discussion
  46   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  47
  48 =head2 Support
  49
  50 Please direct usage questions or support issues to the mailing list:
  51
  52 I<bioperl-l@bioperl.org>
  53
  54 rather than to the module maintainer directly. Many experienced and
  55 reponsive experts will be able look at the problem and quickly
  56 address it. Please include a thorough description of the problem
  57 with code and data examples if at all possible.
  58
  59 =head2 Reporting Bugs
  60
  61 Report bugs to the Bioperl bug tracking system to help us keep track
  62 of the bugs and their resolution. Bug reports can be submitted via
  63 the web:
  64
  65   https://github.com/bioperl/bioperl-live/issues
  66
  67 =head1 AUTHOR - Allen Day
  68
  69 Email allenday@ucla.edu
  70
  71 =head1 APPENDIX
  72
  73 The rest of the documentation details each of the object methods.
  74 Internal methods are usually preceded with a _
  75
  76 =cut
  77
  78
  79 # Let the code begin...
  80
  81
  82 package Bio::DB::Expression;
  83 use strict;
  84 use base qw(Bio::Root::HTTPget Bio::Root::Root);
  85 use Bio::Root::HTTPget;
  86 our $DefaultSource = 'geo';
  87
  88 =head2 new()
  89
  90  Usage   : my $obj = Bio::DB::Expression->new();
  91  Function: Builds a new Bio::DB::Expression object
  92  Returns : an instance of Bio::DB::Expression
  93  Args    :
  94
  95
  96 =cut
  97
  98 sub new {
  99   my($class,@args) = @_;
 100
 101   if( $class =~ /Bio::DB::Expression::(\S+)/ ) {
 102     my ($self) = $class->SUPER::new(@args);
 103     $self->_initialize(@args);
 104     return $self;
 105   } else {
 106     my %param = @args;
 107     @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
 108     my $source = $param{'-source'} || $DefaultSource;
 109
 110     $source = "\L$source";      # normalize capitalization to lower case
 111
 112     # normalize capitalization
 113     return unless( $class->_load_expression_module($source) );
 114     return "Bio::DB::Expression::$source"->new(@args);
 115   }
 116 }
 117
 118 =head2 get_platforms()
 119
 120  Usage   :
 121  Function:
 122  Example :
 123  Returns : a list of Bio::Expression::Platform objects
 124  Args    :
 125
 126 =cut
 127
 128 sub get_platforms {
 129   my ($self,@args) = @_;
 130   $self->throw_not_implemented();
 131 }
 132
 133 =head2 get_samples()
 134
 135  Usage   :
 136  Function:
 137  Example :
 138  Returns : a list of Bio::Expression::Sample objects
 139  Args    :
 140
 141 =cut
 142
 143 sub get_samples {
 144   my ($self,@args) = @_;
 145   $self->throw_not_implemented();
 146 }
 147
 148 =head2 get_contacts()
 149
 150  Usage   :
 151  Function:
 152  Example :
 153  Returns : a list of Bio::Expression::Contact objects
 154  Args    :
 155
 156 =cut
 157
 158 sub get_contacts {
 159   my ($self,@args) = @_;
 160   $self->throw_not_implemented();
 161 }
 162
 163 =head2 get_datasets()
 164
 165  Usage   :
 166  Function:
 167  Example :
 168  Returns : a list of Bio::Expression::DataSet objects
 169  Args    :
 170
 171 =cut
 172
 173 sub get_datasets {
 174   my ($self,@args) = @_;
 175   $self->throw_not_implemented();
 176 }
 177
 178
 179
 180
 181 =head2 _load_expression_module
 182
 183  Title   : _load_expression_module
 184  Usage   : *INTERNAL Bio::DB::Expression stuff*
 185  Function: Loads up (like use) a module at run time on demand
 186  Example :
 187  Returns :
 188  Args    :
 189
 190 =cut
 191
 192 sub _load_expression_module {
 193     my ($self, $source) = @_;
 194     my $module = "Bio::DB::Expression::" . $source;
 195     my $ok;
 196
 197     eval { $ok = $self->_load_module($module) };
 198     if ( $@ ) {
 199         print STDERR $@;
 200         print STDERR <<END;
 201 $self: $source cannot be found
 202 Exception $@
 203 For more information about the Bio::DB::Expression system please see
 204 the Bio::DB::Expression docs.  This includes ways of checking for
 205 formats at compile time, not run time.
 206 END
 207   ;
 208     }
 209     return $ok;
 210 }
 211
 212
 213 1;