Bio/DB/Expression/geo.pm

   1 =head1 NAME
   2
   3 Bio::DB::Expression::geo - *** DESCRIPTION of Class
   4
   5 =head1 SYNOPSIS
   6
   7 *** Give standard usage here
   8
   9 =head1 DESCRIPTION
  10
  11 *** Describe the object here
  12
  13 =head1 FEEDBACK
  14
  15 =head2 Mailing Lists
  16
  17 User feedback is an integral part of the evolution of this and other
  18 Bioperl modules. Send your comments and suggestions preferably to the
  19 Bioperl mailing list.  Your participation is much appreciated.
  20
  21   bioperl-l@bioperl.org                  - General discussion
  22   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  23
  24 =head2 Support
  25
  26 Please direct usage questions or support issues to the mailing list:
  27
  28 I<bioperl-l@bioperl.org>
  29
  30 rather than to the module maintainer directly. Many experienced and
  31 reponsive experts will be able look at the problem and quickly
  32 address it. Please include a thorough description of the problem
  33 with code and data examples if at all possible.
  34
  35 =head2 Reporting Bugs
  36
  37 Report bugs to the Bioperl bug tracking system to help us keep track
  38 of the bugs and their resolution. Bug reports can be submitted via the
  39 web:
  40
  41   https://github.com/bioperl/bioperl-live/issues
  42
  43 =head1 AUTHOR
  44
  45 Allen Day E<lt>allenday@ucla.eduE<gt>
  46
  47 =head1 APPENDIX
  48
  49 The rest of the documentation details each of the object methods.
  50 Internal methods are usually preceded with a '_'.  Methods are
  51 in alphabetical order for the most part.
  52
  53 =cut
  54
  55
  56 # Let the code begin...
  57
  58 package Bio::DB::Expression::geo;
  59 use strict;
  60 use base qw(Bio::DB::Expression);
  61
  62 use Bio::Expression::Contact;
  63 use Bio::Expression::DataSet;
  64 use Bio::Expression::Platform;
  65 use Bio::Expression::Sample;
  66
  67 use constant URL_PLATFORMS => 'http://www.ncbi.nlm.nih.gov/geo/query/browse.cgi?pgsize=100000&mode=platforms&submitter=-1&filteron=0&filtervalue=-1&private=1&sorton=pub_date&sortdir=1&start=1';
  68 use constant URL_PLATFORM => 'http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?form=text&view=full&acc=';
  69 use constant URL_DATASET => 'http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?form=text&view=full&acc=';
  70 use constant URL_SAMPLE => 'http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?form=text&view=full&acc=';
  71
  72 =head2 _initialize()
  73
  74  Usage   : $obj->_initialize(%arg);
  75  Function: Internal method to initialize a new Bio::DB::Expression::geo object
  76  Returns : true on success
  77  Args    : Arguments passed to new()
  78
  79 =cut
  80
  81 sub _initialize {
  82   my($self,%arg) = @_;
  83
  84   foreach my $arg (keys %arg){
  85     my $marg = $arg;
  86     $marg =~ s/^-//;
  87     $self->$marg($arg{$arg}) if $self->can($marg);
  88   }
  89
  90   return 1;
  91 }
  92
  93 =head2 get_platforms()
  94
  95  Usage   :
  96  Function:
  97  Example :
  98  Returns : a list of Bio::Expression::Platform objects
  99  Args    :
 100
 101 =cut
 102
 103 sub get_platforms {
 104   my ($self,@args) = @_;
 105
 106   my $doc = $self->_get_url( URL_PLATFORMS );
 107   $doc =~ s!^.+?>Release date<.+?</tr>(.+)</table>!$1!gs;
 108
 109   my @platforms = ();
 110   my @records = split m!</tr>\s+<tr>!, $doc;
 111
 112   foreach my $record ( @records ) {
 113     my ($platform_acc,$name,$tax_acc,$contact_acc,$contact_name) =
 114       $record =~ m!acc\.cgi\?acc=(.+?)".+?<td.+?>(.+?)<.+?<td.+?>.+?<.+?<td.+?>.+?href=".+?id=(.+?)".+?<td.+?OpenSubmitter\((\d+?)\).+?>(.+?)<!s;
 115     next unless $platform_acc;
 116
 117     my $platform = Bio::Expression::Platform->new(
 118                                                   -accession => $platform_acc,
 119                                                   -name => $name,
 120                                                   -_taxon_id => $tax_acc,
 121                                                   -contact => Bio::Expression::Contact->new(
 122                                                                                             -source => 'geo',
 123                                                                                             -accession => $contact_acc,
 124                                                                                             -name => $contact_name,
 125                                                                                             -db => $self
 126                                                                                            ),
 127                                                   -db => $self,
 128                                                  );
 129     push @platforms, $platform;
 130   }
 131
 132   return @platforms;
 133 }
 134
 135 =head2 get_samples()
 136
 137  Usage   :
 138  Function:
 139  Example :
 140  Returns : a list of Bio::Expression::Sample objects
 141  Args    :
 142
 143 =cut
 144
 145 sub get_samples {
 146   my ($self,@args) = @_;
 147   $self->throw_not_implemented();
 148 }
 149
 150 =head2 get_contacts()
 151
 152  Usage   :
 153  Function:
 154  Example :
 155  Returns : a list of Bio::Expression::Contact objects
 156  Args    :
 157
 158 =cut
 159
 160 sub get_contacts {
 161   my ($self,@args) = @_;
 162   $self->throw_not_implemented();
 163 }
 164
 165 =head2 get_datasets()
 166
 167  Usage   : $db->get_datasets('accession');
 168  Function:
 169  Example :
 170  Returns : a list of Bio::Expression::DataSet objects
 171  Args    :
 172
 173 =cut
 174
 175 sub get_datasets {
 176   my ($self,$platform) = @_;
 177
 178   my @lines = split /\n/, $self->_get_url( URL_PLATFORM . $platform->accession );
 179
 180   my @datasets = ();
 181
 182   foreach my $line ( @lines ) {
 183     my ($dataset_acc) = $line =~ /^\!Platform_series_id = (\S+?)\s*$/;
 184     next unless $dataset_acc;
 185
 186     my $dataset = Bio::Expression::DataSet->new(
 187                                                 -accession => $dataset_acc,
 188                                                 -platform => $platform,
 189                                                 -db => $self,
 190                                                );
 191
 192     push @datasets, $dataset;
 193   }
 194
 195   return @datasets;
 196 }
 197
 198 sub fill_sample {
 199   my ( $self, $sample ) = @_;
 200
 201   my @lines = split /\n/, $self->_get_url( URL_SAMPLE. $sample->accession );
 202
 203   foreach my $line ( @lines ) {
 204     if ( my ($name) = $line =~ /^\!Sample_title = (.+?)\s*$/ ) {
 205       $sample->name( $name );
 206     }
 207     elsif ( my ($desc) = $line =~ /^\!Sample_characteristics.*? = (.+?)\s*$/ ) {
 208       $sample->description( $desc );
 209     }
 210     elsif ( my ($source_name) = $line =~ /^\!Sample_source_name.*? = (.+?)\s*$/ ) {
 211       $sample->source_name( $source_name );
 212     }
 213     elsif ( my ($treatment_desc) = $line =~ /^\!Sample_treatment_protocol.*? = (.+?)\s*$/ ) {
 214       $sample->treatment_description( $treatment_desc );
 215     }
 216   }
 217   return 1;
 218 }
 219
 220 sub fill_dataset {
 221   my ( $self, $dataset ) = @_;
 222
 223   my @lines = split /\n/, $self->_get_url( URL_DATASET . $dataset->accession );
 224
 225   my @samples = ();
 226
 227   foreach my $line ( @lines ) {
 228     if ( my ($sample_acc) = $line =~ /^\!Series_sample_id = (\S+?)\s*$/ ) {
 229       my $sample = Bio::Expression::Sample->new(
 230                                                 -accession => $sample_acc,
 231                                                 -dataset => $dataset,
 232                                                 -db => $self,
 233                                                );
 234       push @samples, $sample;
 235     }
 236     elsif ( my ($pubmed_acc) = $line =~ /^\!Series_pubmed_id = (.+?)\s*$/ ) {
 237       $dataset->pubmed_id( $pubmed_acc );
 238     }
 239     elsif ( my ($web_link) = $line =~ /^\!Series_web_link = (.+?)\s*$/ ) {
 240       $dataset->web_link( $web_link );
 241     }
 242     elsif ( my ($contact) = $line =~ /^\!Series_contact_name = (.+?)\s*$/ ) {
 243       $dataset->contact( $contact );
 244     }
 245     elsif ( my ($name) = $line =~ /^\!Series_title = (.+?)\s*$/ ) {
 246       $dataset->name( $name );
 247     }
 248     elsif ( my ($desc) = $line =~ /^\!Series_summary = (.+?)\s*$/ ) {
 249       $dataset->description( $desc );
 250     }
 251     elsif ( my ($design) = $line =~ /^\!Series_type = (.+?)\s*$/ ) {
 252       $dataset->design( $design );
 253     }
 254     elsif ( my ($design_desc) = $line =~ /^\!Series_overall_design = (.+?)\s*$/ ) {
 255       $dataset->design_description( $design_desc );
 256     }
 257   }
 258
 259   $dataset->samples(\@samples);
 260 }
 261
 262 #################################################
 263
 264 =head2 _platforms_doc()
 265
 266  Usage   :
 267  Function:
 268  Example :
 269  Returns : an HTML document containing a table of all platforms
 270  Args    :
 271
 272
 273 =cut
 274
 275 sub _get_url {
 276   my ($self,$url) = @_;
 277
 278   my $response;
 279   eval {
 280     $response = $self->get( $url );
 281   };
 282   if( $@ ) {
 283     $self->warn("Can't query website: $@");
 284     return;
 285   }
 286   $self->debug( "resp is $response\n");
 287
 288   return $response;
 289 }
 290
 291
 292 1;