Bio::DB::Expression::geo - *** DESCRIPTION of Class

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::DB::Expression::geo - *** DESCRIPTION of Class

SYNOPSIS

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*** Give standard usage here

DESCRIPTION

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*** Describe the object here

FEEDBACK

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Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR

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Allen Day <allenday@ucla.edu>

APPENDIX

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a '_'. Methods are in alphabetical order for the most part.

_initialize()

 Usage   : $obj->_initialize(%arg);
 Function: Internal method to initialize a new Bio::DB::Expression::geo object
 Returns : true on success
 Args    : Arguments passed to new()

get_platforms()

 Usage   :
 Function:
 Example :
 Returns : a list of Bio::Expression::Platform objects
 Args    :

get_samples()

 Usage   :
 Function:
 Example :
 Returns : a list of Bio::Expression::Sample objects
 Args    :

get_contacts()

 Usage   :
 Function:
 Example :
 Returns : a list of Bio::Expression::Contact objects
 Args    :

get_datasets()

 Usage   : $db->get_datasets('accession');
 Function:
 Example :
 Returns : a list of Bio::Expression::DataSet objects
 Args    :

_platforms_doc()

 Usage   :
 Function:
 Example :
 Returns : an HTML document containing a table of all platforms
 Args    :
BioPerl documentation Contained in the BioPerl distribution. 

# Let the code begin...

package Bio::DB::Expression::geo;
use strict;
use base qw(Bio::DB::Expression);

use Bio::Expression::Contact;
use Bio::Expression::DataSet;
use Bio::Expression::Platform;
use Bio::Expression::Sample;

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';
use constant URL_PLATFORM => 'http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?form=text&view=full&acc=';
use constant URL_DATASET => 'http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?form=text&view=full&acc=';
use constant URL_SAMPLE => 'http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?form=text&view=full&acc=';


sub _initialize {
  my($self,%arg) = @_;

  foreach my $arg (keys %arg){
    my $marg = $arg;
    $marg =~ s/^-//;
    $self->$marg($arg{$arg}) if $self->can($marg);
  }

  return 1;
}


sub get_platforms {
  my ($self,@args) = @_;

  my $doc = $self->_get_url( URL_PLATFORMS );
  $doc =~ s!^.+?>Release date<.+?</tr>(.+)</table>!$1!gs;

  my @platforms = ();
  my @records = split m!</tr>\s+<tr>!, $doc;

  foreach my $record ( @records ) {
    my ($platform_acc,$name,$tax_acc,$contact_acc,$contact_name) =
      $record =~ m!acc\.cgi\?acc=(.+?)".+?<td.+?>(.+?)<.+?<td.+?>.+?<.+?<td.+?>.+?href=".+?id=(.+?)".+?<td.+?OpenSubmitter\((\d+?)\).+?>(.+?)<!s;
    next unless $platform_acc;

    my $platform = Bio::Expression::Platform->new(
                                                  -accession => $platform_acc,
                                                  -name => $name,
                                                  -_taxon_id => $tax_acc,
                                                  -contact => Bio::Expression::Contact->new(
                                                                                            -source => 'geo',
                                                                                            -accession => $contact_acc,
                                                                                            -name => $contact_name,
                                                                                            -db => $self
                                                                                           ),
                                                  -db => $self,
                                                 );
    push @platforms, $platform;
  }

  return @platforms;
}


sub get_samples {
  my ($self,@args) = @_;
  $self->throw_not_implemented();
}


sub get_contacts {
  my ($self,@args) = @_;
  $self->throw_not_implemented();
}


sub get_datasets {
  my ($self,$platform) = @_;

  my @lines = split /\n/, $self->_get_url( URL_PLATFORM . $platform->accession );

  my @datasets = ();

  foreach my $line ( @lines ) {
    my ($dataset_acc) = $line =~ /^\!Platform_series_id = (\S+?)\s*$/;
    next unless $dataset_acc;

    my $dataset = Bio::Expression::DataSet->new(
                                                -accession => $dataset_acc,
                                                -platform => $platform,
                                                -db => $self,
                                               );

    push @datasets, $dataset;
  }

  return @datasets;
}

sub fill_sample {
  my ( $self, $sample ) = @_;

  my @lines = split /\n/, $self->_get_url( URL_SAMPLE. $sample->accession );

  foreach my $line ( @lines ) {
    if ( my ($name) = $line =~ /^\!Sample_title = (.+?)\s*$/ ) {
      $sample->name( $name );
    }
    elsif ( my ($desc) = $line =~ /^\!Sample_characteristics.*? = (.+?)\s*$/ ) {
      $sample->description( $desc );
    }
    elsif ( my ($source_name) = $line =~ /^\!Sample_source_name.*? = (.+?)\s*$/ ) {
      $sample->source_name( $source_name );
    }
    elsif ( my ($treatment_desc) = $line =~ /^\!Sample_treatment_protocol.*? = (.+?)\s*$/ ) {
      $sample->treatment_description( $treatment_desc );
    }
  }
  return 1;
}

sub fill_dataset {
  my ( $self, $dataset ) = @_;

  my @lines = split /\n/, $self->_get_url( URL_DATASET . $dataset->accession );

  my @samples = ();

  foreach my $line ( @lines ) {
    if ( my ($sample_acc) = $line =~ /^\!Series_sample_id = (\S+?)\s*$/ ) {
      my $sample = Bio::Expression::Sample->new(
                                                -accession => $sample_acc,
                                                -dataset => $dataset,
                                                -db => $self,
                                               );
      push @samples, $sample;
    }
    elsif ( my ($pubmed_acc) = $line =~ /^\!Series_pubmed_id = (.+?)\s*$/ ) {
      $dataset->pubmed_id( $pubmed_acc );
    }
    elsif ( my ($web_link) = $line =~ /^\!Series_web_link = (.+?)\s*$/ ) {
      $dataset->web_link( $web_link );
    }
    elsif ( my ($contact) = $line =~ /^\!Series_contact_name = (.+?)\s*$/ ) {
      $dataset->contact( $contact );
    }
    elsif ( my ($name) = $line =~ /^\!Series_title = (.+?)\s*$/ ) {
      $dataset->name( $name );
    }
    elsif ( my ($desc) = $line =~ /^\!Series_summary = (.+?)\s*$/ ) {
      $dataset->description( $desc );
    }
    elsif ( my ($design) = $line =~ /^\!Series_type = (.+?)\s*$/ ) {
      $dataset->design( $design );
    }
    elsif ( my ($design_desc) = $line =~ /^\!Series_overall_design = (.+?)\s*$/ ) {
      $dataset->design_description( $design_desc );
    }
  }

  $dataset->samples(\@samples);
}

#################################################


sub _get_url {
  my ($self,$url) = @_;

  my $response;
  eval {
    $response = $self->get( $url );
  };
  if( $@ ) {
    $self->warn("Can't query website: $@");
    return;
  }
  $self->debug( "resp is $response\n"); 

  return $response;
}


1;