Bio::DB::Expression
geo
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Summary
Bio::DB::Expression::geo - *** DESCRIPTION of Class
Package variables
No package variables defined.
Included modules
Bio::Expression::Contact
Bio::Expression::DataSet
Bio::Expression::Platform
Bio::Expression::Sample
Inherit
Synopsis
*** Give standard usage here
Description
*** Describe the object here
Methods
Methods description
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() |
Usage :
Function:
Example :
Returns : a list of Bio::Expression::Platform objects
Args : |
Usage :
Function:
Example :
Returns : a list of Bio::Expression::Sample objects
Args : |
Usage :
Function:
Example :
Returns : a list of Bio::Expression::Contact objects
Args : |
Usage : $db->get_datasets('accession');
Function:
Example :
Returns : a list of Bio::Expression::DataSet objects
Args : |
Methods code
sub _initialize
{ my($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;} | General documentation
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
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.
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/
Allen Day <allenday@ucla.edu>
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.
Usage :
Function:
Example :
Returns : an HTML document containing a table of all platforms
Args :