Bio::GMOD::Query::WormBase - Defaults for programmatically interacting with Wormbase

Bio-GMOD documentation Contained in the Bio-GMOD distribution.

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NAME

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Bio::GMOD::Query::WormBase - Defaults for programmatically interacting with Wormbase

SYNPOSIS

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  my $adaptor = Bio::GMOD::Adaptor::WormBase->new();

DESCRIPTION

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Bio::GMOD::Adaptor::WormBase objects are created internally by the new() method provided by Bio::GMOD::Adaptor. Adaptor::* objects contain appropriate defaults for interacting programmatically with the GMOD of choice.

Defaults are read dynamically from the WormBase server at runtime. This helps to insulate your scripts from changes in the WormBase infrastructure. If using Bio::GMOD offline, defaults will be populated from those hard-coded in this adaptor. You may also supply these defaults as hash=>key pairs to the new method.

For descriptions of all currently known parameters, see Bio::GMOD::Adaptor::WormBase.pm or the default list maintained at http://dev.wormbase.org/db/gmod/defaults

BUGS

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None reported.

SEE ALSO

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Bio::GMOD, Bio::GMOD::Query

AUTHOR

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Todd W. Harris <harris@cshl.edu>.

Copyright (c) 2003-2005 Cold Spring Harbor Laboratory.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

Bio-GMOD documentation Contained in the Bio-GMOD distribution. 
package Bio::GMOD::Query::WormBase;

use strict;

use Ace;
use Bio::GMOD::Util::Rearrange;
use vars qw/@ISA @AVAILABLE_CLASSES/;

@ISA = qw/Bio::GMOD::Query/;

# Adjust this array to describe the classes that can be searched or
# retrieved at your MOD.  Classes should correspond to method names!
@AVAILABLE_CLASSES = qw/gene protein/;

sub available_classes { return @AVAILABLE_CLASSES; }

# Run a query for genes at WormBase
sub gene {
  my ($self,@p) = @_;
  my ($name,@remainder) = rearrange([qw/NAME/],@p);
  my $adaptor = $self->adaptor;
  my $db      = $self->_connect_to_ace;
  my $query   = sprintf($adaptor->gene_fetch_query,$name);
  my @genes = $db->aql($query);
  my @results = _do_grep($db,'Gene',$name) unless @genes;
  if (@results) {
    @genes = map { [ $_,$_->Public_name,$_->Concise_description ] } @results;
  }
  return \@genes;
}

sub protein {
  my ($self,@p) = @_;
  my ($name,@remainder) = rearrange([qw/NAME/],@p);
  my $adaptor = $self->adaptor;
  my $db      = $self->_connect_to_ace;
  my $query   = sprintf($adaptor->protein_fetch_query,$name);
  my @proteins = $db->aql($query);
  my @results = _do_grep($db,'Protein',$name) unless @proteins;
  if (@results) {
    @proteins = map { [ $_,$_->Public_name,$_->Concise_description ] } @results;
  }
  return \@proteins;
}

sub allele {
  my ($self,@p) = @_;
  my ($name,@remainder) = rearrange([qw/NAME/],@p);
  my $adaptor = $self->adaptor;
  my $db      = $self->_connect_to_ace;
  my $query   = sprintf($adaptor->protein_fetch_query,$name);
  my @alleles = $db->aql($query);
  my @results = _do_grep($db,'Variation',$name) unless @alleles;
  if (@results) {
    @alleles = map { [ $_,$_->Public_name,$_->Concise_description ] } @results;
  }
  return \@alleles;
}

sub _connect_to_ace {
  my $self = shift;
  my $adaptor = $self->adaptor;
  my $host = $adaptor->data_mining_server;
  my $port = $adaptor->data_mining_port;
  return $self->{db} if $self->{db};
  my $db = Ace->connect(-host=>$host,-port=>$port) or $self->logit(-msg=>"Couldn't connect to $host:$port: $!",-die=>1);
  $self->{db} = $db;
  return $db;
}

# Do a full database grep in cases where we can't specifically fetch something
sub _do_grep {
  my ($db,$class,$name) = @_;
  my @results = grep { $_->class eq $class } $db->grep(-pattern => $name,
						       -long    => 'true');
  return @results;
}


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