—
—
—
—

              
# $Id: EntrezGene.pm,v 1.8.4.1 2006/10/02 23:10:14 sendu Exp $
#
# BioPerl module for Bio::DB::EntrezGene
#
# Cared for by Brian Osborne bosborne at alum.mit.edu
#
# Copyright Brian Osborne
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
HideShow 68 lines of Pod
=head1 NAME
Bio::DB::EntrezGene - Database object interface to Entrez Gene
=head1 SYNOPSIS
    use Bio::DB::EntrezGene;
    my $db = Bio::DB::EntrezGene->new;
    my $seq = $db->get_Seq_by_id(2); # Gene id
    # or ...
    my $seqio = $db->get_Stream_by_id([2, 4693, 3064]); # Gene ids
    while ( my $seq = $seqio->next_seq ) {
            print "id is ", $seq->display_id, "\n";
    }
=head1 DESCRIPTION
Allows the dynamic retrieval of Sequence objects from the 
Entrez Gene database at NCBI, via an Entrez query using Gene ids.
This module requires the CPAN Bio::ASN1 module.
WARNING: Please do NOT spam the Entrez web server with multiple requests.
NCBI offers Batch Entrez for this purpose.
=head1 NOTES
The Entrez eutils API does not allow Entrez Gene queries by name as
of this writing, therefore there are only get_Seq_by_id and 
get_Stream_by_id methods in this module, and these expect Gene ids. 
There are no get_Seq_by_acc or get_Stream_by_acc methods.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the
evolution of this and other Bioperl modules. Send
your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation
is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via the
web:
  http://bugzilla.open-bio.org/
=head1 AUTHOR - Brian Osborne
Email bosborne at alum.mit.edu
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::DB::EntrezGene;
use strict;
use vars qw($DEFAULTFORMAT $DEFAULTMODE %PARAMSTRING);
use base qw(Bio::DB::NCBIHelper);
BEGIN { 
    $DEFAULTMODE   = 'single';
    $DEFAULTFORMAT = 'asn.1';       
    %PARAMSTRING = ('batch'  => {'db'     => 'gene',
                                                                                         'usehistory' => 'y',
                                                                                         'tool'   => 'bioperl',
                                                                                         'retmode' => 'asn.1'},
                                                   'gi'     => {'db'     => 'gene',
                                                                                         'usehistory' => 'y',
                                                                                         'tool'   => 'bioperl',
                                                                                         'retmode' => 'asn.1'},
                                                  'version' => {'db'     => 'gene',
                                                                                         'usehistory' => 'y',
                                                                                         'tool'   => 'bioperl',
                                                                                         'retmode' => 'asn.1'},
                                                  'single'  => {'db'     => 'gene',
                                                                                         'usehistory' => 'y',
                                                                                         'tool'   => 'bioperl',
                                                                                         'retmode' => 'asn.1'} );
}
# the new way to make modules a little more lightweight
sub new {
  my($class, @args) = @_;
  my $self = $class->SUPER::new(@args);
  # Seems that Bio::SeqIO::entrezgene requires this:
  $self->{_retrieval_type} = "tempfile"; 
  $self->request_format($self->default_format);
  return $self;
}
HideShow 11 lines of Pod
=head2 get_params
 Title   : get_params
 Usage   : my %params = $self->get_params($mode)
 Function: Returns key,value pairs to be passed to NCBI database
           for either 'batch' or 'single' sequence retrieval method
 Returns : A key,value pair hash
 Args    : 'single' or 'batch' mode for retrieval
=cut
sub get_params {
    my ($self, $mode) = @_;
    return defined $PARAMSTRING{$mode} ? %{$PARAMSTRING{$mode}} : 
                %{$PARAMSTRING{$DEFAULTMODE}};
}
HideShow 10 lines of Pod
=head2 default_format
 Title   : default_format
 Usage   : my $format = $self->default_format
 Function: Returns default sequence format for this module
 Returns : string
 Args    : none
=cut
sub default_format {
        return $DEFAULTFORMAT;
}
# from Bio::DB::WebDBSeqI from Bio::DB::RandomAccessI
HideShow 40 lines of Pod
=head1 Routines from Bio::DB::WebDBSeqI and Bio::DB::RandomAccessI
=head2 get_Seq_by_id
 Title   : get_Seq_by_id
 Usage   : $seq = $db->get_Seq_by_id(2)
 Function: Gets a Bio::Seq object by its name
 Returns : A Bio::Seq object
 Args    : Gene id
 Throws  : "id does not exist" exception
=head1 Routines implemented by Bio::DB::NCBIHelper
=head2 get_request
 Title   : get_request
 Usage   : my $url = $self->get_request
 Function: HTTP::Request
 Returns : 
 Args    : %qualifiers = a hash of qualifiers (ids, format, etc)
=head2 get_Stream_by_id
  Title   : get_Stream_by_id
  Usage   : $stream = $db->get_Stream_by_id( [$gid1, $gid2] );
  Function: Gets a series of Seq objects using Gene ids
  Returns : A Bio::SeqIO stream object
  Args    : A reference to an array of Gene ids
=head2 request_format
 Title   : request_format
 Usage   : my $format = $self->request_format;
           $self->request_format($format);
 Function: Get or set sequence format retrieval
 Returns : String representing format
 Args    : $format = sequence format
=cut
# override to force format
sub request_format {
    my ($self) = @_;
    return $self->SUPER::request_format($self->default_format());
}
1;
__END__