Provided by: libbio-perl-perl_1.6.923-1_all bug


       Bio::DB::EntrezGene - Database object interface to Entrez Gene


           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";


       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.


       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.


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AUTHOR - Brian Osborne

       Email bosborne at


       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

        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

        Title   : default_format
        Usage   : my $format = $self->default_format
        Function: Returns default sequence format for this module
        Returns : string
        Args    : none

Routines from Bio::DB::WebDBSeqI and Bio::DB::RandomAccessI

        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

Routines implemented by Bio::DB::NCBIHelper

        Title   : get_request
        Usage   : my $url = $self->get_request
        Function: HTTP::Request
        Returns :
        Args    : %qualifiers = a hash of qualifiers (ids, format, etc)

         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

        Title   : request_format
        Usage   : my $format = $self->request_format;
        Function: Get or set sequence format retrieval
        Returns : String representing format
        Args    : $format = sequence format