Bio::DB::EntrezGene(3)

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

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";
    }

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.

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.

FEEDBACK

  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

  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 the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Brian Osborne
Email bosborne at alum.mit.edu

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

  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

  default_format
 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

  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

Routines implemented by Bio::DB::NCBIHelper

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

  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

  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