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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq