Bio::DB::EntrezGene.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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