Bio::DB::EntrezGene(3)User Contributed Perl DocumentatioBio::DB::EntrezGene(3)NAMEBio::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
perl v5.14.1 2011-07-22 Bio::DB::EntrezGene(3)
