| Bio::DB::EntrezGene(3pm) | User Contributed Perl Documentation | Bio::DB::EntrezGene(3pm) |
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.
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
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.
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
Email bosborne at alum.mit.edu
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
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
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;
$self->request_format($format);
Function: Get or set sequence format retrieval
Returns : String representing format
Args : $format = sequence format
| 2022-02-24 | perl v5.34.0 |