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
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
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