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.\" ========================================================================
.\"
.IX Title "Bio::DB::EntrezGene 3pm"
.TH Bio::DB::EntrezGene 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::DB::EntrezGene \- Database object interface to Entrez Gene
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&    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, "\en";
\&    }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Allows the dynamic retrieval of Sequence objects from the 
Entrez Gene database at \s-1NCBI,\s0 via an Entrez query using Gene ids.
.PP
This module requires the \s-1CPAN\s0 Bio::ASN1 module.
.PP
\&\s-1WARNING:\s0 Please do \s-1NOT\s0 spam the Entrez web server with multiple requests.
\&\s-1NCBI\s0 offers Batch Entrez for this purpose.
.SH "NOTES"
.IX Header "NOTES"
The Entrez eutils \s-1API\s0 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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Brian Osborne"
.IX Header "AUTHOR - Brian Osborne"
Email bosborne at alum.mit.edu
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "get_params"
.IX Subsection "get_params"
.Vb 6
\& Title   : get_params
\& Usage   : my %params = $self\->get_params($mode)
\& Function: Returns key,value pairs to be passed to NCBI database
\&           for either \*(Aqbatch\*(Aq or \*(Aqsingle\*(Aq sequence retrieval method
\& Returns : A key,value pair hash
\& Args    : \*(Aqsingle\*(Aq or \*(Aqbatch\*(Aq mode for retrieval
.Ve
.SS "default_format"
.IX Subsection "default_format"
.Vb 5
\& Title   : default_format
\& Usage   : my $format = $self\->default_format
\& Function: Returns default sequence format for this module
\& Returns : string
\& Args    : none
.Ve
.SH "Routines from Bio::DB::WebDBSeqI and Bio::DB::RandomAccessI"
.IX Header "Routines from Bio::DB::WebDBSeqI and Bio::DB::RandomAccessI"
.SS "get_Seq_by_id"
.IX Subsection "get_Seq_by_id"
.Vb 6
\& 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
.Ve
.SH "Routines implemented by Bio::DB::NCBIHelper"
.IX Header "Routines implemented by Bio::DB::NCBIHelper"
.SS "get_request"
.IX Subsection "get_request"
.Vb 5
\& Title   : get_request
\& Usage   : my $url = $self\->get_request
\& Function: HTTP::Request
\& Returns : 
\& Args    : %qualifiers = a hash of qualifiers (ids, format, etc)
.Ve
.SS "get_Stream_by_id"
.IX Subsection "get_Stream_by_id"
.Vb 5
\&  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
.Ve
.SS "request_format"
.IX Subsection "request_format"
.Vb 6
\& 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
.Ve