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.\" ========================================================================
.\"
.IX Title "Bio::DB::GenPept 3pm"
.TH Bio::DB::GenPept 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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.nh
.SH "NAME"
Bio::DB::GenPept \- Database object interface to GenPept
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&    $gb = Bio::DB::GenPept\->new();
\&
\&    $seq = $gb\->get_Seq_by_id(\*(Aq195055\*(Aq); # Unique ID
\&
\&    # or ...
\&
\&    $seq = $gb\->get_Seq_by_acc(\*(AqDEECTH\*(Aq); # Accession Number
\&
\&    my $seqio = $gb\->get_Stream_by_id([\*(Aq195055\*(Aq, \*(AqDEECTH\*(Aq]);
\&    while( my $seq = $seqio\->next_seq ) {
\&            print "seq is is ", $seq\->display_id, "\en";
\&    }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the GenPept
database at \s-1NCBI,\s0 via an Entrez query.
.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.  Batch Entrez support will likely
be supported in a future version of DB::GenPept.
.PP
Currently the only return format supported by \s-1NCBI\s0 Entrez for GenPept
database is GenPept format, so any format specification passed to
GenPept will be ignored still be forced to GenPept format (which is
just GenBank format).
.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 \- Aaron Mackey, Jason Stajich"
.IX Header "AUTHOR - Aaron Mackey, Jason Stajich"
Email amackey@virginia.edu
Email jason@bioperl.org
.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(\*(AqROA1_HUMAN\*(Aq)
\& Function: Gets a Bio::Seq object by its name
\& Returns : a Bio::Seq object
\& Args    : the id (as a string) of a sequence
\& Throws  : "id does not exist" exception
.Ve
.SS "get_Seq_by_acc"
.IX Subsection "get_Seq_by_acc"
.Vb 5
\&  Title   : get_Seq_by_acc
\&  Usage   : $seq = $db\->get_Seq_by_acc(\*(AqAAC73346\*(Aq);
\&  Function: Gets a Seq objects by accession number
\&  Returns : Bio::Seq object
\&  Args    : accession number to retrieve by
.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 6
\&  Title   : get_Stream_by_id
\&  Usage   : $stream = $db\->get_Stream_by_id( [$uid1, $uid2] );
\&  Function: Gets a series of Seq objects by unique identifiers
\&  Returns : a Bio::SeqIO stream object
\&  Args    : $ref : a reference to an array of unique identifiers for
\&                   the desired sequence entries
.Ve
.SS "get_Stream_by_acc (2)"
.IX Subsection "get_Stream_by_acc (2)"
.Vb 7
\&  Title   : get_Stream_by_acc
\&  Usage   : $seq = $db\->get_Stream_by_acc($acc);
\&  Function: Gets a series of Seq objects by accession numbers
\&  Returns : a Bio::SeqIO stream object
\&  Args    : $ref : a reference to an array of accession numbers for
\&                   the desired sequence entries
\&  Note    : For GenBank, this just calls the same code for get_Stream_by_id()
.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/Set sequence format retrieval
\& Returns : string representing format
\& Args    : $format = sequence format
.Ve