NAME

       Bio::DB::GenPept - Database object interface to GenPept

SYNOPSIS

           $gb = Bio::DB::GenPept->new();

           $seq = $gb->get_Seq_by_id('195055'); # Unique ID

           # or ...

           $seq = $gb->get_Seq_by_acc('DEECTH'); # Accession Number

           my $seqio = $gb->get_Stream_by_id(['195055', 'DEECTH']);
           while( my $seq = $seqio->next_seq ) {
                   print "seq is is ", $seq->display_id, "\n";
           }

DESCRIPTION

       Allows the dynamic retrieval of Sequence objects (Bio::Seq) from the GenPept database at
       NCBI, via an Entrez query.

       WARNING: Please do NOT spam the Entrez web server with multiple requests.  NCBI offers
       Batch Entrez for this purpose.  Batch Entrez support will likely be supported in a future
       version of DB::GenPept.

       Currently the only return format supported by NCBI 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).

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Aaron Mackey, Jason Stajich

       Email amackey@virginia.edu Email jason@bioperl.org

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('ROA1_HUMAN')
        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

   get_Seq_by_acc
         Title   : get_Seq_by_acc
         Usage   : $seq = $db->get_Seq_by_acc('AAC73346');
         Function: Gets a Seq objects by accession number
         Returns : Bio::Seq object
         Args    : accession number to retrive by

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 = $db->get_Stream_by_id( [$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

   get_Stream_by_acc (2)
         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()

   request_format
        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